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WO2025202590A1 - Inhibiteurs de lyase c-s staphylococcique - Google Patents

Inhibiteurs de lyase c-s staphylococcique

Info

Publication number
WO2025202590A1
WO2025202590A1 PCT/GB2025/050350 GB2025050350W WO2025202590A1 WO 2025202590 A1 WO2025202590 A1 WO 2025202590A1 GB 2025050350 W GB2025050350 W GB 2025050350W WO 2025202590 A1 WO2025202590 A1 WO 2025202590A1
Authority
WO
WIPO (PCT)
Prior art keywords
aptamer
seq
nucleic acid
aptamers
certain embodiments
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/GB2025/050350
Other languages
English (en)
Inventor
Barry Murphy
Alexander James
Robert CORNMELL
David Bunka
Arron TOLLEY
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Aptamer Group Plc
Original Assignee
Aptamer Group Plc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Aptamer Group Plc filed Critical Aptamer Group Plc
Publication of WO2025202590A1 publication Critical patent/WO2025202590A1/fr
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

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Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/70Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088Compounds having three or more nucleosides or nucleotides
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/16Aptamers

Definitions

  • the invention relates to the isolation and characterisation of one or more aptamers against staphylococcal C-S lyase.
  • the invention also provides aptamers, aptamer-conjugates, and minimal functional fragments thereof which may be used to inhibit the activity of said lyases and thereby inhibit Staphylococcus associated malodour.
  • nucleic acid sequence having at least about 50%, about 60%, about 70%, about 80%, about 85%, about 90%, about 95% or about 99% identity or more with any one or more of the sequences of (a); or
  • nucleic acid sequence having at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75 or more consecutive nucleotides of sequences (a) or (b).
  • these aptamers were the most effective in inhibiting staphylococcal C-S lyase as compared to other aptamers screened during the selection process.
  • nucleic acid sequence selected from any one or more of SEQ ID NOs: 19 or 28;
  • nucleic acid sequence having at least about 50%, about 60%, about 70%, about 80%, about 85%, about 90%, about 95% or about 99% identity or more with any one or more of the sequences of (a); or
  • the invention provides one or more aptamers capable of specifically binding to staphylococcal C-S lyase, wherein the one or more aptamers comprise:
  • nucleic acid sequence having at least about 50%, about 60%, about 70%, about 80%, about 85%, about 90%, about 95% or about 99% identity or more with any one or more of the sequences of (a); or
  • nucleic acid sequence having at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75 or more consecutive nucleotides of sequences (a) or (b).
  • the invention provides one or more aptamers capable of specifically binding to staphylococcal C-S lyase, wherein the one or more aptamers comprise:
  • nucleic acid sequence having at least about 50%, about 60%, about 70%, about 80%, about 85%, about 90%, about 95% or about 99% identity or more with any one or more of the sequences of (a); or
  • nucleic acid sequence having at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75 or more consecutive nucleotides of sequences (a) or (b).
  • the invention provides one or more aptamers capable of specifically binding to staphylococcal C-S lyase, wherein the one or more aptamers comprise:
  • nucleic acid sequence having at least about 50%, about 60%, about 70%, about 80%, about 85%, about 90%, about 95% or about 99% identity or more with any one or more of the sequences of (a); or
  • nucleic acid sequence having at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75 or more consecutive nucleotides of sequences (a) or (b).
  • these aptamers are highly effective within bacterial cells, as further described herein.
  • the one or more aptamers are isolated.
  • the aptamer is an RNA aptamer (e.g., a single stranded RNA aptamer).
  • the invention further provides aptamers which compete for binding to the staphylococcal C-S lyase with any aptamer as described herein.
  • the invention provides an aptamer-conjugate as further described herein.
  • the aptamers are capable of inhibiting Staphylococcus associated malodour as further described herein.
  • Figure 1 shows the mechanism through which the odourless precursor Cys-Gly-3M3SH is processed in Staphylococcus hominis.
  • Cys-Gly-3M3SH is secreted by axillary apocrine glands in the skin. This is actively taken up by Staphylococcus hominis via the di-/tri-peptide transporter (DtpT).
  • the terminal glycine is cleaved by a dipeptidase (PepA) to release Cys- 3M3SH, which is then further processed by the CS lyase to give the volatile thioalcohol 3- methyl-3-sulfanylhexan-1-ol (3M3SH). This is then excreted from S. hominis and is responsible for body malodour.
  • FIG. 2 shows the Biolayer Interferometry data used to identify potential aptamer candidates.
  • Individual aptamer candidates were synthesised incorporating a biotin group at the 5’ end.
  • Biotinylated aptamer candidates were immobilised on streptavidin coated biosensor probes and interacted with ShPatB in solution.
  • the sensor data was background corrected to remove any interaction between the ShPatB and an unloaded biosensor.
  • the aptamer candidates are chosen based on their association rate (0-120 sec) and dissociation rate (120-240 sec).
  • the best performing candidates in this screen appear to be 9S_7, 9S_8 and 9S_11 (SEQ ID NOs: 25, 26 and 29 respectively).
  • 9S_1_F15 SEQ ID NO: 33
  • 9S_1_F16 SEQ ID NO: 34
  • 9S_10_F8 SEQ ID NO 42
  • 9S_10_F9 SEQ ID NO: 43
  • SEQ ID NO: 21 shows the full nucleic acid sequence of Aptamer 9S_3:
  • SEQ I D NO: 29 shows the full nucleic acid sequence of Aptamer 9S_11 :
  • SEQ ID NO: 30 shows the full nucleic acid sequence of Aptamer 9S_12:
  • SEQ ID NO: 31 shows a minimal fragment (9S_1_F12) of Aptamer 9S_1 :
  • SEQ ID NO: 32 shows a minimal fragment (9S_1_F14) of Aptamer 9S_1 :
  • SEQ ID NO: 45 shows a minimal fragment (9S_10_F15) of Aptamer 9S_10:
  • SEQ ID NO: 46 shows a minimal fragment (9S_10_F18) of Aptamer 9S_10:
  • CUCAAUGCACCCGAGUCCGAGUUGCACCUGACCSEQ ID NO: 47 shows a minimal fragment (9S_10_F19) of Aptamer 9S_10: CUCAAUGCACCCGAGUCCGAGUUGCACCUGACCACUAA
  • SEQ ID NO: 48 shows a minimal fragment (9S_10_F20) of Aptamer 9S_10: CGAGUCCGAGUUGCACCUGACCACUAAAUACGAUCCG
  • SEQ ID NO: 49 shows a minimal fragment (9S_10_F21) of Aptamer 9S_10:
  • SEQ ID NO: 51 shows a minimal fragment (9S_10_F23) of Aptamer 9S_10: CUCAAUGCACCCGAGUCCGAGUUGCACCUGACCACUAAAUACGAUCCG
  • the staphylococcal C-S lyase is pyridoxal phosphate (PLP)-dependent.
  • the staphylococcal C-S lyase may be from Staphylococcus nepalensis, Staphylococcus cohnii, Staphylococcus hominis, Staphylococcus lugdunensis, Staphylococcus devriesei, Staphylococcus haemolyticus, Staphylococcus petrasii, Staphylococcus vitulinis or Staphylococcus sciuri.
  • the staphylococcal C-S lyase is a cysteine-thiol lyase (C-T lyase).
  • the staphylococcal C-S lyase is selected from one or more of Staphylococcus hominis (Sh) PatB (SEQ ID NO:1 or 2), Staphylococcus lugdunensis (SI) PatB (SEQ ID NO: 3), Staphylococcus devriesei (Sd) PatB (SEQ ID NO: 4), Staphylococcus haemolyticus (Sha) PatB (SEQ ID NO: 5) or Staphylococcus petrasii (Sp) PatB (SEQ ID NO: 6).
  • the invention provides one or more aptamers capable of specifically binding to Staphylococcus hominis PatB as set forth in SEQ ID NO: 1.
  • the aptamers of the invention specifically bind to a protein having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or more sequence identity to SEQ ID NO: 1.
  • the invention provides one or more aptamers capable of specifically binding to the form of Staphylococcus hominis PatB as set forth in SEQ ID NO: 2.
  • the aptamers of the invention specifically bind to a protein having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or more sequence identity to SEQ ID NO:2.
  • the invention provides one or more aptamers capable of specifically binding to Staphylococcus hominis PatB as set forth in any one of SEQ ID NO: 3, 4, 5 or 6.
  • sequence identity refers to the percentage of amino acids in a candidate sequence that are identical with the amino acids in said sequences after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percentage amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, CLUSTALW or Megalign (DNASTAR) software. For example, % amino acid sequence identity values can be generated using sequence comparison computer programs found on the European Bioinformatics Institute website (http://www.ebi.ac.uk).
  • the term “high affinity” is understood to mean, for example, an aptamer that binds to the staphylococcal C-S lyase with a binding dissociation equilibrium constant (K D ) of less than about 1 pM, less than about 900nM, less than about 800nM, less than about 700nM, less than about 600nM, less than about 500nM, less than about 400nM, less than about 300nM, less than about 200nM, less than about 100nM, less than about 50nM, less than about 10nM, less than about 9nM, less than about 8nM, less than about 7nM, less than about 6nM, less than about 5nM, less than about 4nM, less than about 3nM, less than about 2nM, less than about 1nM or less.
  • K D binding dissociation equilibrium constant
  • the invention provides an aptamer capable of specifically binding to staphylococcal C-S lyase, wherein the aptamer comprises a nucleic acid sequence of SEQ ID NO: 32, 34 or 42 wherein the nucleic acid sequence further comprises at least 1, 2, 3, 4,
  • immobilised staphylococcal C-S lyase e.g., SEQ ID NO:1
  • a solution comprising the first labelled aptamer but not the second unlabelled aptamer.
  • excess unbound aptamer may be removed, and the amount of label associated with immobilised staphylococcal C-S lyase (e.g., SEQ ID NO:1) measured.
  • the amount of label associated with immobilised staphylococcal C-S lyase (e.g., SEQ ID NO:1) is substantially reduced in the test sample relative to the control sample, then that indicates that the second aptamer is competing with the first aptamer for binding to staphylococcal C- S lyase (e.g., SEQ ID NO:1).
  • the detectable label of the aptamer is a fluorescent protein such as Green Fluorescent Protein (GFP) or any other fluorescent protein known to those skilled in the art.
  • the detectable label of the aptamer is an enzyme.
  • the enzyme may be selected from horseradish peroxidase, alkaline phosphatase, urease, p- galactosidase, or any other enzyme known to those skilled in the art.
  • the nature of the detection will be dependent on the detectable label used.
  • the label may be detectable by virtue of its colour e.g. gold nanoparticles.
  • a colour can be detected quantitatively by an optical reader or camera e.g. a camera with imaging software.
  • the detectable label of the aptamer is a fluorescent label e.g. a quantum dot.
  • the detection means may comprise a fluorescent plate reader, strip reader or similar which is configured to record fluorescence intensity.
  • the detection means may, for example, be colorimetric, chemiluminescence and/or electrochemical (for example, using an electrochemical detector).
  • electrochemical sensing is through conjugation of a redox reporter (e.g. methylene blue or ferrocene) to one end of the aptamer and a sensor surface to the other end.
  • a redox reporter e.g. methylene blue or ferrocene
  • a change in aptamer conformation upon target binding changes the distance between the reporter and sensor to provide a readout.
  • the detectable label of the aptamer may further comprise enzymes such as horseradish peroxidase (HRP), Alkaline phosphatase (APP) or similar, to catalytically turnover a substrate to give an amplified signal.
  • enzymes such as horseradish peroxidase (HRP), Alkaline phosphatase (APP) or similar, to catalytically turnover a substrate to give an amplified signal.
  • the aptamer of the invention is conjugated to one or more molecule(s).
  • An “aptamer-conjugate” as used herein is a complex formed by conjugating an aptamer or target binding nucleic acid molecule with one or more molecule(s).
  • the aptamer may be conjugated to another aptamer (“aptamer-aptamer”), a peptide (“aptamer-peptide”) or small molecule (“aptamer-small molecule). Techniques of conjugating an aptamer to one or more molecule(s) are further described herein.
  • the aptamer region of the conjugate is capable of specifically binding to staphylococcal C-S lyase.
  • the one or more molecule(s) of the conjugate may be capable of targeting the aptamer to a desired bacterial cell as described herein.
  • the one or more molecule(s) of the conjugate may be capable of otherwise modulating or improving the performance of the aptamer or imparting other beneficial properties to the aptamer.
  • “capable of specifically binding” refers to the ability of the aptamer to selectively attach itself to the target molecule.
  • Selective binding means that the interaction between the molecule is highly specific, typically the result of molecular recognition where the aptamer has a binding site that matches the shape, charge, or chemical properties of the target molecule. This specific interaction allows the aptamer to recognise and attach to the target molecule while having minimal binding or affinity for other molecules in the sample.
  • An aptamer may be conjugated to one or more molecule(s) using any chemical modification technique which allows for the attachment of the modified aptamer to one or more compatibly modified molecule(s), while preserving the binding affinity and specificity of both components.
  • aptamer and/or one or more molecule(s) may be introduced to the aptamer and/or one or more molecule(s).
  • Common function groups used for conjugation will be known to those skilled in the art.
  • Aptly common function groups used for conjugation include, for example, primary amines (NH2), sulfhydryl groups (SH), ‘Click chemistry’ groups such as an azide or alkyne and carboxyl groups (COOH). This may be introduced during the solid phase synthesis of the aptamer using phosphoramidites carrying the functional group; or may be achieved through chemical modification of the aptamer post synthesis, or one or more molecule(s) having existing functional groups.
  • the functional groups may be activated using any suitable techniques known to those skilled in the art, e.g., using cross-linking reagents or chemical reactions that create reactive sites for conjugation.
  • Common reagents include N-hydroxysuccinimide (NHS) and maleimide.
  • the aptamer region of the aptamer-conjugate comprises one or more primary amines (NH2), sulfhydryl groups (SH), azide, alkyne and/or carboxyl groups (COOH).
  • NH2 primary amines
  • SH sulfhydryl groups
  • COOH carboxyl groups
  • the one or more molecule(s) comprises one or more primary amines (NH2), sulfhydryl groups (SH), azide, alkyne and/or carboxyl groups (COOH).
  • NH2 primary amines
  • SH sulfhydryl groups
  • COOH carboxyl groups
  • the appropriately modified aptamer and one or more molecule(s) may then be combined under any suitable condition which allows specific conjugation, whilst minimising any side reactions.
  • the specific reaction conditions e.g., pH, temperature, time
  • the aptamer-conjugate is then purified to remove any unreacted aptamers and/or molecules and reaction by-products. Typical purification methods may include, for example, size exclusion chromatography, affinity chromatography, dialysis, or the like.
  • the aptamer-conjugate may then be further characterised and/or stored under any suitable conditions.
  • Recombinant His tagged ShPatB protein (SEQ ID NO: 2) was supplied by Unilever, human Microbiome Department. The protein was characterised by UV spectroscopy and SDS- PAGE analysis for quality control purposes. The protein was immobilised onto His-Tag Isolation and Pulldown magnetic DynabeadsTM (ThermoFisher Scientific, UK), according to manufacturer’s protocols. The protein loading density was determined spectrophotometrically.
  • the aptamer selection process was carried out starting from synthetic ssDNA oligonucleotide sequences of an aptamer library (manufactured by IDT, Belgium).
  • the nucleotide sequences of the aptamer library have the following structure (in a 5’ to 3’ direction): T7S - T7 - P1 - R - P2, wherein T7 is a promoter region which is recognised and bound by the T7 RNA polymerase, T7S is a primer region, P1 is a first primer region, R is a randomized region (40 nucleotides in length) and P2 is a further primer region wherein R or a portion thereof are involved in target molecule binding.
  • nominated aptamers or Optimers must retain their function on skin.
  • axilla buffer scrubs were collected using an established collection method (Williamson, P.; Kligman, A. M. A New Method for the Quantitative Investigation of Cutaneous Bacteria. The Journal of Investigative Dermatology 1965, 45 (6), 498-503, herein incorporated by reference). Collected buffer scrub wash was split into 6x 2ml aliquots.

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Abstract

L'invention concerne l'isolement et la caractérisation d'un ou plusieurs aptamères contre la C-S lyase staphylococcique. L'invention concerne également des aptamères, des conjugués d'aptamères et des fragments fonctionnels minimaux de ceux-ci qui peuvent être utilisés pour inhiber l'activité desdites lyases et ainsi inhiber les mauvaises odeurs associées à Staphylococcus.
PCT/GB2025/050350 2024-03-28 2025-02-24 Inhibiteurs de lyase c-s staphylococcique Pending WO2025202590A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB2404469.5 2024-03-28
GBGB2404469.5A GB202404469D0 (en) 2024-03-28 2024-03-28 Aptamers against staphylococcal c-s lyase

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WO2025202590A1 true WO2025202590A1 (fr) 2025-10-02

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Citations (9)

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Publication number Priority date Publication date Assignee Title
WO1991005541A1 (fr) 1989-10-10 1991-05-02 The Gillette Company Inhibiteurs a base d'une amino acide beta-lyase enzyme utilises comme deodorants
WO1991011988A1 (fr) 1990-02-12 1991-08-22 The Gillette Company Substrats enzymatiques servant d'alternatives en tant que deodorants
US5213791A (en) * 1989-10-10 1993-05-25 The Gillette Company Amino acid β-lyase enzyme inhibitors as deodorants
WO1995007069A1 (fr) 1993-09-09 1995-03-16 The Gillette Company Serines d'o-acyle utilisees comme deodorants
WO2000034232A1 (fr) 1998-12-08 2000-06-15 Givaudan Sa Carbonates de serine
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EP1846436B1 (fr) 2005-01-31 2012-09-12 Firmenich S.A. Inhibition des mauvaises odeurs de transpiration
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Publication number Priority date Publication date Assignee Title
WO1991005541A1 (fr) 1989-10-10 1991-05-02 The Gillette Company Inhibiteurs a base d'une amino acide beta-lyase enzyme utilises comme deodorants
US5213791A (en) * 1989-10-10 1993-05-25 The Gillette Company Amino acid β-lyase enzyme inhibitors as deodorants
WO1991011988A1 (fr) 1990-02-12 1991-08-22 The Gillette Company Substrats enzymatiques servant d'alternatives en tant que deodorants
WO1995007069A1 (fr) 1993-09-09 1995-03-16 The Gillette Company Serines d'o-acyle utilisees comme deodorants
WO2000034232A1 (fr) 1998-12-08 2000-06-15 Givaudan Sa Carbonates de serine
EP1846436B1 (fr) 2005-01-31 2012-09-12 Firmenich S.A. Inhibition des mauvaises odeurs de transpiration
WO2010031657A2 (fr) * 2008-09-17 2010-03-25 Henkel Ag & Co. Kgaa Utilisation de dérivés d'urée et de sels de phenacyl thiazolium pour le traitement d'odeurs corporelles
US20200383891A1 (en) * 2017-12-20 2020-12-10 Conopco, Inc., D/B/A Unilever Deodorant compositions
WO2020214784A1 (fr) 2019-04-16 2020-10-22 The Procter & Gamble Company Aptamères pour applications de contrôle des odeurs

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M. EGERT ET AL: "Identification of compounds inhibiting the C-S lyase activity of a cell extract from a Staphylococcus sp. isolated from human skin", LETTERS IN APPLIED MICROBIOLOGY, vol. 57, no. 6, 23 September 2013 (2013-09-23), GB, pages 534 - 539, XP055576047, ISSN: 0266-8254, DOI: 10.1111/lam.12146 *
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