WO2024187120A1 - Formulations comprising stabilized sars-cov-2 peptides and uses thereof - Google Patents
Formulations comprising stabilized sars-cov-2 peptides and uses thereof Download PDFInfo
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P31/12—Antivirals
- A61P31/14—Antivirals for RNA viruses
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/12—Viral antigens
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/39—Medicinal preparations containing antigens or antibodies characterised by the immunostimulating additives, e.g. chemical adjuvants
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
- A61K2039/55511—Organic adjuvants
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/60—Medicinal preparations containing antigens or antibodies characteristics by the carrier linked to the antigen
- A61K2039/6093—Synthetic polymers, e.g. polyethyleneglycol [PEG], Polymers or copolymers of (D) glutamate and (D) lysine
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/62—Medicinal preparations containing antigens or antibodies characterised by the link between antigen and carrier
- A61K2039/627—Medicinal preparations containing antigens or antibodies characterised by the link between antigen and carrier characterised by the linker
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/64—Medicinal preparations containing antigens or antibodies characterised by the architecture of the carrier-antigen complex, e.g. repetition of carrier-antigen units
- A61K2039/645—Dendrimers; Multiple antigen peptides
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K2039/70—Multivalent vaccine
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K9/00—Medicinal preparations characterised by special physical form
- A61K9/10—Dispersions; Emulsions
- A61K9/107—Emulsions ; Emulsion preconcentrates; Micelles
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K9/00—Medicinal preparations characterised by special physical form
- A61K9/14—Particulate form, e.g. powders, Processes for size reducing of pure drugs or the resulting products, Pure drug nanoparticles
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
- C12N2770/00011—Details
- C12N2770/20011—Coronaviridae
- C12N2770/20022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
- C12N2770/00011—Details
- C12N2770/20011—Coronaviridae
- C12N2770/20033—Use of viral protein as therapeutic agent other than vaccine, e.g. apoptosis inducing or anti-inflammatory
Definitions
- COVID-19 has been declared a high-risk global health emergency by the World Health Organization (WHO) and has, as of September 2022, caused 603,711,760 cases of respiratory disease and 6,484,136 deaths worldwide. Subsequent variants have posed an ongoing public health challenge, including thwarting the efficacy of vaccine, antibody, and molecular therapeutics.
- WHO World Health Organization
- SARS-CoV-2 contains a surface protein that undergoes a conformational change upon engagement with the host cell, resulting in formation of a six-helix bundle that brings the host and viral membranes together.
- peptide-based inhibition of viral fusion processes is mechanistically feasible and clinically effective (e.g., Fuzeon (i.e., enfurvirtide), approved by the FDA in 2003)
- Fuzeon i.e., enfurvirtide
- the biophysical and pharmacologic liabilities of peptides including loss of bioactive shape and rapid proteolysis in vivo (e.g., 100 mg self-injected twice daily)
- new strategies for the preventing and/or treating COVID-19 infections are urgently required to effectively mitigate outbreaks.
- the instant disclosure provides dry powders, anhydrous compositions, and emulsions comprising peptides that are useful for the treatment and/or prevention of coronavirus infections.
- dry powders, anhydrous compositions, or emulsions comprising a peptide that binds to a SARS-CoV-2 spike protein.
- the peptides comprised within the dry powders, anhydrous compositions, and emulsions provided herein are particularly advantageous because they prevent coronavirus fusion to a host cell.
- a dry powder comprising a peptide that binds to a SARS-CoV-2 spike protein.
- an anhydrous composition comprising a peptide that binds to a SARS-CoV-2 spike protein.
- the anhydrous composition is a liquid composition.
- an emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein.
- the emulsion composition comprises an aqueous phase and a non-aqueous phase.
- the peptide is comprised within the non-aqueous phase.
- the dry powder, anhydrous composition, or emulsion is for mucosal surface delivery.
- the dry powder, anhydrous composition, or emulsion is not for systemic delivery. [0010] In an embodiment, the dry powder, anhydrous composition, or emulsion is for nasal, nasopharyngeal, and/or pulmonary administration. [0011] In an embodiment, the peptide inhibits infection of a cell by SARS-CoV-2 in a pseudovirus and/or a live SARS-CoV-2 virus assay. [0012] In an embodiment, the peptide is at most 50 amino acids in length. In an embodiment, the peptide is 38 amino acids in length.
- the peptide is or comprises a peptide of Formula (I): or a pharmaceutically acceptable salt thereof, wherein: each R 1 and R 2 is H or a C 1 to C 10 alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heteroarylalkyl, or heterocyclylalkyl, any of which is substituted or unsubstituted; each R 3 is independently alkylene, alkenylene, or alkynylene, any of which is substituted or unsubstituted; Page 2 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO (208172) z is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and each [Xaa] w is DISGINASVVNIQ (SEQ ID NO: 35), each [Xaa] x is EIDRLN (SEQ ID NO: 36), and each [Xaa]y is VAKNLNESLIDLQELGK (SEQ ID NO: 37).
- R 1 is an alkyl. In an embodiment, R 1 is a methyl group.
- R2 is an alkyl. In an embodiment, R2 is a methyl group.
- R3 is an alkenylene.
- the peptide is or comprises a peptide of Formula I-A: or a pharmaceutically R 3 is alkenylene;
- [Xaa]w is DISGINASVVNIQ (SEQ ID NO: 35);
- [Xaa]x is EIDRLN (SEQ ID NO: 36);
- [Xaa]y is VAKNLNESLIDLQELGK (SEQ ID NO: 37); wherein optionally the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the peptide is or comprises a peptide of Formula Ia: or a pharmaceutically w , [Xaa] x , and [Xaa] y are as defined above for Formula I-A, and wherein optionally the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)-(C 1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the peptide is or comprises a peptide of the formula: Page 3 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO (208172) O [Xaa] x NH or as group aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)-(C1-4 alkyl). In an embodiment, the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)CH 3 .
- the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the peptide further comprises PEG and/or a cholesterol.
- the cholesterol is thiocholesterol.
- the peptide further comprises PEG(n)-cholesterol, wherein the PEG(n)-cholesterol is conjugated to the N-terminus or C-terminus of the peptide, and wherein n is 1-36, optionally wherein n is 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36.
- the peptide further comprises PEG(n)-thiocholesterol, wherein the PEG(n)-thiocholesterol is conjugated to the N- terminus or C-terminus of the peptide, and wherein n is 1-36, optionally wherein n 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36.
- the peptide is a peptide of Formula II: or a pharmaceutically Page 4 of 91 BUSINESS.31107393.1 Attorney Ref.
- R 3 is alkenylene;
- R 4 is **-C(O)-(C 2-6 alkylene)-[O-CH 2 CH 2 ] m -N(R 5 )C(O)-(C 1-6 alkylene)-R 6 , wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa]y;
- R 5 is hydrogen or C 1-4 alkyl;
- R6 is one of the following: , each of which is R7 represents independently for each occurrence C1-3 alkyl, hydroxyl, or C1-3 alkoxyl;
- [Xaa]w is DISGINASVVNIQ (SEQ ID NO: 35);
- [Xaa] x is EIDRLN (SEQ ID NO: 36);
- [Xaa]y is VAKNLNESLIDLQELGK (SEQ ID NO: 37);
- m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16; and t
- the peptide is a peptide of Formula IIa: or a pharmaceutically w, [Xaa]x, and [Xaa]y are as defined above for Formula II, and wherein optionally the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the peptide is a peptide of formula: or Page 5 of 91 BUSINESS.31107393.1 Attorney Ref.
- R3, R4, [Xaa]w, [Xaa]x, and [Xaa]y are as optionally the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- R 3 is C 7-15 alkenylene. In an embodiment, R 3 is C 9-13 alkenylene. In an embodiment, R3 is C11 alkenylene.
- the peptide is a peptide of Formula III: or a pharmaceutically
- R4 is **-C(O)-(C2-6 alkylene)-[O-CH2CH2]m-N(R5)C(O)-(C1-6 alkylene)-R6, wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa] y ;
- R5 is hydrogen or C1-4 alkyl;
- R 6 is one of the following: , each of which is R7 represents independently for each occurrence C1-3 alkyl, hydroxyl, or C1-3 alkoxyl;
- [Xaa] w is DISGINASVVNIQ (SEQ ID NO: 35);
- [Xaa]x is EIDRLN (SEQ ID NO: 36);
- [Xaa] y is VAKNLNESLIDLQELGK (SEQ ID NO: 37);
- m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or
- No.406693-002WO (208172) z is 2, 3, 4, 5, or 6; and t is 0, 1, 2, or 3; wherein optionally the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C 1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the peptide is a peptide of Formula IIIa: or a pharmaceutically [Xaa]x, and [Xaa]y are as defined above for Formula III, and wherein optionally the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- R4 is **-C(O)-(C2-3 alkylene)-[O-CH2CH2]m-N(R5)C(O)-(C1-2 alkylene)-R6, wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa] y .
- R 4 is **-C(O)-(CH 2 CH 2 )-[O-CH 2 CH 2 ] m - N(R5)C(O)-(CH2)-R6, wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa] y .
- the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C 1-4 alkyl).
- the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)CH3.
- the carboxylic acid group of the C-terminal lysine in [Xaa] y is replaced with -C(O)NH 2 .
- the peptide is a peptide of Formula IV: or a pharmaceutically acceptable salt thereof, wherein: R 4 is -C(O)-(C 2-6 alkylene)-[O-CH 2 CH 2 ] m -N(R 5 )C(O)-(C 1-6 alkylene)-R 6 ; R5 is hydrogen or C1-4 alkyl; Page 7 of 91 BUSINESS.31107393.1 Attorney Ref.
- R 6 is one of the following: , each of which is occurrence 3 or C1-3 alkoxyl; R 8 is -C(O)-(C 1-4 alkyl); [Xaa]w is DISGINASVVNIQ (SEQ ID NO: 35); [Xaa] x is EIDRLN (SEQ ID NO: 36); [Xaa]z is VAKNLNESLIDLQELG (SEQ ID NO: 77); m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16; p is 2, 3, 4, 5, 6, 7, or 8; z is 2, 3, 4, 5, or 6; and t is 0, 1, 2, or 3.
- the peptide is a peptide of Formula IVa: or a [Xaa] z , p, and z are as defined above in Formula IV. [0031] In an embodiment, the peptide is a peptide of Formula IVb: or a and [Xaa] z are as defined above in Formula IV. [0032] In an embodiment, the peptide is a peptide of Formula IVc: Page 8 of 91 BUSINESS.31107393.1 Attorney Ref.
- the peptide is a peptide of Formula V: or a wherein R 4 is -C(O)-(C 2-6 alkylene)-[O-CH 2 CH 2 ] m -N(R 5 )C(O)-(C 1-6 alkylene)-R 6 ; R5 is hydrogen or C1-4 alkyl; R 6 is one of the following: is 3 alkyl, hydroxyl, or C1-3 alkoxyl; R8 is -C(O)-(C1-4 alkyl); [Xaa]w is DISGINASVVNIQ (SEQ ID NO: 35); [Xaa]x is EIDRLN (SEQ ID NO: 36); [Xaa] z is VAKNLNESLIDLQELG (SEQ ID NO: 77); m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16; and t is 0, 1,
- R8 is -C(O)CH3.
- R4 is -C(O)-(C2-3 alkylene)- [O-CH 2 CH 2 ] m -N(R 5 )C(O)-(C 1-2 alkylene)-R 6 .
- R 4 is -C(O)-(CH 2 CH 2 )-[O- CH2CH2]m-N(R5)C(O)-(CH2)-R6.
- R5 is hydrogen. Page 9 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) [0035] In an embodiment, substituted by t occurrences of R7.
- substituted by t occurrences of R7 [0036] In an embodiment, substituted by t occurrences of R7. [0037] In an embodiment, substituted by t occurrences of R7. [0038] In an embodiment, substituted by t occurrences of R 7 . [0039] In an embodiment, substituted by t occurrences of R 7 . Page 10 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) [0040] In an embodiment, substituted by t occurrences of R7. [0041] In an embodiment, t an m an m is 8.
- the peptide is a peptide of Formula VI: or a wherein R4 is -C(O)-(CH2CH2)-[O-CH2CH2]8-N(H)C(O)-(CH2)-R6; [Xaa]z is VAKNLNESLIDLQELG (SEQ ID NO: 77).
- a method of treating a coronavirus infection in a human subject in need thereof comprising administering to the human subject a therapeutically effective amount of any one of the dry powders, anhydrous compositions, or emulsions disclosed herein.
- a method of preventing a coronavirus infection in a human subject in need thereof comprising administering to the human subject a therapeutically effective amount of any one of the dry powders, anhydrous compositions, or Page 11 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) emulsions disclosed herein.
- a method of treating a coronavirus infection in a subject in need thereof comprising administering to the subject a therapeutically effective amount of any one of the dry powders, anhydrous compositions, or emulsions disclosed herein, wherein the subject is a cow, a pig, a horse, a cat, a dog, a rat, a mouse, or a bat.
- a method of preventing a coronavirus infection in a subject in need thereof comprising administering to the subject a therapeutically effective amount of any one of the dry powders, anhydrous compositions, or emulsions disclosed herein, wherein the subject is a cow, a pig, a horse, a cat, a dog, a rat, a mouse, or a bat.
- a method of inhibiting coronavirus fusion to a host cell in a subject the method comprising administering to the subject any one of the dry powders, anhydrous compositions, or emulsions disclosed herein.
- the subject is a human, a cow, a pig, a horse, a cat, a dog, a rat, a mouse, or a bat.
- the coronavirus is a betacoronavirus.
- the coronavirus is SARS-CoV-2.
- the coronavirus is a variant of SARS-CoV- 2.
- the variant is Wuhan-Hu-1, B.1.427/B.1.429, B.1.617.2, D614G B.1, Brazilian variant P.1, B.1.1.7, B.1.351, B.1.525, B.1.526, B.1.617.1, B.1.617.3, P.2, B.1.621, B.1.621.1, B.1.1.529, BA.1, BA.1.1, BA.2, BA.3, BA.4, or BA.5.
- the variant is B.1.351, Cluster 5, Lineage B.1.1.207, Lineage B.1.1.7, Variant of Concern 202102/02, Lineage B.1.1.317, Lineage B.1.1.318, Lineage B.1.351, Lineage B.1.429, Lineage B.1.525, Lineage P.1 (also known as Lineage B.1.1.28), Lineage B.1.1.529, Lineage BA.1, Lineage BA.1.1, Lineage BA.2, Lineage BA.3, Lineage BA.4 Lineage BA.5, D614G, E484K, N501Y, S477G/N, or P681H.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for use in a method of treating a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for use in a method of preventing a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for treating a Page 12 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for preventing a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for the manufacture of a medicament for treating a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for the manufacture of a medicament for preventing a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for use in a method of inhibiting coronavirus fusion to a host cell in a subject.
- FIG.1 depicts a mechanism of action of SARS-CoV-2 S fusion inhibitor peptides.
- FIG.2 provides the amino acid sequence of the S protein (SEQ ID NO: 1) of SARS- CoV-2.
- FIG. 3 is a schematic representation of the SARS-CoV-2 spike (S) protein, including the sequence composition of the heptad repeat domain 1 (HR1) (SEQ ID NO: 2) and heptad repeat domain 2 (HR2) (SEQ ID NO: 3) fusion domains.
- FIG. 4 shows an alignment of the HR1 and HR2 regions of SARS-CoV-2 and SARS-CoV-1 (“SARS, C.2004”) viruses highlighting the sequence homology, with striking sequence identity between the HR2 regions of SARS-CoV-2 and SARS-CoV-1 (SEQ ID NOs: 79 and 80).
- FIG. 5 shows a variety of non-natural amino acids containing olefinic tethers that can be used to generate hydrocarbon stapled SARS-CoV-2 S peptides bearing staples spanning i, i+3; i, i+4; and i, i+7 positions.
- Single staple scanning is used to generate a library of singly Page 13 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) stapled SARS-CoV-2-19 HR2 peptides for conjugation to PEG-thiocholesterol or PEG- cholesterol moieties.
- FIG. 6 shows a variety of staple compositions in multiply stapled peptides and staple scanning to generate a library of multiply stapled SARS-CoV-2 HR2 peptides for conjugation to PEG-thiocholesterol or PEG-cholesterol moieties.
- FIG. 7 shows a variety of staple compositions in tandem stitched peptides to generate a library of stitched SARS-CoV-2 HR2 peptides for conjugation to PEG- thiocholesterol or PEG-cholesterol moieties.
- FIG. 7 shows a variety of staple compositions in tandem stitched peptides to generate a library of stitched SARS-CoV-2 HR2 peptides for conjugation to PEG- thiocholesterol or PEG-cholesterol moieties.
- FIG. 8 is an illustration of an exemplary approach to designing, synthesizing, and identifying optimal stapled peptide constructs to target the SARS-CoV-2 fusion apparatus, including the generation of Ala scan, staple scan, and variable N- and C-terminal deletion, addition, and derivatization libraries for conjugation to PEG-thiocholesterol or PEG- cholesterol moieties.
- Singly and doubly stapled and stitched constructs, including alanine and staple and stitch scans are used to identify optimal stapled peptides for conjugation to PEG- thiocholesterol or PEG-cholesterol moieties and application in in vitro and in vivo analyses.
- FIG. 9 is a helical wheel depiction of a portion of the SARS-CoV-2 HR2 domain structured as an amphipathic alpha-helix (SEQ ID NO: 4), illustrating the predominantly hydrophobic binding interface, with flanking charged or polar residues at the perimeter of the binding interface and at the non-interacting face. The arrow refers to the hydrophobic moment.
- FIG.10 shows a synthetic schema for converting thiocholesterol or cholesterol into a carboxylic acid for facile on-resin derivatization of stapled peptides with cholesterol- containing moieties.
- DCM dichloromethane
- TFA trifluoroacetic acid.
- FIG.11A-11B shows a synthetic schema of the steps for on-resin derivatization of the stapled peptide sequence (SEQ ID NO: 74) with a PEG-linked thiocholesterol moiety (FIG. 11A) and a synthetic schema of the steps for on-resin derivatization of the stapled peptide sequence (SEQ ID NO: 74) with a PEG-linked cholesterol moiety (FIG.11B).
- FIG. 11A shows a synthetic schema of the steps for on-resin derivatization of the stapled peptide sequence (SEQ ID NO: 74) with a PEG-linked thiocholesterol moiety (FIG.11A)
- FIG.11B shows a synthetic schema of the steps for on-resin derivatization of the stapled peptide sequence (SEQ ID NO: 74) with a PEG-linked cholesterol moiety (FIG.11B).
- FIG. 12 shows exemplary unstapled (SEQ ID NOs: 5 and 6) and stapled SARS- CoV-2 HR2 peptide sequences (SEQ ID NOs: 7-21) generated by single i, i+7 staple scanning of a core template sequence (amino acids 1178-1199) bearing N- and C-terminal sequence extensions (e.g., amino acids 1168-1205) and C-terminal derivatization with PEG- thiocholesterol or PEG-cholesterol moieties of varying PEG linker length.
- FIG. 14 shows that a stapled HR2 peptide bearing a PEG4-thiocholesterol moiety appended on-resin (Staple D, SEQ ID NO: 10) exhibits consistent and potent anti-viral activity in the pseudovirus assay whether the cells were treated with peptide (1 ⁇ M) before or after viral inoculation across a series of SARS-CoV-2 pseudovirus variants.
- the corresponding unstapled peptide (SEQ ID NO: 6) is ineffective when applied after viral inoculation and exhibits less anti-viral activity compared to the stapled sequence even when applied before viral inoculation with a series of SARS-CoV-2 pseudovirus variants (pseudovirus: D614G B.1, Wuhan-Hu-1, B.1.526, B.1.427/B.1.429, B.1.1.7; cells: 293T- ACE2; read-out taken at 72 h).
- SARS-CoV-2 pseudovirus variants pseudovirus: D614G B.1, Wuhan-Hu-1, B.1.526, B.1.427/B.1.429, B.1.1.7; cells: 293T- ACE2; read-out taken at 72 h.
- FIG. 15 shows the differential antiviral activity of an unstapled and stapled HR2 peptides bearing a PEG4-thiocholesterol moiety appended on-resin, with peptide of SEQ ID NO: 10 (Staple D) showing the most potent dose-responsive anti-viral activity, followed by the unstapled peptide of SEQ ID NO: 6.
- the stapled peptide of SEQ ID NO: 17 (Staple K) was the least active in this pseudovirus assay (pseudovirus: B.1.526; cells: 293T-ACE2; serial 2-fold dilution starting at 1 ⁇ M; read-out: 72 h).
- FIG. 17 shows the differential antiviral activity of a series of i, i+7 stapled HR2 peptides bearing a PEG4-thiocholesterol moiety appended on-resin.
- peptides of SEQ ID NOs: 11, 14, and 15 show little to no activity (as measured by concentration of virus in ⁇ M on the X-axis) and peptides of SEQ ID NOs: 13 and 16 (Staples G and J) exhibit moderate activity
- the peptide of SEQ ID NO: 10 (Staple D), consistent with the pseudovirus assays results shown in FIG.15, stands out as having uniquely potent activity among the various stapled HR2 peptides in this SARS-CoV-2 live virus assay (live virus: USA- WA1/2020; cells: VeroB6; peptide dose-range 4-1000 nM (i.e., each group of bars, from Page 15 of 91 BUSINESS.31107393.1 Attorney Re
- No.406693-002WO bottom to top, represent a decreasing 2-fold dilution of peptide; i.e., 1000 nM, 500 nM, 250 nM, 125 nM, 62.5 nM, 31.25 nM, 15.625 nM, 7.8125 nM, 3.90625 nM)).
- FIG. 18A-18B shows the differential antiviral activity of an i, i+7 staple scan of the indicated HR2 peptide sequence (SEQ ID NOs: 7-21) bearing a C-terminal PEG4- thiocholesterol moiety against SARS-CoV-2 (virus: live Beta strain; cells: VeroB6; peptide dose 4 ⁇ M), with the most active peptide sequences noted with an asterisk (FIG. 18A).
- a discrete subset of staple positions afford potent anti-viral activity (SEQ ID NOs: 10, 13, 17, 20), as summarized on a helical wheel depiction of the helical portion of the HR2 sequence (FIG.18B).
- FIG. 19 shows the antiviral activity of an i, i+7 stapled HR2 peptide of SEQ ID NO:10 bearing a PEG4-thiocholesterol moiety against a GFP expressing SARS-CoV-2 Omicron variant B.1.1.529.1 (BA1) pseudovirus (cells; 293T-ACE2 cells; peptide serial 2-fold dilution from 2000 nM; 48 h read-out).
- BA1 pseudovirus
- FIG. 20 shows the antiviral activity of an i, i+7 stapled HR2 peptide of SEQ ID NO:10 bearing a PEG4-thiocholesterol moiety against live SARS-CoV-2 beta and delta strains (cells: VeroB6; peptide dose-range 15-4000 nM (i.e., each group of bars, from bottom to top, represent a decreasing 2-fold dilution of peptide; i.e., 4000 nM, 2000 nM, 1000 nM, 500 nM, 250 nM, 125 nM, 62.5 nM, 31.25 nM, 15.625 nM)).
- FIG. 21 shows the antiviral activity of an i, i+7 stapled HR2 peptide of SEQ ID NO:13 bearing a PEG4-thiocholesterol moiety, as measured against GFP-expressing SARS- CoV pseudoviruses, including SARS-CoV-2 Wuhan-hu-1, SARS-CoV-2 Omicron BA1.1.529.1 (BA1), SARS-CoV-2 Omicron BA1.1.529.2 (BA2), and SARS-CoV-1 (Urbani) (cells; 293T-ACE2 cells; peptide serial 2-fold dilution from 10 ⁇ M; 48 h read-out).
- FIG. 1 shows the antiviral activity of an i, i+7 stapled HR2 peptide of SEQ ID NO:13 bearing a PEG4-thiocholesterol moiety, as measured against GFP-expressing SARS- CoV pseudoviruses, including SARS-CoV-2 Wuhan-hu-1, SARS-CoV-2 Omicron BA
- SARS-CoV-2 Wuhan-hu-1 SARS-CoV-2 Omicron BA1.1.529.1 (BA1), SARS-CoV-2 Omicron BA1.1.529.2 (BA2), and SARS-CoV-1 (Urbani) (cells; 293T-ACE2 cells; peptide serial 2-fold dilution from 10 ⁇ M; 48 h read-out).
- FIG.23 shows the antiviral activity of i, i+7 stapled HR2 peptides of SEQ ID NO: 13 and SEQ ID NO: 20 bearing a PEG4-thiocholesterol moiety, as measured against live SARS-CoV-2 beta strain virus (cells: VeroB6; 4 ⁇ M dosing).
- FIGs.24A-24B shows a sequence map of an i, i+7 stapled HR2 peptide of SEQ ID NO: 10 (Staple D spanning positions K1181 and E1188), highlighting the amino acid positions Page 16 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO (208172) that are alternatively in contact with the HR1 core or unbound (solvent exposed) (SEQ ID NO: 81) (FIG. 24A).
- Mutagenesis studies revealed a series of exemplary positions that are relatively unaffected by substitution of the native residue with alanine, as assessed in the context of SEQ ID NO: 10 with a C-terminal PEG4 thiocholesterol moiety against GFP- expressing SARS-CoV-1 (Urbani) in a pseudovirus assay (cells; 293T-ACE2 cells; peptide 4- fold serial dilution from 1.25 ⁇ M; 48 h read-out) (FIG.24B).
- the peptide of SEQ ID NO: 10 (Staple D) bearing a PEG8 linker moiety exhibits the most potent, dose-responsive activity in this pseudovirus assay across a series of five SARS-CoV-2 variants (as measured by number of green cells or percent GFP positive shown on the X-axis), with PEG3 having comparatively less activity among the constructs of variable PEG-linker length (pseudoviruses/variants: Wuhan-Hu-1 (FIG.
- FIG. 25A shows B.1.427/B.1.429 (FIG. 25B), B.1.617.2 (FIG. 25C), D614G B.1(FIG. 25D), Brazilian variant P.1 (FIG. 25E); cells: 293T-ACE2; serial 2-fold dilution starting at 1 ⁇ M (i.e., from bottom to top for each cluster of bars: 1 ⁇ M, 500 nM, 250 nM, 125 nM, 62.5 nM, 31.25 nM, 15.625 nM, 7.8125 nM); read-out: 48 h). [0084] FIG.
- the peptide of SEQ ID NO: 10 (Staple D) bearing a PEG8 linker moiety exhibits the most potent, dose-responsive activity in this SARS-CoV-2 live virus assay, with PEG3 having comparatively less activity among the constructs of variable PEG-linker length (live virus: S.
- No.406693-002WO (208172) serial 2-fold dilution starting at 2 ⁇ M from bottom to top for each cluster of bars: 2 ⁇ M, 1 ⁇ M, 500 nM, 250 nM, 125 nM, 62.5 nM, 31.2 nM, 15.6 nM; read-out: 48 h).
- FIG. 1 500 nM, 250 nM, 125 nM, 62.5 nM, 31.2 nM, 15.6 nM; read-out: 48 h).
- VSV Vesicular Stomatitis Virus
- MMV murine leukemia virus
- SEQ ID NO: 6 unstapled peptide
- FIG.31 shows that an unstapled peptide derivatized with PEG4-thiocholesterol on resin (SEQ ID NO: 6) exhibits somewhat improved anti-viral activity compared to an unstapled peptide derivatized in solution with a GSGSGC-PEG4-cholesterol moiety (shown in SEQ ID NO:71) in this SARS-CoV-2 live virus assay (live virus: S. African B.1.351; cells: VeroB6; peptide dose-range 4-1000 nM with two-fold dilutions).
- FIG.32 shows that an unstapled HR2 peptide (SEQ ID NO: 6) and a stapled HR2 peptide (SEQ ID NO: 10) derivatized with PEG4-thiocholesterol on resin show no non-specific cytotoxicity when applied to 293T-ACE2 cells in the pseudovirus assay, whereas the corresponding unstapled HR2 peptide derivatized in solution with a GSGSGC-PEG4- cholesterol moiety kills cells within the dosing range (pseudovirus: D614G B.1; cells: 293T- ACE2; serial 2-fold dilution starting at 2500 nM (from bottom to top, 2500 nM, 1250 nM, 630 nM, 315 nM, 158 nM, 78 nM); read-out: 48 h).
- FIG.33 shows a direct fluorescence polarization binding curve of SEQ ID NO: 10 derivatized at the C-terminus with PEG8-Chol and at the N-terminus with a FITC- ⁇ -Ala in place of the acetyl, combined with a serial dilution of a recombinant five-helix bundle (5HB) lacking the 3 rd HR2 group. Addition of the FITC-HR2 peptide completes the fusogenic six helix bundle. (peptide: 5 nM; 5-HB protein serial dilution from 1000 nM). [0092] FIG.
- FIG. 34 shows the differential antiviral activity of SEQ ID NO: 10 derivatized at the C-terminus with PEG8-Chol against a collection of GFP expressing SARS-CoV-2 variant pseudoviruses (293T-ACE2 cells; peptide serial dilution from 1000 nM; 48 h read-out).
- FIG. 35 shows the differential antiviral activity of SEQ ID NO: 10 derivatized at Page 18 of 91 BUSINESS.31107393.1 Attorney Ref.
- FIG. 36 shows the differential antiviral activity of SEQ ID NO: 10 derivatized at the C-terminus with PEG8-Chol against SARS-CoV-2 beta and delta live viruses (cells: Vero; peptide serial dilution from 100 nM serial dilution of peptide starting at 100 nM; 48 hour read- out).
- FIG.37 shows the antiviral activity of SEQ ID NO: 10 derivatized at the C-terminus with PEG8-Chol against GFP expressing Alphacoronavirus NL63 pseudovirus (293T-ACE2 cells; peptide serial 3-fold dilution from 10 ⁇ M; 48 h read-out).
- the instant disclosure provides compositions comprising peptides that are useful for the treatment and/or prevention of coronavirus infections.
- provided herein are dry powders, anhydrous compositions, or emulsions comprising a peptide that binds to a SARS-CoV-2 spike protein.
- peptides comprised within the dry powders, anhydrous compositions, and emulsions provided herein are particularly advantageous because they prevent coronavirus fusion to a host cell.
- Definitions [0097] As used herein, the following definitions shall apply unless otherwise indicated. These definitions apply regardless of whether a term is used by itself or in combination with other terms, unless otherwise indicated. Hence, the definition of “alkyl” applies to “alkyl” as well as the “alkyl” portions of “-O-alkyl” etc.
- the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75 th Ed.
- heteroatom means one or more of oxygen, sulfur, nitrogen, phosphorus, or silicon (including, any oxidized form of nitrogen, sulfur, phosphorus, or silicon; the quaternized form of any basic nitrogen; or a substitutable nitrogen of a heterocyclic ring, for example N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or NR + (as in N-substituted pyrrolidinyl)).
- N as in 3,4-dihydro-2H-pyrrolyl
- NH as in pyrrolidinyl
- NR + as in N-substituted pyrrolidinyl
- alkylene chain is a polymethylene group, i.e., –(CH2)n–, wherein n is a positive integer, preferably from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, or from 2 to 3.
- a substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.
- the term “-(C0 alkylene)-” refers to a bond. Accordingly, the term “-(C0-3 alkylene)-” encompasses a bond (i.e., C0) and a -(C1-3 alkylene)- group.
- alkenylene refers to a bivalent alkenyl group.
- a substituted alkenylene chain is a polymethylene group containing at least one double bond in which one or more hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.
- halogen means F, Cl, Br, or I.
- aryl used alone or as part of a larger moiety as in “aralkyl,” “aralkoxy,” or “aryloxyalkyl,” refers to monocyclic or bicyclic ring systems having a total of 5 to 14 ring members, wherein at least one ring in the system is aromatic and wherein each ring in the system contains 3 to 7 ring members.
- aryl may be used interchangeably with the term “aryl ring.”
- aryl refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, anthracyl, and the like, which may bear one or more substituents.
- aryl is a group in which an aromatic ring is fused to one or more non-aromatic rings, such as indanyl, phthalimidyl, naphthimidyl, phenanthridinyl, or tetrahydronaphthyl, and the like.
- phenylene refers to a multivalent phenyl group having the appropriate number of open valences to account for groups attached to it. For example, “phenylene” is a bivalent phenyl group when it has two groups attached to it ); “phenylene” is a trivalent Page 20 of 91 BUSINESS.31107393.1 Attorney Ref.
- arylene refers to a multivalent (e.g., bivalent) aryl group.
- heteroaryl and “heteroar—,” part of a larger moiety, e.g., “heteroaralkyl,” or “heteroaralkoxy,” refer to groups having 5 to 10 ring atoms, preferably 5, 6, or 9 ring atoms; having 6, 10, or 14 ⁇ electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms.
- heteroatom refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen.
- Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl.
- heteroaryl and “heteroar—,” as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where unless otherwise specified, the radical or point of attachment is on the heteroaromatic ring or on one of the rings to which the heteroaromatic ring is fused.
- Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H–quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, and tetrahydroisoquinolinyl.
- a heteroaryl group may be mono– or bicyclic.
- heteroaryl may be used interchangeably with the terms “heteroaryl ring,” “heteroaryl group,” or “heteroaromatic,” any of which terms include rings that are optionally substituted.
- heteroarylkyl refers to an alkyl group substituted by a heteroaryl, wherein the alkyl and heteroaryl portions independently are optionally substituted.
- heteroarylene refers to a multivalent heteroaryl group having the appropriate number of open valences to account for groups attached to it.
- heteroarylene is a bivalent heteroaryl group when it has two groups attached to it; “heteroarylene” is a trivalent heteroaryl group when it has three groups attached to it.
- heterocycle As used herein, the terms “heterocycle,” “heterocyclyl,” “heterocyclic radical,” and “heterocyclic ring” are used interchangeably and refer to a stable 5– to 7–membered monocyclic or 7– to 10–membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, as defined above.
- the term “nitrogen” includes a substituted nitrogen.
- the nitrogen in a saturated or partially unsaturated ring having 0–3 heteroatoms selected from oxygen, sulfur or nitrogen, the nitrogen may be N (as in 3,4–dihydro–2H–pyrrolyl), NH (as in pyrrolidinyl), or + NR (as in N– substituted pyrrolidinyl).
- a heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted.
- saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothiophenyl pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, 2-oxa-6- azaspiro[3.3]heptane, and quinuclidinyl.
- heterocycle used interchangeably herein, and also include groups in which a heterocyclyl ring is fused to one or more aryl, heteroaryl, or cycloaliphatic rings, such as indolinyl, 3H–indolyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl.
- a heterocyclyl group may be mono– or bicyclic.
- heterocyclylalkyl refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.
- oxo-heterocyclyl refers to a heterocyclyl substituted by one or more oxo group.
- heterocyclylene refers to a multivalent heterocyclyl group having the appropriate number of open valences to account for groups attached to it. For example, “heterocyclylene” is a bivalent heterocyclyl group when it has two groups attached to it; “heterocyclylene” is a trivalent heterocyclyl group when it has three groups attached to it.
- oxo-heterocyclylene refers to a multivalent oxo-heterocyclyl group having the appropriate number of open valences to account for groups attached to it.
- partially unsaturated refers to a ring moiety that includes at least one double or triple bond.
- partially unsaturated is intended to encompass rings having multiple sites of unsaturation but is not intended to include aryl or heteroaryl moieties, as herein defined.
- a molecule disclosed herein may contain “optionally substituted” moieties.
- substituted means that one or more hydrogens of the designated moiety are replaced with a suitable substituent.
- an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from Page 22 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) a specified group, the substituent may be either the same or different at every position.
- Combinations of substituents envisioned herein are preferably those that result in the formation of stable or chemically feasible compounds.
- R * is C1–6 aliphatic
- R * is optionally substituted with halogen, – R ⁇ , -(haloR ⁇ ), -OH, –OR ⁇ , –O(haloR ⁇ ), –CN, –C(O)OH, –C(O)OR ⁇ , –NH2, –NHR ⁇ , –NR ⁇ 2, or –NO2, wherein each R ⁇ is independently selected from C1–4 aliphatic, –CH2Ph, –O(CH2)0– 1 Ph, or a 5–6–membered saturated, partially unsaturated, or aryl ring having 0–4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and wherein each R ⁇ is unsubstituted or where preceded by halo is substituted only with one or more halogens.
- An optional substituent on a substitutable nitrogen is independently –R ⁇ , –NR ⁇ 2, –C(O)R ⁇ , –C(O)OR ⁇ , –C(O)C(O)R ⁇ , –C(O)CH 2 C(O)R ⁇ , -S(O) 2 R ⁇ , -S(O) 2 NR ⁇ 2 , –C(S)NR ⁇ 2 , – C(NH)NR ⁇ 2, or –N(R ⁇ )S(O)2R ⁇ ; wherein each R ⁇ is independently hydrogen, C1–6 aliphatic, unsubstituted –OPh, or an unsubstituted 5–6–membered saturated, partially unsaturated, or aryl ring having 0–4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, two independent occurrences of R ⁇ , taken together with their intervening atom(s) form an unsub
- the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response, and the like, and are commensurate with a reasonable benefit/risk ratio.
- Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge et al., describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1–19, incorporated herein by reference.
- Pharmaceutically acceptable salts of the compounds disclosed herein include those derived from suitable inorganic and organic acids and bases.
- Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods used in the art such as ion exchange.
- inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid
- organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods used in the art such as ion exchange.
- salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, gluconate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2–hydroxy–ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2–naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pect
- Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N + (C1–4alkyl)4 salts.
- Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
- Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and Page 25 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
- structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, Z and E double bond isomers, and Z and E conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present molecules are within the scope of the disclosure. Unless otherwise stated, all tautomeric forms of the compounds of the disclosure are within the scope of the disclosure.
- the disclosure includes compounds that differ only in the presence of one or more isotopically enriched atoms.
- Diastereomeric mixtures can be separated into their individual diastereomers on the basis of their physical chemical differences by methods known to those skilled in the art, such as, for example, by chromatography and/or fractional crystallization.
- Enantiomers can be separated by converting the enantiomeric mixture into a diastereomeric mixture by reaction with an appropriate optically active compound (e.g., chiral auxiliary such as a chiral alcohol or Mosher’s acid chloride), separating the diastereomers and converting (e.g., hydrolyzing) the individual diastereomers to the corresponding pure enantiomers.
- an appropriate optically active compound e.g., chiral auxiliary such as a chiral alcohol or Mosher’s acid chloride
- converting e.g., hydrolyzing
- a particular enantiomer of a molecule disclosed herein may be prepared by asymmetric synthesis.
- molecule contains a basic functional group (such as amino) or an acidic functional group (such as carboxylic acid) diastereomeric salts are formed with an appropriate optically active acid or base, followed by resolution of the diastereomers thus formed by fractional crystallization or chromatographic means known in the art, and subsequent recovery of the pure enantiomers.
- Individual stereoisomers of the molecules disclosed herein may, for example, be substantially free of other isomers, or may be admixed, for example, as racemates or with all other, or other selected, stereoisomers.
- Chiral center(s) in a molecule disclosed herein can have the S or R configuration as defined by the IUPAC 1974 Recommendations.
- alkyl refers to a saturated straight or branched hydrocarbon, such as a straight or branched group of 1-12, 1-10, or 1-6 carbon atoms, referred to herein as C 1 -C 12 alkyl, C1-C10 alkyl, and C1-C6 alkyl, respectively.
- Exemplary alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, 2-methyl-1-propyl, 2-methyl-2-propyl, 2-methyl- 1-butyl, 3-methyl-1-butyl, 2-methyl-3-butyl, 2,2-dimethyl-1-propyl, 2-methyl-1-pentyl, 3- methyl-1-pentyl, 4-methyl-1-pentyl, 2-methyl-2-pentyl, 3-methyl-2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl-1-butyl, 3,3-dimethyl-1-butyl, 2-ethyl-1-butyl, butyl, isobutyl, t-butyl, pentyl, isopentyl, neopentyl, hexyl, heptyl, octyl, etc.
- cycloalkyl refers to a monovalent saturated cyclic, bicyclic, or bridged cyclic (e.g., adamantyl) hydrocarbon group of 3-12, 3-8, 4-8, or 4-6 carbons, referred to herein, e.g., as “C 3 -C 6 cycloalkyl,” derived from a cycloalkane.
- exemplary cycloalkyl groups include cyclohexyl, cyclopentyl, cyclobutyl, and cyclopropyl.
- cycloalkylene refers to a bivalent cycloalkyl group.
- haloalkyl refers to an alkyl group that is substituted with at least one halogen.
- exemplary haloalkyl groups include -CH 2 F, -CHF 2 , -CF 3 , -CH 2 CF 3 , -CF 2 CF 3 , and the like.
- haloalkylene refers to a bivalent haloalkyl group.
- hydroxyalkyl refers to an alkyl group that is substituted with at least one hydroxyl.
- Exemplary hydroxyalkyl groups include -CH2CH2OH, -C(H)(OH)CH3, -CH2C(H)(OH)CH2CH2OH, and the like.
- alkenyl and alkynyl are art-recognized and refer to unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double or triple bond respectively.
- alkoxyl or “alkoxy” are art-recognized and refer to an alkyl group, as defined above, having an oxygen radical attached thereto. Representative alkoxyl groups include methoxy, ethoxy, propyloxy, tert-butoxy, and the like.
- haloalkoxyl refers Page 27 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO 208172 to an alkoxyl group that is substituted with at least one halogen.
- exemplary haloalkoxyl groups include -OCH 2 F, -OCHF 2 , -OCF 3 , -OCH 2 CF 3 , -OCF 2 CF 3 , and the like.
- a cyclopentane substituted with an oxo group is cyclopentanone.
- the symbol “ ” indicates a point of attachment.
- any substituent or variable occurs more than one time in any constituent or the molecules disclosed herein, its definition on each occurrence is independent of its definition at every other occurrence, unless otherwise indicated.
- One or more molecules disclosed herein may exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like, and it is intended that the disclosure embrace both solvated and unsolvated forms.
- “Solvate” means a physical association of a molecule disclosed herein with one or more solvent molecules. This physical association involves varying degrees of ionic and covalent bonding, including hydrogen bonding. In an embodiment the solvate will be capable of isolation, for example when one or more solvent molecules are incorporated in the crystal lattice of the crystalline solid.
- Solvate encompasses both solution-phase and isolatable solvates.
- suitable solvates include ethanolates, methanolates, and the like.
- “Hydrate” is a solvate wherein the solvent molecule is H2O.
- IC 50 is art-recognized and refers to the concentration of a compound that is required to achieve 50% inhibition of the target.
- EC 50 is art recognized and refers to the concentration of a compound that is required to achieve a response that is 50% of the maximum target effect relative to the baseline.
- Emax is art recognized and refers to the concentration of a compound that is required to achieve maximal target effect.
- the term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo or ex vivo.
- the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, emulsions (e.g., such as an oil/water or water/oil emulsions), and various types of wetting agents.
- the compositions also can include stabilizers and preservatives.
- salts of the molecules disclosed herein are contemplated as being pharmaceutically acceptable.
- salts of acids and bases that are non- pharmaceutically acceptable may also find use, for example, in the preparation or purification of a pharmaceutically acceptable compound.
- a molecule disclosed herein contains both a basic moiety (such as, but not limited to, a pyridine or imidazole) and an acidic moiety (such as, but not limited to, a carboxylic acid) zwitterions (“inner salts”) may be formed.
- acidic and basic salts used within the scope of the disclosure are pharmaceutically acceptable (i.e., non-toxic, physiologically acceptable) salts.
- Such salts of the molecules disclosed herein may be formed, for example, by reacting a molecule disclosed herein with an amount of acid or base, such as an equivalent amount, in a medium such as one in which the salt precipitates or in an aqueous medium followed by lyophilization.
- compositions are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are compositions disclosed herein that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the disclosure that consist essentially of, or consist of, the recited processing steps.
- compositions specifying a percentage are by weight unless otherwise specified.
- the term “effective amount” refers to the amount of a compound sufficient to effect beneficial or desired results (e.g., a therapeutic, ameliorative, inhibitory, or preventative result).
- an effective amount can be administered in one or more administrations, applications or dosages and is not intended to be limited to a particular formulation or administration route.
- the term “treating” includes any effect, e.g., lessening, reducing, modulating, ameliorating, or eliminating, that results in the improvement of the condition, disease, disorder, and the like, or ameliorating a symptom thereof.
- the term “subject” includes any human or non-human animal. In an embodiment, the subject is a human or non-human mammal. In an embodiment, the subject is a human.
- the instant disclosure provides dry powders, anhydrous compositions, and emulsions comprising a peptide.
- the instant disclosure provides a dry Page 29 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) powder comprising a peptide that binds to a SARS-CoV-2 spike protein.
- the instant disclosure provides an anhydrous composition comprising a peptide that binds to a SARS-CoV-2 spike protein.
- the instant disclosure provides an emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a stapled SARS-CoV-2 peptide based on a portion of the HR2 region.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise stapled SARS-CoV-2 peptides derived from SARS-CoV-2 HR2 (1168-1205) (DISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGK (SEQ ID NO:6)).
- the stapled SARS-CoV-2 peptides derived from SEQ ID NO:9 include SAH- SARS-CoV-2-A; SAH-SARS-CoV-2-B; SAH-SARS-CoV-2-C; SAH-SARS-CoV-2-D; SAH- SARS-CoV-2-E; SAH-SARS-CoV-2-F; SAH-SARS-CoV-2-G; SAH-SARS-CoV-2-H; SAH- SARS-CoV-2-I; SAH-SARS-CoV-2-J; SAH-SARS-CoV-2-K; SAH-SARS-CoV-2-L; SAH- SARS-CoV-2-M; SAH-SARS-CoV-2-N; or SAH-SARS-CoV-2-O (e.g., SEQ ID NOs: 7-21), as shown in Table 1 below.
- the two formulae indicated by the “*” include: or [00149] In some cases, the two formulae indicated by the “*” include: Page 31 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) or .
- amino acids e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 amino acids added
- N and/or C terminal deletions e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 amino acids deleted.
- the SARS-CoV-2 peptides are derived from SEQ ID NO:4.
- the bolded and underlined sequence used herein e.g., in Table 1 identifies the stapling amino acids at the N- and C-termini and the intervening sequence between staples for each disclosed peptide.
- the peptide is single-stapled peptide.
- SEQ ID NO: 6 includes one or more variants. For instance, if positions 25 or 29 of SEQ ID NO: 6 are substituted, they are substituted by an ⁇ , ⁇ -disubstituted non-natural amino acid with olefinic side chains or are substituted by any amino acid. In an embodiment, if one or more of positions 1, 2, 5, 7, 8, 10, 12, 16, 17, 19, 23, 24, 26, 28, 30, 31, 33, and 36 of SEQ ID NO: 6 are substituted, they are substituted by conservative amino acid substitutions. In an embodiment, if one or more of positions 3, 4, 6, 9, 11, 13, 15, 18, 20, 22, 27, 32, 34, 35, 37, or 38 in SEQ ID NO: 6 are substituted, they are substituted by any amino acid.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide that is 19 to 50 (e.g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) amino acids in length.
- the peptide is 19 to 60 (e.g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60) amino acids in length.
- the peptide ranges from 19 to 100, 38 to 100, 19 to 60, 38 to 60, 19 to 50, 38 to 50, 19 to 45, 38 to 45, 19 Page 32 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) to 40 and 38 to 40 amino acids in length.
- the peptide described above have one or more (1, 2, 3, 4, 5, 6) of the properties listed below: (i) is alpha-helical; (ii) is protease resistant; (iii) inhibits fusion of SARS-CoV-2 with a host cell; and/or (iv) inhibits infection of a cell by SARS-CoV-2.
- the peptide inhibits infection of a cell by SARS- CoV-2 in pseudovirus and/or live SARS-CoV-2 virus assays and/or wherein the peptide prevents infection of a cell by SARS-CoV-2 in the pseudovirus and/or the live SARS-CoV-2 virus assays.
- the peptide includes an amino acid sequence that has 2 to 18, 2 to 17, 2 to 16, 2 to 15, 2 to 14, 2 to 13, 2 to 12, 2 to 11, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, or 2 substitutions, insertions, and/or deletions relative to SEQ ID NO: 6, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:17, or SEQ ID NO:20.
- a peptide having substitutions, insertions, and/or deletions relative to SEQ ID NO: 6, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:17, or SEQ ID NO:20 as described above (i) is alpha- helical; (ii) is protease resistant; (iii) inhibits fusion of SARS-CoV-2 with a host cell; and/or (iv) inhibits infection of a cell by SARS-CoV-2.
- the peptide inhibits infection of a cell by SARS-CoV-2 in pseudovirus and/or live SARS-CoV-2 virus assays and/or wherein the peptide prevents infection of a cell by SARS-CoV-2 in the pseudovirus and/or the live SARS-CoV-2 virus assays.
- the peptide binds to a polypeptide comprising or consisting of the sequence of SEQ ID NO:78.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide that comprises 0-10 (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) amino acid substitutions compared to one of the single-stapled peptides (e.g., SEQ ID NOs: 7-21) in Table 1.
- the peptide is at least 75% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 94%, at least 95% identical) to one of the single-stapled peptides (e.g., SEQ ID NOs: 7-21) in Table 1.
- the peptide is 19 to 50 (e.g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) amino acids in length.
- the peptide is 19 to 60 (e.g., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60) amino acids in length.
- the peptide ranges from 19 to 100, 38 to 100, 19 to 60, 38 to 60, 19 to 50, 38 to 50, 19 to 45, 38 to 45, 19 to 40 and 38 to 40 amino acids in length.
- the peptide has one or more (1, 2, 3, 4, 5, 6) of the properties listed below: (i) is alpha-helical; (ii) is protease resistant; (iii) inhibits fusion of SARS-CoV-2 with a host cell; and/or (iv) inhibits infection of a cell by SARS-CoV-2.
- the peptide inhibits infection of a cell Page 33 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO (208172) by SARS-CoV-2 in pseudovirus and/or live SARS-CoV-2 virus assays and/or wherein the peptide prevents infection of a cell by SARS-CoV-2 in the pseudovirus and/or the live SARS- CoV-2 virus assays.
- the peptide binds to a polypeptide comprising or consisting of the sequence of SEQ ID NO:78.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide comprising or consisting of any one of the amino acid sequences of SEQ ID NOs: 5 or 6, except that at least two (e.g., 2, 3, 4, 5, 6) amino acids of SEQ ID NOs: 5 or 6 are replaced with a non-natural amino acid capable of forming a staple.
- the non-natural amino acid is an ⁇ , ⁇ -disubstituted non-natural amino acid with at least one olefinic side chain.
- the peptide is a peptide comprising or consisting of any one of the amino acid sequences of SEQ ID NOs: 5 or 6, except that at least two (e.g., 2, 3, 4, 5, 6) amino acids of SEQ ID NOs: 5 or 6 are replaced with a non-natural amino acid capable of forming a staple.
- the non-natural amino acid is an ⁇ , ⁇ -disubstituted non-natural amino acid with at least one olefinic side chain.
- the peptide is 19 to 50 (e.g., 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) amino acids in length.
- the peptide is 19 to 60 (e.g., 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60) amino acids in length.
- the peptide ranges from 19 to 100, 38 to 100, 19 to 60, 38 to 60, 19 to 50, 38 to 50, 19 to 45, 38 to 45, 19 to 40 and 38 to 40 amino acids in length.
- the peptide has one or more (1, 2, 3, 4, 5, 6) of the properties listed below: (i) is alpha-helical; (ii) is protease resistant; (iii) inhibits fusion of SARS-CoV-2 with a host cell; and/or (iv) inhibits infection of a cell by SARS-CoV-2.
- the peptide inhibits infection of a cell by SARS-CoV-2 in pseudovirus and/or live SARS-CoV-2 virus assays and/or wherein the peptide prevents infection of a cell by SARS-CoV-2 in the pseudovirus and/or the live SARS- CoV-2 virus assays.
- the peptide binds to a polypeptide comprising or consisting of the sequence of SEQ ID NO:78.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise peptides that comprise 0-10 (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) amino acid substitutions compared to one of the unmodified peptides (e.g., SEQ ID NOs: 5 or 6) in Table 1.
- peptides that are at least 75% (e.g., at least 75%, at least 80%, at least 85%, at least 90%, at least 95% identical) to one of the unmodified peptides (e.g., SEQ ID NOs: 5 or 6) in Table 1.
- the substitution as described herein is a conservative substitution.
- the peptide is 19 to 50 (e.g., 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) amino acids in length.
- the peptide is 19 to 60 (e.g., 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60) amino acids in length.
- the peptide ranges from 19 to 100, 38 to 100, 19 to 60, 38 to 60, 19 to 50, 38 to 50, 19 to 45, 38 to 45, 19 to 40 and 38 to 40 amino acids in length.
- the peptide described above have one or more (1, 2, 3, 4, 5, 6) of the properties listed below: (i) is alpha-helical; (ii) is protease resistant; (iii) inhibits fusion of SARS-CoV-2 with a host cell; and/or (iv) inhibits infection of a cell by SARS-CoV-2.
- the peptide inhibits infection of a cell by SARS- CoV-2 in pseudovirus and/or live SARS-CoV-2 virus assays and/or wherein the peptide prevents infection of a cell by SARS-CoV-2 in the pseudovirus and/or the live SARS-CoV-2 virus assays.
- the peptide binds to a polypeptide comprising or consisting of the sequence of SEQ ID NO:78.
- any substitution as described herein can be a conservative substitution. In an embodiment, any substitution as described herein is a non-conservative substitution.
- the non-natural amino acids that may be used as stapling amino acids are: (R)-2-(2'-propenyl)alanine; (R)-2-(4′-pentenyl)alanine; (R)- ⁇ -(7'-octenyl)alanine; (S)- ⁇ -(2′-propenyl)alanine; (S)- ⁇ -(4′-pentenyl)alanine; (S)-2-(7'-octenyl)alanine; ⁇ , ⁇ -Bis(4′- pentenyl)glycine; and ⁇ , ⁇ -Bis(7′-octeny)glycine.
- an internal staple replaces the side chains of 2 amino acids, i.e., each staple is between two amino acids separated by, for example, 6 amino acids.
- the amino acids forming the staple are at each of positions i and i+7 of the staple.
- cross-links between X1 and X8 are useful hydrocarbon stapled forms of that peptide.
- the use of an i and i+4 staple, multiple cross-links (e.g., 2, 3, 4, or more), or a tandem stitch is also contemplated.
- Peptide stapling is a term coined from a synthetic methodology wherein two olefin-containing side-chains (e.g., cross-linkable side chains) present in a peptide chain are covalently joined (e.g., “stapled together”) using a ring-closing metathesis (RCM) reaction to form a cross-linked ring (see, e.g., Blackwell et al., J. Org. Chem., 66: 5291-5302, 2001; Angew et al., Chem. Int. Ed. 37:3281, 1994).
- RCM ring-closing metathesis
- the structural-stabilization may be by, e.g., stapling the peptide (see, e.g., Walensky, J. Med. Chem., 57:6275-6288 (2014), the contents of Page 35 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) which are incorporated by reference herein in its entirety).
- the staple is a hydrocarbon staple.
- a staple used herein is a lactam staple; a UV-cycloaddition staple; an oxime staple; a thioether staple; a double-click staple; a bis-lactam staple; a bis- arylation staple; or a combination of any two or more thereof.
- Stabilized peptides as described herein include stapled peptides as well as peptides containing multiple staples or any other chemical strategies for structural reinforcement (see. e.g., Balaram P. Cur. Opin. Struct. Biol. 1992;2:845; Kemp DS, et al., J. Am. Chem.
- a peptide is “structurally-stabilized” in that it maintains its native secondary structure. For example, stapling allows a peptide, predisposed to have an ⁇ -helical secondary structure, to maintain its native ⁇ -helical conformation. This secondary structure increases resistance of the peptide to proteolytic cleavage and heat, and may increase target binding affinity, hydrophobicity, plasma membrane binding, and/or cell permeability. Accordingly, the stapled (cross-linked) peptides described herein have improved biological activity and pharmacology relative to a corresponding non-stapled (un-cross-linked) peptide.
- the modification(s) to introduce structural stabilization e.g., internal cross-linking, e.g., stapling
- structural stabilization e.g., internal cross-linking, e.g., stapling
- the modification(s) to introduce structural stabilization may be positioned on the face of the SARS-CoV-2 HR2 helix that does not interact with the recombinant 5-helix bundle of SARS-CoV-2 or corresponding native fusion apparatus.
- the modification(s) to introduce stabilization (e.g., internal cross-linking, e.g., stapling) into the SARS-CoV-2 HR2 peptides described herein may be positioned on the face of the SARS-CoV-2 HR2 helix that does interact with the 5-helix bundle of SARS-CoV-2.
- a SARS-CoV-2 HR2 peptide described herein is stabilized by introducing a staple (e.g., a hydrocarbon staple) at the interface of the interacting and non-interacting helical faces of the SARS-CoV-2 HR2 protein.
- a SARS-CoV-2 HR2 peptide described herein is stabilized by introducing a staple (e.g., a hydrocarbon staple) or staples at the border between the hydrophobic interacting surface and the non-interacting faces of the SARS-CoV-2 HR2 protein.
- a staple e.g., a hydrocarbon staple
- staples e.g., a hydrocarbon staple
- staples e.g., a hydrocarbon staple
- No.406693-002WO (208172) internal cross-linking, e.g., stapling) into the SARS-CoV-2 HR2 peptides described herein are positioned at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to residues: (i) 11 and 18 of SEQ ID NO: 6; (ii) 12 and 19 of SEQ ID NO: 6; (iii) 13 and 20 of SEQ ID NO: 6; (iv) 14 and 21 of SEQ ID NO: 6; (v) 15 and 22 of SEQ ID NO: 6; (vi) 16 and 23 of SEQ ID NO: 6; (vii) 17 and 24 of SEQ ID NO: 6; (viii) 18, and 25 of SEQ ID NO: 6; (ix) 19 and 26 of SEQ ID NO: 6; (x) 20 and 27 of SEQ ID NO: 6; (xi) 21 and 28 of SEQ ID NO: 6; (xii) 22 and 29 of SEQ ID NO: 6; (xiii
- the SARS-CoV-2 HR2 peptides described herein may also contain one or more (e.g., 1, 2, 3, 4, or 5) amino acid substitutions (relative to an amino acid sequence set forth in any one of SEQ ID NOs: 5 or 6), e.g., one or more (e.g., 1, 2, 3, 4, or 5) conservative and/or non-conservative amino acid substitutions.
- the SARS-CoV-2 HR2 peptides described herein may also contain at least one, at least 2, at least 3, at least 4, or at least 5 amino acids added to the N-terminus of the peptide.
- the SARS-CoV-2 HR2 peptides described herein may also contain at least one, at least 2, at least 3, at least 4, or at least 5 amino acids added to the C-terminus of the peptide.
- the N-terminal aspartic acid in any one of the peptides disclosed herein is replaced with -N(H)C(O)-(C1-4 alkyl).
- the carboxylic acid group of the C-terminal lysine in any one of the peptides disclosed herein is replaced with C(O)NH 2 .
- the N-terminal aspartic acid in SEQ ID NO: 6, SEQ ID NO:10, or SEQ ID NO:20 is replaced with -N(H)C(O)-(C 1-4 alkyl).
- the carboxylic acid group of the C-terminal lysine in SEQ ID NO: 6, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:17, or SEQ ID NO:20 is replaced with C(O)NH 2 .
- the C-terminal lysine of any of the peptides discloses herein is replaced with ornithine (e.g., L-ornithine), L-2,3-diaminopropionic acid, L-2,7- diaminoheptanoic acid, diamino butyric acid (e.g., L-2,4-diamino butyric acid), an amino acid having an alpha carbon amine, or a diamine.
- ornithine e.g., L-ornithine
- L-2,3-diaminopropionic acid e.g., L-2,7- diaminoheptanoic acid
- diamino butyric acid e.g., L-2,4-diamino butyric acid
- an amino acid having an alpha carbon amine e.g., L-2,4-diamino butyric acid
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide that is or comprises a peptide of Formula (I): O O z or a pharmaceutically acceptable salt thereof, wherein: each R 1 and R 2 are independently H or a C 1 to C 10 alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heteroarylalkyl, or heterocyclylalkyl; R 3 is alkyl, alkenyl, alkynyl, or [R 4 —K—R 4 ] n ; each of which is substituted with 0-6 R 5 ; R4 is alkyl, alkenyl, or alkynyl; R 5 is halo, alkyl, OR 6 , N(R 6 ) 2 , SR 6 , SOR 6 , SO 2 R 6 , CO 2 R 6 , R 6 , a fluorescent moiety, or
- the peptide binds to a polypeptide comprising or consisting of the sequence of SEQ ID NO:78.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide that is or comprises a peptide of Formula (I-A): Page 38 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) or a pharmaceutically x, and [Xaa]y are as defined above for [00172]
- the peptide consists of Formula (I-A).
- R 3 of Formula (I-A) is alkenylene.
- the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa] y is replaced with - C(O)NH2.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide that is or comprises a peptide of Formula Ia: or a pharmaceutically acceptable salt thereof, wherein R3, [Xaa]w, [Xaa]x, and [Xaa]y are as defined above for Formula I.
- the peptide consists of Formula (Ia).
- the amino group of the N-terminal aspartic acid in [Xaa] w of Formula (Ia) is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the peptide comprises or consists of: y BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) Formula (Ic), or a pharmaceutically w, [Xaa]x, and [Xaa]y are as defined above for Formula I.
- the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C 1-4 alkyl), and optionally the carboxylic acid group of the C- terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- R 3 of any one of Formular (I)-(Id) i.e., I, Ia, Ib, Ic, Id
- R3 is C9-13 alkenylene.
- R3 is C11 alkenylene.
- the carboxylic acid group of the C-terminal lysine in [Xaa] y is replaced with -C(O)NH 2 [00181]
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula II: or a pharmaceutically acceptable salt thereof, wherein: R3 is alkenylene; R 4 is **-C(O)-(C 2-6 alkylene)-[O-CH 2 CH 2 ] m -N(R 5 )C(O)-(C 1-6 alkylene)-R 6 , wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa]y; R 5 is hydrogen or C 1-4 alkyl; R6 is one of the following: Page 40 of 91 BUSINESS.31107393.1 Attorney Ref.
- R 3 of Formula II is alkenylene.
- R 4 is **- C(O)-(C2-6 alkylene)-[O-CH2CH2]m-N(R5)C(O)-(C1-6 alkylene)-R6, wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa] y .
- R5 is hydrogen or C1-4 alkyl.
- R 6 is one of the following: , of R 7 ; [00184] In an embodiment, R7 represents independently for each occurrence C1-3 alkyl, hydroxyl, or C 1-3 alkoxyl.
- m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16.
- t is 0, 1, 2, or 3.
- the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C- terminal lysine in [Xaa] y is replaced with -C(O)NH 2 .
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula IIa: Page 41 of 91 BUSINESS.31107393.1 Attorney Ref.
- the peptide comprises or consists of: or a pharmaceutically acceptable salt thereof, wherein R 3 , R 4 , [Xaa] w , [Xaa] x , and [Xaa] y are as defined above for Formula II, and wherein optionally the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)-(C 1-4 alkyl). In an embodiment, the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl).
- R 3 of Formular (II), (IIa), (IIb), (IIc), or (IId) is C 7-15 alkenylene.
- R3 is C9-13 alkenylene.
- R3 is C11 alkenylene.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula III: or a pharmaceutically
- R4 is **-C(O)-(C2-6 - m- - 6 -R6, wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa] y ;
- R5 is hydrogen or C1-4 alkyl;
- R 6 is one of the following: , each of which is R7 represents independently for each occurrence C1-3 alkyl, hydroxyl, or C1-3 alkoxyl;
- [Xaa] w is DISGINASVVNIQ (SEQ ID NO: 35);
- [Xaa]x is EIDRLN (SEQ ID NO: 36);
- R4 is **-C(O)-(C2-6 alkylene)-[O-CH2CH2]m-N(R5)C(O)-(C1-6 alkylene)-R 6 , wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa]y.
- R 5 is hydrogen or C 1-4 alkyl.
- R 6 is one of the Page 43 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) following: , optionally wherein an each occurrence C1-3 alkyl, hydroxyl, or C 1-3 alkoxyl.
- m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16.
- p is 2, 3, 4, 5, 6, 7, or 8.
- z is 2, 3, 4, 5, or 6.
- t is 0, 1, 2, or 3.
- the amino group of the N-terminal aspartic acid in [Xaa]w is replaced with -N(H)C(O)-(C1-4 alkyl).
- the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula (IIIa): or a pharmaceutically [Xaa] x , and [Xaa] y are as defined above in Formula III.
- the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)-(C1-4 alkyl), and optionally the carboxylic acid group of the C- terminal lysine in [Xaa]y is replaced with -C(O)NH2.
- R4 is **-C(O)-(C2-3 alkylene)-[O-CH 2 CH 2 ] m -N(R 5 )C(O)-(C 1-2 alkylene)-R 6 , wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa]y.
- R4 is **-C(O)-(CH 2 CH 2 )-[O-CH 2 CH 2 ] m -N(R 5 )C(O)-(CH 2 )-R 6 , wherein ** is the point of attachment to the amino group in the side chain of the C-terminal lysine in [Xaa]y.
- the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with - N(H)C(O)-(C1-4 alkyl). In an embodiment, the amino group of the N-terminal aspartic acid in [Xaa] w is replaced with -N(H)C(O)CH 3 . In an embodiment, the carboxylic acid group of the C-terminal lysine in [Xaa]y is replaced with -C(O)NH2. [00195] In an aspect, the dry powders, anhydrous compositions, and emulsions disclosed Page 44 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO herein comprise a peptide of Formula (IV): or a R4 is -C(O)- 6 - m- - 6 - R 5 is hydrogen or C 1-4 alkyl; R 6 is one of the following: , each of which is R 7 represents independently for each occurrence C 1-3 alkyl, hydroxyl, or C 1-3 alkoxyl; R8 is -C(O)-(C1-4 alkyl); [Xaa] w is DISGINASVVNIQ (SEQ ID NO: 35); [Xaa]x is EIDRLN (SEQ ID NO: 36); [Xaa] z is VAKNLNESLIDLQELG (SEQ ID NO: 77); m is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16; p is 2, 3, 4, 5, 6, 7, or 8; z is 2, 3, 4, 5, or 6; and t is 0, 1, 2, or 3.
- R4 is -C(O)-(C2-6 alkylene)-[O-CH2CH2]m-N(R5)C(O)-(C1-6 alkylene)-R6.
- R5 is hydrogen or C1-4 alkyl.
- R6 is one of the following: , [00197]
- R7 represents independently for each occurrence C1-3 alkyl, Page 45 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) hydroxyl, or C 1-3 alkoxyl.
- R 8 is -C(O)-(C 1-4 alkyl).
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula IVa: or a [Xaa] z , p, and z are as [00199]
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula IVb: or a and [Xaa]z are as defined above for Formula IV.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula IVc: or a and [Xaa] z are as defined above for Formula IV.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula V: Page 46 of 91 BUSINESS.31107393.1 Attorney Ref.
- R 4 is -C(O)-(C 2-6 alkylene)-[O-CH 2 CH 2 ]m-N(R 5 )C(O)-(C 1-6 alkylene)-R6.
- R5 is hydrogen or C1-4 alkyl.
- R6 is one of the following: , optionally wherein [00203]
- R7 represents independently for each occurrence C1-3 alkyl, hydroxyl, or C 1-3 alkoxyl.
- R 8 is -C(O)-(C 1-4 alkyl).
- [Xaa]w is DISGINASVVNIQ (SEQ ID NO: 35); [Xaa]x is EIDRLN (SEQ ID NO: 36); and [Xaa] z is VAKNLNESLIDLQELG (SEQ ID NO: 77).
- m is 3, 4, 5, 6, 7, 8, Page 47 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) 9, 10, 11, 12, 13, 14, 15, or 16.
- t is 0, 1, 2, or 3.
- R 8 is -C(O)CH 3 .
- R 4 is -C(O)-(C 2-3 alkylene)- [O-CH2CH2]m-N(R5)C(O)-(C1-2 alkylene)-R6.
- R4 is -C(O)-(CH2CH2)-[O- CH 2 CH 2 ] m -N(R 5 )C(O)-(CH 2 )-R 6 .
- R 5 is hydrogen.
- R 6 substituted by t occurrences of R 7 . [00205] In an embodiment, t occurrences of R 7 . [00206] In an embodiment, t occurrences of R 7 . [00207] In an embodiment, t occurrences of R7.
- t BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) occurrences of R 7 .
- t an m an m is 8.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula VI: O [Xaa] x HN R NH 4 H or a pharmaceutically acceptable salt thereof, wherein: R 4 is -C(O)-(CH 2 CH 2 )-[O-CH 2 CH 2 ] 8 -N(H)C(O)-(CH 2 )-R 6 ; [Xaa] x is EIDRLN (SEQ ID NO: 36); and [Xaa] z is VAKNLNESLIDLQELG (SEQ ID NO: 77).
- R4 is -C(O)-(CH2CH2)-[O-CH2CH2]8-N(H)C(O)-(CH2)-R6.
- [Xaa]x is ; z (SEQ ID NO: 77).
- each of the [Xaa] w of Formula (I), the [Xaa] x of Formula (I), and the [Xaa]y of Formulae (I), (Ia), (II), (IIa) is as described for any one of constructs 1-15 of Table 2.
- the [Xaa]w, the [Xaa]x, and the [Xaa]y is: DISGINASVV (SEQ ID NO: 26), IQKEID (SEQ ID NO: 27), and LNEVAKNLNESLIDLQELGK (SEQ ID NO: 28), respectively.
- the [Xaa] w , the [Xaa] x , and the [Xaa] y is: DISGINASVVN (SEQ ID NO: 29), QKEIDR (SEQ ID NO: 30), and NEVAKNLNESLIDLQELGK (SEQ ID NO: 31), respectively.
- Table 2 [Xaa]w, [Xaa]x, and [Xaa]y sequences for Formula (I) constructs 1-15.
- SARS-CoV-2 HR2 peptides can include any amino acid sequence described herein.
- the peptide of Formula (I) comprising the sequences set forth above in Table 2 has one or more of the properties listed below: (i) binds the recombinant SARS-CoV-25-helix bundle S protein and/or the corresponding native fusion apparatus; (ii) is alpha-helical; (iii) is protease resistant; (iv) inhibits fusion of SARS-CoV-2 with a host cell; and/or (v) inhibits infection of a cell by SARS-CoV-2.
- the peptide binds to a polypeptide comprising or consisting of the sequence of SEQ ID NO:78.
- the tether of Formula (I) can include an alkyl, alkenyl, or alkynyl moiety (e.g., C5, C8, C11, or C12 alkyl, a C5, C8, or C11 alkenyl, or C5, C8, C11, or C12 alkynyl).
- the tethered amino acid can be alpha disubstituted (e.g., C1-C3 or methyl).
- x is 2, 3, or 6.
- each y is independently an integer between 0 and 15, or 3 and 15.
- R1 and R2 are each independently H or C1-C6 alkyl.
- R1 Page 51 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) and R 2 are each independently C 1 -C 3 alkyl.
- at least one of R 1 and R 2 are methyl.
- R 1 and R 2 can both be methyl.
- R3 is alkyl (e.g., C8 alkyl) and x is 3.
- R3 is C11 alkyl and x is 6.
- R 3 is alkenyl (e.g., C 8 alkenyl) and x is 3.
- x is 6 and R3 is C11 alkenyl.
- R3 is a straight chain alkyl, alkenyl, or alkynyl.
- R 3 is —CH 2 —CH 2 —CH 2 —CH ⁇ CH— CH2—CH2—CH2—.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide of Formula (I), or a pharmaceutically acceptable salt thereof, wherein: each R 1 and R 2 is H or a C 1 to C 10 alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heteroarylalkyl, or heterocyclylalkyl, any of which is substituted or unsubstituted; each R3 is independently alkylene, alkenylene, or alkynylene, any of which is substituted or unsubstituted; z is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and (a) each [Xaa]w is DISGINASVV (SEQ ID NO: 26), each [Xaa]x is IQKEID (SEQ ID NO: 27), and each [Xaa]y is LNEVAKNLNESLIDLQELGK (SEQ ID NO: 28);
- R 1 is an alkyl. In an embodiment, R 1 is a methyl group. In an embodiment, R3 is an alkyl. In an embodiment, R3 is a methyl group. In an embodiment, R2 is an alkenyl. In an embodiment, z is 1. [00221] In another aspect of Formula (I), the two alpha, alpha disubstituted stereocenters are both in the R configuration or S configuration (e.g., i, i+4 cross-link), or one stereocenter is R and the other is S (e.g., i, i+7 cross-link).
- Formula (I) is depicted as:
- the C’ and C” can or they can both be in the S configuration.
- the C’ disubstituted stereocenter is in the R configuration and the C” disubstituted stereocenter is in the S configuration.
- the R3 double bond of Formula (I) can be in the E or Z stereochemical configuration.
- R3 is [R4—K—R4]n; and R4 is a straight chain alkyl, alkenyl, or alkynyl.
- the instant disclosure provides a dry powder comprising a peptide of the following formula: Page 53 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) O [Xaa] x HN R NH 4 H [Xaa]z is VAKNLNESLIDLQELG (SEQ ID NO: 77).
- O [Xaa] x HN R NH 4 [Xaa] z is VAKNLNESLIDLQELG (SEQ ID NO: 77).
- the instant disclosure provides an emulsion comprising a Page 54 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) peptide of the following formula: O [Xaa] x HN R NH 4 H [Xaa] z is VAKNLNESLIDLQELG (SEQ ID NO: 77).
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 6 or 7 (or a modified version thereof), wherein: the side chains of two amino acids separated by six amino acids are replaced by an internal staple.
- the dry powders, anhydrous compositions, and emulsions disclosed herein comprise a peptide that is 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 amino acids in length.
- the peptide is 19-45 amino acids (i.e., 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45) in length.
- the peptide is 36-45 amino acids (i.e., 36, 37, 38, 39, 40, 41, 42, 43, 44, or 45) in length. In an embodiment, the peptide is 38-45 amino acids (i.e., 38, 39, 40, 41, 42, 43, 44, or 45) in length. In an embodiment, the peptide is 36-42 amino acids (i.e., 36, 37, 38, 39, 40, 41, 42) in length. In an embodiment, the stapled peptide is 38-42 amino acids (i.e., 38, 39, 40, 41, 42) in length. In an embodiment, the peptide is 36 amino acids in length. In an embodiment, the stapled peptide is 38 amino acids in length.
- Exemplary COVID- 19 HR2 stapled peptides are shown in Table 1 and described in Formula (I).
- the peptide comprises or consists of a stapled version of the amino acid sequence of any one of Page 55 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) SEQ ID NOs: 7-21 (e.g., the product of a ring-closing metathesis reaction performed on a peptide comprising the amino acid sequence of any one of SEQ ID NOs: 7-21, respectively).
- the peptide comprises or consists of a stapled version of the amino acid sequence of SEQ ID NO: 5 (e.g., the product of a ring-closing metathesis reaction performed on a peptide comprising the amino acid sequence of SEQ ID NO: 5).
- the peptide comprises or consists of a stapled version of the amino acid sequence of SEQ ID NO: 6 (e.g., the product of a ring-closing metathesis reaction performed on a peptide comprising the amino acid sequence of SEQ ID NO: 6).
- the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 11 and 18 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 12 and 19 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 13 and 20 of SEQ ID NO:6.
- the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 14 and 21 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 15 and 22 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 16 and 23 of SEQ ID NO:6.
- the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 17 and 24 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 18 and 25 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 19 and 26 of SEQ ID NO:6.
- the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 20 and 27 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 21 and 28 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 22 and 29 of SEQ ID Page 56 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) NO:6.
- the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 23 and 30 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 24 and 31 of SEQ ID NO:6. In certain embodiments, the two amino acids each separated by six amino acids are at the amino acid positions in the SARS-CoV-2 HR2 peptide corresponding to positions 25 and 32 of SEQ ID NO:6. [00229] While hydrocarbon tethers are provided herein, other tethers can also be employed in the peptides described herein.
- the tether can include one or more of an ether, thioether, ester, amine, amide, or triazole moiety.
- a naturally occurring amino acid side chain can be incorporated into the tether.
- a tether can be coupled with a functional group such as the hydroxyl in serine, the thiol in cysteine, the primary amine in lysine, the acid in aspartate or glutamate, or the amide in asparagine or glutamine. Accordingly, it is possible to create a tether using naturally occurring amino acids rather than using a tether that is made by coupling two non-naturally occurring amino acids.
- Triazole-containing (e.g., 1, 4 triazole or 1, 5 triazole) crosslinks can be used (see, e.g., Kawamoto et al. 2012 Journal of Medicinal Chemistry 55:1137; WO 2010/060112).
- other methods of performing different types of stapling are well known in the art and can be employed with the SARS-CoV-2 HR2 peptides described herein (see, e.g., Lactam stapling: Shepherd et al., J. Am. Chem.
- tethers spanning from amino acids i to i+7 are provided herein Page 57 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) in order to provide a tether that is primarily on a single face of the alpha helix, the tethers can be synthesized to span any combinations of numbers of amino acids and also used in combination to install multiple tethers.
- the hydrocarbon tethers (i.e., cross links) described herein can be further manipulated.
- a double bond of a hydrocarbon alkenyl tether (e.g., as synthesized using a ruthenium-catalyzed ring closing metathesis (RCM)) can be oxidized (e.g., via epoxidation, aminohydroxylation or dihydroxylation) to provide one of compounds below: H O O H O H H H O N [Xaa] 3 N N [Xaa] 3 N [00233] can be further functionalized.
- the epoxide can be treated with a nucleophile, which provides additional functionality that can be used, for example, to attach a therapeutic agent.
- a nucleophile which provides additional functionality that can be used, for example, to attach a therapeutic agent.
- Such derivatization can alternatively be achieved by synthetic manipulation of the amino or carboxy terminus of the peptide or via the amino acid side chain.
- Other agents can be attached to the functionalized tether, e.g., an agent that facilitates entry of the peptide into cells.
- alpha disubstituted amino acids are used in the peptide to improve the stability of the alpha helical secondary structure.
- the peptides can further comprise a drug, a toxin, a derivative of polyethylene glycol; a second peptide; a carbohydrate, etc.
- PEG polyethelene glycol
- PEG is a water-soluble polymer and can be represented as linked to the peptide as formula: XO--(CH2CH2O)n--CH2CH2--Y where n is 2 to 10,000 and X is H or a terminal modification, e.g., a C1-4 alkyl; and Y is an amide, carbamate or urea linkage to an amine group (including but not limited to, the epsilon amine of lysine or the N-terminus) of the peptide. Y may also be a maleimide linkage to a thiol group (including but not limited to, the thiol group of cysteine). Page 58 of 91 BUSINESS.31107393.1 Attorney Ref.
- PEG as used herein functions as a linker or spacer between one of the peptides and a cholesterol or thiocholesterol moiety.
- n 5.
- n 6.
- n 7.
- n 8.
- the PEG molecule includes a cholesterol moiety.
- the cholesterol moiety is thiocholesterol.
- the sulfur of the thioether moiety in thiocholesterol is replaced by an oxygen atom to produce an ether moiety in the cholesterol derivatization.
- the peptide further comprises PEG and/or cholesterol.
- the cholesterol is thiocholesterol.
- the peptide further comprises PEG(n)- cholesterol, wherein the PEG(n)-cholesterol is conjugated to the N-terminus or C-terminus of the peptide, and wherein n is 1-36, optionally wherein n is 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36.
- the peptide further comprises PEG(n)- thiocholesterol, wherein the PEG(n)-thiocholesterol is conjugated to the N-terminus or C- terminus of the peptide, and wherein n is 1-36, optionally wherein n 4, 5, 6, 7, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36.
- PEG having degradable linkages in the backbone can be used.
- PEG can be prepared with ester linkages that are subject to hydrolysis. Conjugates having degradable PEG linkages are described in WO 99/34833; WO 99/14259, and U.S.6,348,558.
- the PEG is attached to a peptide described herein through an intermediate linker.
- the linker is made up of from 1 to 20 amino acids linked by peptide bonds, wherein the amino acids are selected from the 20 naturally occurring amino acids. Some of these amino acids may be glycosylated, as is well understood by those in the art.
- the 1 to 20 amino acids are selected from glycine, alanine, proline, asparagine, glutamine, and lysine.
- a linker is made up of a majority of amino acids that are sterically unhindered, such as glycine and alanine.
- Non- peptide linkers are also possible.
- alkyl linkers may further be substituted by any non- sterically hindering group such as lower alkyl (e.g., C 1 -C 6 ), lower acyl, halogen (e.g., Cl, Br), CN, NH2, phenyl, etc.
- U.S. Pat. No.5,446,090 describes a bifunctional PEG linker and its use in forming conjugates having a peptide at each of the PEG linker termini.
- the peptides are further modified, e.g., to further facilitate mucoadhesion, membrane binding, or increase in vivo stability.
- acylating or PEGylating a peptide increases bioavailability, increases blood circulation, alters pharmacokinetics, alters immunogenicity, and/or decreases the needed frequency of administration.
- the peptides disclosed herein have an enhanced ability to bind to or penetrate cell membranes (e.g., relative to non-stapled peptides). See, e.g., International Publication No. WO 2017/147283, which is incorporated by reference herein in its entirety.
- Excipients and Formulations [00249]
- a dry powder comprising a peptide that binds to a SARS-CoV-2 spike protein and one or more excipient.
- anhydrous composition comprising a peptide that binds to a SARS-CoV-2 spike protein and one or more excipient.
- an emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein and one or more excipient.
- the dry powders, anhydrous compositions, and emulsions disclosed herein are formulated to minimize systemic absorption.
- the dry powders, anhydrous compositions, and emulsions disclosed herein may include excipients that do not enhance absorption across a biological membrane.
- the dry powders, anhydrous compositions, and emulsions disclosed herein are formulated for mucosal surface delivery.
- the dry powders, anhydrous compositions, and emulsions disclosed herein further comprise a surfactant, a stabilizing agent, and/or a cyclodextrin.
- the dry powders, anhydrous compositions, and emulsions disclosed herein further comprise a surfactant.
- the surfactant is polysorbate 80, polysorbate 20, Brij-35, Poloxamer 188, sodium taurocholate, sodium deoxycholate sodium, glycodeoxycholate, palmitic acid, palmitoleic acid, stearic acid, oleyl alcohol, oleic acid, capric acid, DHA, or EPA.
- the surfactant is a phospholipid surfactant.
- the phospholipid surfactant is dodecylphosphocholine (DPC), l,2-didecyl- Page 61 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO (208172) 5n-glycero-3-phosphocholine (DDPC or didecylphosphatidylcholine), 1-didecanoyl-sn- glycero-3-phosphocholine (LLPC or lysolauroylphosphatidylcholine), 1,2-dioctanoyl-sn- glycero-3-phosphocholine (D8PC or dioctanoylphosphatidylcholine), or 1,2-dilauroyl-sn- glycero-3-phospho(l'-rac-glycerol) (DLPG or dilauroylphosphatidylglycerol).
- DDPC didecylphosphatidylcholine
- LLPC 1-didecanoyl-sn- glycero-3-phosphocholine
- D8PC dioctanoylphosphatidylcholine
- DLPG 1,2-dilauroyl-s
- the dry powders, anhydrous compositions, and emulsions disclosed herein further comprise a cyclodextrin.
- the cyclodextrin is alpha- cyclodextrin, beta-cyclodextrin, or gamma-cyclodextrin.
- the cyclodextrin is ⁇ -cyclodextrin, ⁇ -cyclodextrin, ⁇ -cyclodextrin, hydroxypropyl- ⁇ -cyclodextrin, hydroxyethyl- ⁇ -cyclodextrin, hydroxypropyl- ⁇ -cyclodextrin, hydroxyethyl- ⁇ -cyclodextrin, dihydroxypropyl- ⁇ -cyclodextrin, glucosyl- ⁇ -cyclodextrin, glucosyl- ⁇ -cyclodextrin, diglucosyl- ⁇ -cyclodextrin, maltosyl- ⁇ -cyclodextrin, maltosyl- ⁇ -cyclodextrin, maltosyl- ⁇ -cyclodextrin, maltosyl- ⁇ -cyclodextrin, maltosyl- ⁇ -cyclodextrin, maltosyl- ⁇ -cyclodextrin, maltosyl-
- the cyclodextrin comprises succinyl- ⁇ -cyclodextrin, succinyl- ⁇ - cyclodextrin, succinyl- ⁇ -cyclodextrin, sulfobutylether- ⁇ -cyclodextrin, sulfobutylether- ⁇ - cyclodextrin, sulfobutylether- ⁇ -cyclodextrin, carboxymethyl- ⁇ -cyclodextrin, carboxymethyl- ⁇ -cyclodextrin, carboxymethyl- ⁇ -cyclodextrin, 2-carboxyethyl- ⁇ -cyclodextrin, 2- carboxyethyl- ⁇ -cyclodextrin, 2-carboxyethyl- ⁇ -cyclodextrin, phosphate- ⁇ -cyclodextrin, phosphate- ⁇ -cyclodextrin, phosphate- ⁇ -cyclodextrin, phosphate- ⁇ -cyclodextrin
- the dry powders, anhydrous compositions, and emulsions disclosed herein further comprise a stabilizing agent.
- the stabilizing agent is any sugar or sugar-alcohol such as a monosaccharide, a disaccharide, a polysaccharide, a glucan (e.g., water-soluble glucan), e.g., fructose, glucose, mannose, sorbose, sorbitol, xylose, maltose, lactose, sucrose, dextran, trehalose, pullulan, dextrin, cyclodextrin, soluble starch, hydroxyethyl starch, or carboxymethylcellulose, or any combination thereof.
- glucan e.g., water-soluble glucan
- the dry powders, anhydrous compositions, and emulsions disclosed herein further comprise a bioadhesive excipient.
- a bioadhesive excipient is a cellulose derivative (e.g., hydroxypropyl methyl cellulose (HPMC), Page 62 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO hydroxyethyl cellulose (HEC), or carboxymethyl cellulose (CMC)), chitosan, a poly(acrylic acid) derivate (e.g., carbomer (Carbopol®) or polycarbophil), alginate, xanthan gum, pectin, gelatin, a natural gum (such as guar gum or tragacanth gum), polyethylene oxide (PEO), polyvinylpyrrolidone (PVP), polyvinyl alcohol (PVA), or a thiolated polymer (such as thiolated chitosan or a thiolated polymer of acrylic acid), or any combination thereof.
- a poly(acrylic acid) derivate e.g., carbomer (Carbopol®) or polycarbophil
- alginate e.g., carbomer (Carbopol®) or polycarbophil
- alginate e.g., xanthan gum, pec
- the dry powder disclosed herein is dried from a liquid form by freeze-drying, spray-drying, tray-drying, or other techniques known in the art.
- the dry powder is in the form of a flaky solid from freeze drying or a dried solid cake.
- the dry powder contains less than 5%, 4%, 3%, 2%, or 1% water content.
- the anhydrous composition disclosed herein is a liquid composition. In an embodiment, the anhydrous composition contains less than 5%, 4%, 3%, 2%, or 1% water content.
- the anhydrous compositions disclosed herein comprise an excipient selected from waxes, emollients, thickening agents/viscosity increasing agents, humectants, pH modifiers, water repelling agents, anti-foaming agents, surfactants, solubilizers, wetting agents, antioxidants, and solvents.
- an excipient selected from waxes, emollients, thickening agents/viscosity increasing agents, humectants, pH modifiers, water repelling agents, anti-foaming agents, surfactants, solubilizers, wetting agents, antioxidants, and solvents.
- the anhydrous compositions disclosed herein comprise a viscosity increasing agent selected from co-polymers of carboxymethylcellulose and acrylic acid, N-vinylpyrrolidone, polyalkylene glycols (e.g., poly(ethylene glycol)), polyalkylene oxides (e.g., polyethylene oxide), polyvinyl alcohols, polyvinylpyrrolidone, polysiloxanes, poly(vinyl acetates), cellulose, derivatized celluloses, hydroxypropylcellulose, and alginates, copolymers thereof and mixtures thereof.
- a viscosity increasing agent selected from co-polymers of carboxymethylcellulose and acrylic acid, N-vinylpyrrolidone, polyalkylene glycols (e.g., poly(ethylene glycol)), polyalkylene oxides (e.g., polyethylene oxide), polyvinyl alcohols, polyvinylpyrrolidone, polysiloxanes, poly(vinyl acetates
- the anhydrous compositions disclosed herein comprise a solvent selected from acetone, methyl alcohol, ethanol, isopropanol, butyl alcohol, ethyl acetate, dimethyl isosorbide, propylene glycol, glycerol, ethylene glycol, polyethylene glycol, and diethylene glycol monoethyl ether or mixtures thereof.
- the emulsions disclosed herein comprise oil and an aqueous medium.
- the emulsion is an oil in water emulsion.
- Routes of Administration [00262]
- the dry powder is for mucosal surface delivery. In an embodiment, the dry powder is not for systemic delivery.
- the anhydrous composition is for mucosal surface delivery.
- the anhydrous composition, Page 63 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) is not for systemic delivery.
- the emulsion is for mucosal surface delivery.
- the emulsion is not for systemic delivery.
- the dry powder is for nasal, nasopharyngeal, and/or pulmonary administration.
- the anhydrous composition is for nasal, nasopharyngeal, and/or pulmonary administration.
- the emulsion is for nasal, nasopharyngeal, and/or pulmonary administration.
- a coronavirus e.g., betacoronavirus such as SARS-CoV-2
- coronavirus disease e.g., COVID-19
- the subject is an animal.
- the subject is a mammal such as a non-primate (e.g., cow, pig, horse, cat, dog, rat, etc.) or a primate (e.g., monkey or human).
- the subject is a domesticated animal (e.g., a dog or cat).
- the subject is a bat or other species that spread coronavirus.
- the subject is a human.
- the subject is a non-human animal (e.g., a non-human animal such as a pig, horse, cow, cat, or dog).
- the dry powders, anhydrous compositions, or emulsions described herein are useful for treating a subject having a coronavirus (e.g., betacoronavirus) infection.
- the dry powders, anhydrous compositions, or emulsions described herein can also be useful for treating a human or non-human animal subject having a coronavirus disease.
- the coronavirus is 229E (alpha coronavirus); NL63 (alpha coronavirus); OC43 (beta coronavirus); HKU1 (beta coronavirus); Middle East respiratory syndrome (MERS); SARS-CoV; or SARS-CoV-2.
- the coronavirus infection is an infection of a SARS-CoV-2 variant selected from one of D614G B.1 (RVP- 702), Wuhan-Hu-1 QHD43416.1 (RVP-701), New York variant B.1.526 (RVP-726) Iota, Californian variant B.1.526 (RVP-713), or UK variant B.1.1.7 with E484K (RVP-717).
- the coronavirus disease is caused by a COVID-19 infection.
- the coronavirus is Wuhan-Hu-1, B.1.427/B.1.429, B.1.617.2, D614G B.1, Brazilian variant P.1, B.1.1.7, B.1.351, B.1.525, B.1.526, B.1.617.1, B.1.617.3, P.2, B.1.621, B.1.621.1, B.1.1.529, BA.1, BA.1.1, BA.2, BA.3, BA.4 or BA.5.
- the coronavirus infection is an infection of one of B.1.351, Cluster 5, Lineage B.1.1.207, Lineage B.1.1.7, Variant of Concern 202102/02, Lineage B.1.1.317, Lineage B.1.1.318, Lineage B.1.351, Lineage B.1.429, Lineage B.1.525, Lineage P.1 (also known as Page 64 of 91 BUSINESS.31107393.1 Attorney Ref.
- the coronavirus infection is an infection of one of 229E (alpha coronavirus); NL63 (alpha coronavirus); OC43 (beta coronavirus); HKU1 (beta coronavirus); Middle East respiratory syndrome (MERS); SARS-CoV; or SARS- COVID-19.
- the coronavirus disease is caused by a COVID-19 infection.
- the human or non-human animal subject in need thereof is administered any one of the dry powders, anhydrous compositions, or emulsions disclosed herein.
- the treatment blocks transmission of a coronavirus between human subjects.
- the treatment controls the spread of coronavirus infection in a population of human subjects.
- the human subject or non-human animal subject is infected with a coronavirus (e.g., betacoronavirus).
- the human subject or non- human animal subject is at risk of being infected with a coronavirus (e.g., betacoronavirus).
- the human subject or non-human animal subject is at risk of developing a coronavirus disease (e.g., betacoronavirus).
- a human subject or non-human animal subject is at risk of being infected with a coronavirus or at risk of developing a coronavirus disease if the subject lives in an area (e.g., city, state, country) subject to an active coronavirus outbreak (e.g., an area where at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 30, at least 40, or more people have been diagnosed as infected with a coronavirus).
- an area e.g., city, state, country
- an active coronavirus outbreak e.g., an area where at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 30, at least 40, or more people have been diagnosed as infected with a coronavirus.
- a human subject or non-human animal subject is at risk of being infected with a coronavirus or developing a coronavirus disease if the subject lives in an area near (e.g., a bordering city, state, country) a second area (e.g., city, state, country) subject to an active coronavirus outbreak (e.g., an area near a second area where at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 20, at least 30, at least 40, or more people have been diagnosed as infected with a coronavirus).
- the coronavirus disease is caused by a SARS-CoV-2 infection.
- the subject or non-human animal subject has or is at risk of developing COVID-19.
- methods include selecting a subject or non-human animal subject and administering to the subject an effective amount of one or more of the dry powders, anhydrous Page 65 of 91 BUSINESS.31107393.1 Attorney Ref.
- the administration is by a topical respiratory application which includes application to the nasal mucosa, sinus mucosa, oropharyngeal mucosa, or respiratory tree, including the lungs.
- topical application includes application to the skin or eyes.
- a subject can be selected for treatment based on, e.g., determining that the subject is at risk to acquire or has a coronavirus (e.g., betacoronavirus such as SARS-CoV-2) infection.
- a coronavirus e.g., betacoronavirus such as SARS-CoV-2
- the dry powders, anhydrous compositions, or emulsions described herein increase bioavailability, increase blood circulation, alter pharmacokinetics, decrease immunogenicity and/or decrease the needed frequency of administration.
- An effective amount can be administered in one or more administrations, applications or dosages.
- the dry powders, anhydrous compositions, or emulsions disclosed herein can be administered from one or more times per day to one or more times per week, including once every other day.
- treatment of a subject with a therapeutically effective amount of any one of the dry powders, anhydrous compositions, or emulsions described herein can include a single treatment or a series of treatments.
- effective amounts can be administered at least once.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for use in a method of treating a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for use in a method of preventing a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for treating a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for the manufacture of a medicament for treating a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for the manufacture of a medicament for preventing a coronavirus infection in a subject in need thereof.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for use in a method of inhibiting coronavirus fusion to a host cell in a subject.
- a dry powder, anhydrous composition, or emulsion comprising a peptide that binds to a SARS-CoV-2 spike protein for the manufacture of a medicament for inhibiting coronavirus fusion to a host cell in a subject.
- EXAMPLES [00283] The examples in this Section are offered by way of illustration and not by way of limitation.
- Example 1 Design and Synthesis of Stapled SARS-CoV-2 Peptides Derivatized with C- terminal PEG(n)-Thiocholesterol or PEG(n)-Cholesterol Moieties [00284] To design peptides that could block the fusion of the coronavirus to a host cell (FIG. 1), a series of stapled peptides bearing differentially localized chemical staples and derivatized with PEG(n)-thiocholesterol or PEG(n)-cholesterol moieties at the C-termini were designed and then synthesized on resin by solid phase synthesis.
- the differentially localized chemical staples were located within the SARS-CoV-2 HR2 domain (i.e., amino acids 1168-1205) of the sequence of the surface (S) glycoprotein of the severe acute respiratory syndrome coronavirus 2 (see, FIGs.2-4), and preferably within the alpha-helical region (i.e., amino acids 1179-1197; see, FIG.9), by replacing native residues with ⁇ , ⁇ -disubstituted non-natural olefinic residues (e.g., “X” for S-pentenyl alanine and “8” for R-octenyl alanine installed at select i, i+7 positions or “X” for S-pentenyl alanine installed at each of select i, i+4 positions) and combinations thereof in the form of double staples or stitches, followed by ruthenium-catalyzed olefin metathesis (see, FIGs.
- Some preferred designs incorporate staples on the non- interacting amphiphilic face of the core SARS-CoV-2 HR2 helix (e.g., SEQ ID NO: 4) or at positions at the border of the hydrophobic interaction face with the amphiphilic face of the helix (see, FIG.9).
- Stapled SARS-CoV-2 HR2 constructs bearing C-terminal derivatization with PEG(n)-thiocholesterol or PEG(n)-cholesterol moieties were designed by replacing two naturally occurring amino acids with the non-natural (R)-2-(((9H–fluoren-9- yl)methoxy)carbonylamino)-2-methyl-dec-9-enoic acid (R8) and S-2-(4′-pentenyl) alanine (S5) amino acids at i, i+7 positions (i.e.
- flanking 7 amino acids to generate a staple spanning two ⁇ -helical turns, or with two S5 non-natural amino acids at i, i+4 positions to generate a staple spanning one ⁇ -helical turn.
- Asymmetric syntheses of ⁇ , ⁇ -disubstituted amino acids were performed as previously described in detail (Schafmeister et al., J. Am. Chem. Soc., 2000; Walensky et al., Science, 2004; Bird et al. Current Protocols in Chemical Biology, 2011, each of which is incorporated by reference in its entirety). [00286] “Staple scanning” was performed to respectively identify residues and binding surfaces critical for interaction, which dictates the design of optimized constructs and negative control mutants.
- the peptide N-termini were capped with acetyl or a fluorophore (e.g. FITC, rhodamine), depending upon the experimental application.
- Doubly stapled peptides were generated by installing two-S5-S5, two R8-S5, or other combinations of crosslinking non-natural amino acids. Multiply stapled or stitched peptides are generated using similar principles.
- carboxy-thiocholesterol or carboxy-cholesterol were synthesized according to the procedure described above (see, Methods and FIG.10).
- the completed resin-bound peptide was capped with an acetyl group (by use of acetic anhydride) followed by deprotection of the C-terminal side chain lysine amine by treatment with 2% hydrazine.
- the Fmoc was removed from the C-terminal NH of the PEG(n) amino acid and the amine acylated with carboxy-thiocholesterol or carboxy-cholesterol.
- the final peptide product was obtained after Page 68 of 91 BUSINESS.31107393.1 Attorney Ref. No.406693-002WO (208172) peptide deprotection and cleavage, and purification by reverse phase high performance liquid chromatography/mass spectrometry (LC/MS). See the full synthetic schemas in FIG. 11A- 11B.
- FIG.12 Exemplary i, i+7 stapled SARS-CoV-2 HR2 peptides derivatized with PEG(n)- thiocholesterol and PEG(n)-cholesterol generated by use of the synthetic schemas are listed in FIG.12 (SEQ ID NOs: 7-21).
- Example 2 Identifying optimally stapled SARS-CoV-2 HR2 peptides bearing a C-terminal PEG4-thiocholesterol to achieve anti-viral activity in pseudotype and live virus assays [00289]
- SEQ ID NO: 5 unstapled peptide with C-terminal amide
- SEQ ID NO: 6 unstapled peptide with C-terminal PEG4-thiocholesterol
- the stapled HR2 peptide of SEQ ID NO:10 (Staple D) showed the most potent, dose- responsive anti-viral activity followed by the unstapled peptide of SEQ ID NO: 6; notably, the stapled peptide of SEQ ID NO: 17 (Staple K) was the least active in the pseudovirus assay despite its staple also localized to the non-interacting face of the HR2 helix (see, FIG. 15).
- the select few constructs that afford potent antiviral activity discretely colocalize to a focal region of the HR2 alpha-helical surface, as demonstrated by a helical wheel depiction (FIG. 18B).
- the stapled lipopeptide corresponding to SEQ ID NO:10 (Staple D) bearing a C-terminal PEG4 thiocholesterol moiety was most active against the Omicron variant (FIG. 19), with potent antiviral activity also demonstrated against SARS-CoV-2 live viral strains, including Beta and Delta (FIG.20).
- Additional constructs corresponding to SEQ ID NOs: 13 and 20 bearing a C- terminal PEG4 thiocholesterol moiety also demonstrated consistent antiviral activity against a diversity of SARS-CoV-2 variant and SARS-CoV-1 pseudoviruses and live SARS-CoV-2 Beta strain virus (FIGs. 21-23).
- the tolerance for mutagenesis within the HR2 sequence, which alternatively has contacts with the HR1 core or is solvent exposed (FIG. 24A) was demonstrated for exemplary alanine substitutions in SEQ ID NO:10 bearing a C-terminal PEG4 thiocholesterol moiety, as revealed by retention of antiviral potency in a SARS-CoV-1 pseudoviral assay (FIGs.24B).
- No.406693-002WO (208172) responsive antiviral activity; (2) stapling can not only enhance peptide activity compared to the unstapled analog but also achieve antiviral activity whether administered before or after viral inoculation in culture; and (3) corroborative pseudoviral and live virus assays effectively identified a select few uniquely potent stapled HR2 peptides (SEQ ID NOs: 10, 13, 17, and 20) among a complete panel of differentially i, i+7 stapled peptides with lesser or no activity, underscoring that discerning the optimal staple position to achieve potent antiviral activity is unpredictable and must be determined experimentally in SARS-CoV-2 antiviral assays.
- Example 3 Determining the optimal PEG linker length within stapled SARS-CoV-2 HR2 peptides bearing a C-terminal PEG(n)-thiocholesterol to achieve anti-viral activity in pseudotype and live virus assays [00293] To determine the optimal PEG-chain length to link the stapled HR2 peptide to the thiocholesterol or cholesterol moiety, a series of PEG(n) analogs were generated according to the above-described synthetic method, where n equals 3, 4, 5, 6, 7, and 8.
- Example 4 Specificity of the Anti-viral Mechanism of Action of stapled SARS-CoV-2 HR2 peptides bearing a C-terminal PEG(n)-thiocholesterol [00296]
- the unstapled HR2 peptide of SEQ ID NO:6 and the corresponding i, i+7 stapled HR2 peptide of SEQ ID NO:10 showed no cytotoxic activity across the anti-viral dose-effective range, as measured by DRAQ7 and Hoechst 33342 staining, whereas the unstapled HR2 peptide bearing a GSGSGC linker and C-terminally appended PEG4-cholesterol (DeVries et al, Science, 2021) killed cells within the dosing range (pseudovirus: D614G B.1; cells: 293T-ACE2; serial 2-fold dilution starting at 1 ⁇ M; read-out: 48 h) (see, FIG.32).
- Example 5 SARS-CoV-25-HB Binding Activity and Broad SARS-CoV-2 Anti-viral Activity Across Variants of a stapled SARS-CoV-2 HR2 peptide bearing a C-terminal PEG8-Chol [00298] A direct fluorescence polarization binding assay revealed low nanomolar binding Page 72 of 91 BUSINESS.31107393.1 Attorney Ref.
- No.406693-002WO (208172) affinity of a stapled lipopeptide of composition corresponding to SEQ ID NO: 10 derivatized at the C-terminus with PEG8-Chol and at the N-terminus with FITC- ⁇ -Ala in place of the acetyl, to a recombinant five-helix bundle (5-HB) of SARS-CoV-2, with the addition of the FITC-stapled lipopeptide completing the fusogenic six helix bundle (peptide: 5 nM; 5-HB protein of sequence MQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSGGSGGDI SGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGSSGGQKLIANQFNSAIGKIQDSLS STASALGKLQDVVNQNAQALNTLVKQLSSGGSGGDISGINASVVNIQKEIDRLNEVA KNLNESLIDLQELGSS
- the stapled lipopeptide of SEQ ID NO:10 derivatized at the C-terminus with PEG8-Chol demonstrated potent antiviral activity against (a) a spectrum of SARS-CoV-2 variant pseudoviruses (293-ACE2 cells, GFP-expressing pseudoviruses, peptide (serial dilution from 1000 nM), 48 hour read-out) (FIG.
- Example 6 Preparation of a Stapled SARS-CoV-2 Peptide Derivatized with a C-terminal PEG(8)-Cholesterol Moiety
- the following compound was prepared based on procedures described in Example 1 above: a structurally stabilized peptide conjugate represented by the following formula: O [Xaa] x HN R NH 4 wherein R4 is -C(O)-(CH2CH2)-[O-CH2CH2]8-N(H)C(O)-(CH2)-R6; Page 73 of 91 BUSINESS.31107393.1 Attorney Ref.
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