Lyn Jones, PhD
Biography
Lyn Jones, PhD
Lyn Jones completed his PhD studies in synthetic organic chemistry at the University of Nottingham, and his postdoctoral research at The Scripps Research Institute, California in chemical biology. He joined Pfizer Sandwich (UK) as a medicinal chemistry team leader, eventually becoming Head of Chemical Biology and Lead Discovery Technologies. He transferred to Pfizer Cambridge (USA) to become Head of Chemistry for Rare Disease Research, and Head of Chemical Biology. He then helped establish Jnana Therapeutics as Head of Chemistry and Chemical Biology, before moving to Dana-Farber Cancer Institute in Boston as Chief Scientist of the Center for Protein Degradation. He is currently Principal Investigator and Faculty Member of the Department of Pediatric Oncology and Chemical Biology Program at DFCI, and his lab focusses on the development of next-generation covalent chemical biology with the objective of expanding the druggable proteome.
Researcher
Physician
Recent Awards
- Fellow of the Learned Society of Wales
- Fellow of the Royal Society of Public Health
- Fellow of the AAAS
- RSC Capps Green Zomaya Lecture
- Fellow of the Royal Society of Biology
- Fellow of the Linnean Society
- Fellow of the Royal Society of Chemistry
- RSC Rising Star in Industry Prize
Research
Our lab lab focusses on the development of next-generation covalent chemical biology with the objective of expanding the druggable proteome.
Covalent modulators possess superior potency, selectivity and pharmacodynamic duration compared to reversible binding small molecule ligands. Traditional approaches target the cysteine side chain, but the residue is rarely present in protein binding sites and its nucleophilicity hinders the development of selective chemical probes and drugs. Additionally, cysteine-targeting anticancer drugs suffer from the emergence of resistance due to mutation of the cysteine to serine. To address these issues, we are building next-generation covalent chemical biology and drug discovery platforms targeting residues beyond cysteine. We are rationally designing novel electrophilic warheads that enable the site-specific modification of tyrosine, lysine, and histidine. Modalities under investigation in our lab include: - covalent inhibitors that block oncoproteins previously deemed undruggable - synthetic neoenzymes that rewire cancer cells - covalent protein therapeutics (avoiding the need for genetic code expansion) - chemoproteomics-based technologies that identify cryptic and allosteric sites across the cancer proteome
Research Departments
Publications
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Ligandability assessment of interferonopathy-associated proteins using chemoproteomics. Br J Pharmacol. 2025 Nov 12. View in: Pubmed
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Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation. Mol Cell. 2025 Aug 21; 85(16):3184-3201.e14. View in: Pubmed
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Property-Based Optimization of Cereblon-Based Molecular Glue Degraders. ACS Med Chem Lett. 2025 Aug 14; 16(8):1456-1462. View in: Pubmed
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Introduction to the themed collection on 'Induced-Proximity Pharmacology'. RSC Med Chem. 2025 Jun 03. View in: Pubmed
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Advances in sulfonyl exchange chemical biology: expanding druggable target space. Chem Sci. 2025 Jun 11; 16(23):10119-10140. View in: Pubmed
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Structure-guided design of a truncated heterobivalent chemical probe degrader of IRE1a. RSC Med Chem. 2025 Mar 18. View in: Pubmed
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Novel Corrector for Variants of SLC6A8: A Therapeutic Opportunity for Creatine Transporter Deficiency. ACS Chem Biol. 2024 11 15; 19(11):2372-2382. View in: Pubmed
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Synthetic modification of protein surfaces to mediate induced-proximity pharmacology. RSC Med Chem. 2024 Aug 09. View in: Pubmed
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Photoaffinity labelling with small molecules. Nature Reviews Methods Primers. 2024; 4:30. View in: Pubmed
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Development of sulfonyl fluoride chemical probes to advance the discovery of cereblon modulators. RSC Med Chem. 2024 Feb 21; 15(2):607-611. View in: Pubmed
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The Minimum Protein Staple? - Towards 'bio'-Baldwin's rules via inter-phosphosite linking in the MEK1 activation loop. Chem Sci. 2024 Jan 24; 15(4):1306-1317. View in: Pubmed
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Covalent Stapling of the Cereblon Sensor Loop Histidine Using Sulfur-Heterocycle Exchange. ACS Med Chem Lett. 2023 Nov 09; 14(11):1576-1581. View in: Pubmed
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The promise of targeted protein degradation approaches. Trends Pharmacol Sci. 2023 Nov; 44(11):746-749. View in: Pubmed
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ReSPONDINg TACtically, degrading strategically. Trends Pharmacol Sci. 2023 Nov; 44(11):753-754. View in: Pubmed
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Development of a covalent cereblon-based PROTAC employing a fluorosulfate warhead. RSC Chem Biol. 2023 Nov 01; 4(11):906-912. View in: Pubmed
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Clinical Translation of Targeted Protein Degraders. Clin Pharmacol Ther. 2023 09; 114(3):558-568. View in: Pubmed
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Covalent drug discovery using sulfur(VI) fluoride exchange warheads. Expert Opin Drug Discov. 2023 07; 18(7):725-735. View in: Pubmed
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Catalytic Degraders Effectively Address Kinase Site Mutations in EML4-ALK Oncogenic Fusions. J Med Chem. 2023 04 27; 66(8):5524-5535. View in: Pubmed
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HiBiT-SpyTag: A Minimal Tag for Covalent Protein Capture and Degrader Development. ACS Chem Biol. 2023 04 21; 18(4):933-941. View in: Pubmed
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Structural rationalization of GSPT1 and IKZF1 degradation by thalidomide molecular glue derivatives. RSC Med Chem. 2023 Mar 22; 14(3):501-506. View in: Pubmed
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Cereblon target validation using a covalent inhibitor of neosubstrate recruitment. Methods Enzymol. 2023; 681:155-167. View in: Pubmed
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Covalent drugs targeting histidine - an unexploited opportunity? RSC Med Chem. 2022 Oct 19; 13(10):1121-1126. View in: Pubmed
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Advancing targeted protein degrader discovery by measuring cereblon engagement in cells. Methods Enzymol. 2023; 681:169-188. View in: Pubmed
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Introduction to the themed collection on Covalent Drug Discovery. RSC Med Chem. 2022 Aug 17; 13(8):893-894. View in: Pubmed
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Cereblon covalent modulation through structure-based design of histidine targeting chemical probes. RSC Chem Biol. 2022 Aug 31; 3(9):1105-1110. View in: Pubmed
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Targeted protein degraders: a call for collective action to advance safety assessment. Nat Rev Drug Discov. 2022 06; 21(6):401-402. View in: Pubmed
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Small molecule modulation of protein polymerization. Chem Soc Rev. 2022 Apr 04; 51(7):2392-2396. View in: Pubmed
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Physicochemistry of Cereblon Modulating Drugs Determines Pharmacokinetics and Disposition. ACS Med Chem Lett. 2021 Nov 11; 12(11):1861-1865. View in: Pubmed
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Human amyotrophic lateral sclerosis excitability phenotype screen: Target discovery and validation. Cell Rep. 2021 06 08; 35(10):109224. View in: Pubmed
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LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome. Cell. 2021 May 13; 184(10):2680-2695.e26. View in: Pubmed
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Labeling Preferences of Diazirines with Protein Biomolecules. J Am Chem Soc. 2021 05 05; 143(17):6691-6700. View in: Pubmed
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Correction: Fragment-based covalent ligand discovery. RSC Chem Biol. 2021 Apr 01; 2(2):670-671. View in: Pubmed
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Fragment-based covalent ligand discovery. RSC Chem Biol. 2021 Apr 01; 2(2):354-367. View in: Pubmed
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Design of next-generation covalent inhibitors: Targeting residues beyond cysteine. Annual Reports in Medicinal Chemistry. 2021; 56:95-134. View in: Pubmed
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PF-07059013: A Noncovalent Modulator of Hemoglobin for Treatment of Sickle Cell Disease. J Med Chem. 2021 01 14; 64(1):326-342. View in: Pubmed
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Target Validation Using PROTACs: Applying the Four Pillars Framework. SLAS Discov. 2021 04; 26(4):474-483. View in: Pubmed
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Dehydroamino acid chemical biology: an example of functional group interconversion on proteins. RSC Chem Biol. 2020 Dec 01; 1(5):298-304. View in: Pubmed
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Critical Assessment of Targeted Protein Degradation as a Research Tool and Pharmacological Modality. Trends Pharmacol Sci. 2020 05; 41(5):305-317. View in: Pubmed
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Pharmacological Correction of Proteinopathies via Lysosomal Degradation. Biochemistry. 2020 02 18; 59(6):727-728. View in: Pubmed
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Structure-based design and analysis of SuFEx chemical probes. RSC Med Chem. 2020 Jan 01; 11(1):10-17. View in: Pubmed
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Precision Retargeting: A Selective Covalent Inhibitor Illuminates CDK7 Biology. Cell Chem Biol. 2019 06 20; 26(6):779-780. View in: Pubmed
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Expanding chemogenomic space using chemoproteomics. Bioorg Med Chem. 2019 08 01; 27(15):3451-3453. View in: Pubmed
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Quantifying drug-target engagement in live cells using sulfonyl fluoride chemical probes. Methods Enzymol. 2019; 622:201-220. View in: Pubmed
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Emerging Utility of Fluorosulfate Chemical Probes. ACS Med Chem Lett. 2018 Jul 12; 9(7):584-586. View in: Pubmed
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Reactive Chemical Probes: Beyond the Kinase Cysteinome. Angew Chem Int Ed Engl. 2018 07 20; 57(30):9220-9223. View in: Pubmed
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Small-Molecule Kinase Downregulators. Cell Chem Biol. 2018 01 18; 25(1):30-35. View in: Pubmed
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Microfluidic-Enabled Intracellular Delivery of Membrane Impermeable Inhibitors to Study Target Engagement in Human Primary Cells. ACS Chem Biol. 2017 12 15; 12(12):2970-2974. View in: Pubmed
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Highly potent and selective NaV1.7 inhibitors for use as intravenous agents and chemical probes. Bioorg Med Chem Lett. 2017 11 01; 27(21):4805-4811. View in: Pubmed
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In vitro and in vivo effects of 2,4 diaminoquinazoline inhibitors of the decapping scavenger enzyme DcpS: Context-specific modulation of SMN transcript levels. PLoS One. 2017; 12(9):e0185079. View in: Pubmed
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Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay. PLoS One. 2017; 12(9):e0184843. View in: Pubmed
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A flow cytometry-based screen identifies MBNL1 modulators that rescue splicing defects in myotonic dystrophy type I. Hum Mol Genet. 2017 08 15; 26(16):3056-3068. View in: Pubmed
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Covalent Enzyme Inhibition through Fluorosulfate Modification of a Noncatalytic Serine Residue. ACS Chem Biol. 2017 08 18; 12(8):2015-2020. View in: Pubmed
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Structure-Based Design of Highly Selective Inhibitors of the CREB Binding Protein Bromodomain. J Med Chem. 2017 07 13; 60(13):5349-5363. View in: Pubmed
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Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane. Chem Commun (Camb). 2017 May 04; 53(37):5182-5185. View in: Pubmed
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Clinical chemoproteomics-Opportunities and obstacles. Sci Transl Med. 2017 04 19; 9(386). View in: Pubmed
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Selective Downregulation of JAK2 and JAK3 by an ATP-Competitive pan-JAK Inhibitor. ACS Chem Biol. 2017 05 19; 12(5):1183-1187. View in: Pubmed
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Design of Potent mRNA Decapping Scavenger Enzyme (DcpS) Inhibitors with Improved Physicochemical Properties To Investigate the Mechanism of Therapeutic Benefit in Spinal Muscular Atrophy (SMA). J Med Chem. 2017 04 13; 60(7):3094-3108. View in: Pubmed
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Applications of chemogenomic library screening in drug discovery. Nat Rev Drug Discov. 2017 Apr; 16(4):285-296. View in: Pubmed
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Quantitative measurement of intracellular HDAC1/2 drug occupancy using a trans-cyclooctene largazole thiol probe. MedChemComm. 2017; 8:767-770. View in: Pubmed
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Quantitative measurement of intracellular HDAC1/2 drug occupancy using a trans-cyclooctene largazole thiol probe. Medchemcomm. 2017 Apr 01; 8(4):767-770. View in: Pubmed
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Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes. J Am Chem Soc. 2017 01 18; 139(2):680-685. View in: Pubmed
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Discovery of a JAK3-Selective Inhibitor: Functional Differentiation of JAK3-Selective Inhibition over pan-JAK or JAK1-Selective Inhibition. ACS Chem Biol. 2016 12 16; 11(12):3442-3451. View in: Pubmed
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Chemoselective Preparation of Clickable Aryl Sulfonyl Fluoride Monomers: A Toolbox of Highly Functionalized Intermediates for Chemical Biology Probe Synthesis. Chembiochem. 2016 10 17; 17(20):1925-1930. View in: Pubmed
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Selectivity Determination of a Small Molecule Chemical Probe Using Protein Microarray and Affinity Capture Techniques. ACS Comb Sci. 2016 10 10; 18(10):611-615. View in: Pubmed
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Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists. Sci Rep. 2016 08 16; 6:30859. View in: Pubmed
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Identification of novel macrolides with antibacterial, anti-inflammatory and type I and III IFN-augmenting activity in airway epithelium. J Antimicrob Chemother. 2016 10; 71(10):2767-81. View in: Pubmed
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Modern advances in heterocyclic chemistry in drug discovery. Org Biomol Chem. 2016 Jul 12; 14(28):6611-37. View in: Pubmed
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Development of a cell viability assay to assess drug metabolite structure-toxicity relationships. Bioorg Med Chem Lett. 2016 08 15; 26(16):4003-6. View in: Pubmed
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Understanding the chemically-reactive proteome. Mol Biosyst. 2016 05 24; 12(6):1728-30. View in: Pubmed
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Design and development of histone deacetylase (HDAC) chemical probes for cell-based profiling. Mol Biosyst. 2016 05 24; 12(6):1781-9. View in: Pubmed
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Protein labelling. Mol Biosyst. 2016 05 24; 12(6):1725-7. View in: Pubmed
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Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells. Org Biomol Chem. 2016 Jul 14; 14(26):6179-83. View in: Pubmed
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An industry perspective on drug target validation. Expert Opin Drug Discov. 2016 07; 11(7):623-5. View in: Pubmed
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Label-free technologies for target identification and validation. MedChemComm. 2016; 7:769-777. View in: Pubmed
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Transcriptional Profiling of a Selective CREB Binding Protein Bromodomain Inhibitor Highlights Therapeutic Opportunities. Chem Biol. 2015 Dec 17; 22(12):1588-96. View in: Pubmed
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Recent advances in the molecular design of synthetic vaccines. Nat Chem. 2015 Dec; 7(12):952-60. View in: Pubmed
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Cell permeable affinity- and activity-based probes. Future Med Chem. 2015; 7(16):2131-41. View in: Pubmed
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Molecular hybridization yields triazole bronchodilators for the treatment of COPD. Bioorg Med Chem Lett. 2015 Nov 15; 25(22):5121-6. View in: Pubmed
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A library approach to rapidly discover photoaffinity probes of the mRNA decapping scavenger enzyme DcpS. Mol Biosyst. 2015 Oct; 11(10):2709-12. View in: Pubmed
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Know your target, know your molecule. Nat Chem Biol. 2015 Jun; 11(6):368-72. View in: Pubmed
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Direct photocapture of bromodomains using tropolone chemical probes. MedChemComm. 2015; 6:1018-1023. View in: Pubmed
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Sulfonyl fluorides as privileged warheads in chemical biology. Chem Sci. 2015 May 01; 6(5):2650-2659. View in: Pubmed
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Rational targeting of active-site tyrosine residues using sulfonyl fluoride probes. ACS Chem Biol. 2015 Apr 17; 10(4):1094-8. View in: Pubmed
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TAK1 selective inhibition: state of the art and future opportunities. Future Med Chem. 2015; 7(1):23-33. View in: Pubmed
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Click chemistry patents and their impact on drug discovery and chemical biology. Pharm Pat Anal. 2015; 4(2):109-19. View in: Pubmed
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Chemical biology & drug discovery. Eur J Med Chem. 2014 Dec 17; 88:1-2. View in: Pubmed
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Aryloxymaleimides for cysteine modification, disulfide bridging and the dual functionalization of disulfide bonds. Chem Commun (Camb). 2014 Jul 11; 50(54):7139-42. View in: Pubmed
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Rare diseases. Foreword. Future Med Chem. 2014 Jun; 6(9):969-70. View in: Pubmed
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Understanding and applying tyrosine biochemical diversity. Mol Biosyst. 2014 May; 10(5):952-69. View in: Pubmed
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Synthetic phosphorylation of p38a recapitulates protein kinase activity. J Am Chem Soc. 2014 Feb 05; 136(5):1698-701. View in: Pubmed
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Target validation using in-cell small molecule clickable imaging probes. MedChemComm. 2013; 5:247-254. View in: Pubmed
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TAK1 inhibition in the DFG-out conformation. Chem Biol Drug Des. 2013 Nov; 82(5):500-5. View in: Pubmed
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Selection of a novel anti-nicotine vaccine: influence of antigen design on antibody function in mice. PLoS One. 2013; 8(10):e76557. View in: Pubmed
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A mild synthesis of N-functionalised bromomaleimides, thiomaleimides and bromopyridazinediones. Tetrahedron Lett. 2013 Jul 03; 54(27):3493-3495. View in: Pubmed
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Chemical motifs that redox cycle and their associated toxicity. MedChemComm. 2013; 4:1175-1180. View in: Pubmed
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Target validation using chemical probes. Nat Chem Biol. 2013 Apr; 9(4):195-9. View in: Pubmed
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Developing irreversible inhibitors of the protein kinase cysteinome. Chem Biol. 2013 Feb 21; 20(2):146-59. View in: Pubmed
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Medicinal chemistry of glucagon-like peptide receptor agonists. Prog Med Chem. 2013; 52:45-96. View in: Pubmed
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Chemistry and biology of biomolecule nitration. Chem Biol. 2012 Sep 21; 19(9):1086-92. View in: Pubmed
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Molecular scaffolds using multiple orthogonal conjugations: applications in chemical biology and drug discovery. Angew Chem Int Ed Engl. 2012 Jun 25; 51(26):6320-6. View in: Pubmed
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Welcome to Pharmaceutical Patent Analyst. Foreword. Pharm Pat Anal. 2012 Mar; 1(1):1-2. View in: Pubmed
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Quantitative affinity-based chemical proteomics of TrkA inhibitors. MedChemComm. 2011; 3:322-325. View in: Pubmed
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Click-enabled heterotrifunctional template for sequential bioconjugations. Org Biomol Chem. 2012 Jan 21; 10(3):548-54. View in: Pubmed
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Uptake, efficacy, and systemic distribution of naked, inhaled short interfering RNA (siRNA) and locked nucleic acid (LNA) antisense. Mol Ther. 2011 Dec; 19(12):2163-8. View in: Pubmed
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Inhalation by design. Future Med Chem. 2011 Oct; 3(13):1563-5. View in: Pubmed
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Dual-pharmacology muscarinic antagonist and ß2 agonist molecules for the treatment of chronic obstructive pulmonary disease. Future Med Chem. 2011 Oct; 3(13):1585-605. View in: Pubmed
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Efficient conversion of a nonselective norepinephrin reuptake inhibitor into a dual muscarinic antagonist-ß2-agonist for the treatment of chronic obstructive pulmonary disease. J Med Chem. 2011 Oct 13; 54(19):6998-7002. View in: Pubmed
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Optimized glucuronidation of dual pharmacology ß-2 agonists/M3 antagonists for the treatment of COPD. MedChemComm. 2011; 2:870-876. View in: Pubmed
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Small molecules targeting hepatitis C virus-encoded NS5A cause subcellular redistribution of their target: insights into compound modes of action. J Virol. 2011 Jul; 85(13):6353-68. View in: Pubmed
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Comparison of the non-nucleoside reverse transcriptase inhibitor lersivirine with its pyrazole and imidazole isomers. Chem Biol Drug Des. 2011 May; 77(5):393-7. View in: Pubmed
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Squaramides: physical properties, synthesis and applications. Chem Soc Rev. 2011 May; 40(5):2330-46. View in: Pubmed
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In-cell click labelling of small molecules to determine subcellular localisation. J Chem Biol. 2011 Apr; 4(2):49-53. View in: Pubmed
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Inhalation by design: dual pharmacology ß-2 agonists/M3 antagonists for the treatment of COPD. Bioorg Med Chem Lett. 2011 May 01; 21(9):2759-63. View in: Pubmed
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Aromatic chloride to nitrile transformation: medicinal and synthetic chemistry. MedChemComm. 2010; 1:309-318. View in: Pubmed
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Thermodynamic optimisation in drug discovery: a case study using carbonic anhydrase inhibitors. ChemMedChem. 2009 Dec; 4(12):1985-9. View in: Pubmed
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Pyrazole NNRTIs 3: optimisation of physicochemical properties. Bioorg Med Chem Lett. 2009 Oct 01; 19(19):5603-6. View in: Pubmed
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Physicochemical drug properties associated with in vivo toxicological outcomes: a review. Expert Opin Drug Metab Toxicol. 2009 Aug; 5(8):921-31. View in: Pubmed
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Novel indazole non-nucleoside reverse transcriptase inhibitors using molecular hybridization based on crystallographic overlays. J Med Chem. 2009 Feb 26; 52(4):1219-23. View in: Pubmed
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Relaying stereochemistry through aromatic ureas: 1,9 and 1,15 remote stereocontrol. Chem Commun (Camb). 2009 Feb 07; (5):547-9. View in: Pubmed
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Helix persistence and breakdown in oligoureas of metaphenylenediamine: apparent diastereotopicity as a spectroscopic marker of helix length in solution. J Am Chem Soc. 2008 Nov 12; 130(45):15193-202. View in: Pubmed
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Optimization of 5-aryloxyimidazole non-nucleoside reverse transcriptase inhibitors. ChemMedChem. 2008 Nov; 3(11):1756-62. View in: Pubmed
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Conformation and stereodynamics of 2,2'-disubstituted N,N'-diaryl ureas. Org Biomol Chem. 2008 Aug 21; 6(16):2908-13. View in: Pubmed
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Design and synthesis of a fluorescent muscarinic antagonist. Bioorg Med Chem Lett. 2008 Jan 15; 18(2):825-7. View in: Pubmed
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Synthetic chemistry-led creation of a difluorinated biaryl ether non-nucleoside reverse transcriptase inhibitor. Org Biomol Chem. 2007 Nov 07; 5(21):3431-3. View in: Pubmed
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Novel selective inhibitors of neutral endopeptidase for the treatment of female sexual arousal disorder. Bioorg Med Chem. 2007 Jan 01; 15(1):142-59. View in: Pubmed
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A concise synthesis of trifluoromethyl-substituted 4-aryloxy pyrazoles. Synlett. 2006; 2006(9):1404-1406. View in: Pubmed
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A concise and selective synthesis of novel 5-aryloxyimidazole NNRTIs. Org Lett. 2006 Apr 13; 8(8):1725-7. View in: Pubmed
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Oxaziridine-mediated amination of primary amines: scope and application to a one-pot pyrazole synthesis. Org Lett. 2005 Feb 17; 7(4):713-6. View in: Pubmed
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Active immunization with a glycolipid transition state analogue protects against endotoxic shock. Angew Chem Int Ed Engl. 2002 Nov 15; 41(22):4241-4. View in: Pubmed
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Antibody catalysis of the oxidation of water. Science. 2001 Sep 07; 293(5536):1806-11. View in: Pubmed
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The therapeutic potential for catalytic antibodies: from a concept to a promise. Mini Rev Med Chem. 2001 Jul; 1(2):125-32. View in: Pubmed
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Conversion of enediynes into quinones by antibody catalysis and in aqueous buffers: implications for an alternative enediyne therapeutic mechanism. J Am Chem Soc. 2001 Apr 18; 123(15):3607-8. View in: Pubmed
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Total synthesis of (+)-zaragozic acid C. J Org Chem. 2000 Oct 20; 65(21):7020-32. View in: Pubmed
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Antibodies have the intrinsic capacity to destroy antigens. Proc Natl Acad Sci U S A. 2000 Sep 26; 97(20):10930-5. View in: Pubmed
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Cleavage of the cyclohexyl-subunit of rapamycin results in loss of immunosuppressive activity. Bioorg Med Chem Lett. 1999 Feb 08; 9(3):459-62. View in: Pubmed
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