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Das D, Duncton MAJ, Georgiadis TM, Pellicena P, Clark J, Sobol RW, Georgiadis MM, King-Underwood J, Jobes DV, Chang C, Gao Y, Deacon AM, Wilson DM. A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1. Int J Mol Sci 2023; 24:16637. [PMID: 38068959 PMCID: PMC10706420 DOI: 10.3390/ijms242316637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM ("SAR by X-ray Poses Quickly") platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or "undruggable" targets, allows for (i) hit generation; (ii) the mapping of protein-ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.
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Affiliation(s)
- Debanu Das
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | | | | | | | - Jennifer Clark
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
- Department of Pathology & Laboratory Medicine, Warrant Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Millie M. Georgiadis
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - David V. Jobes
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Mid-Atlantic BioTherapeutics, Inc., Doylestown, PA 18902, USA
| | - Caleb Chang
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Yang Gao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashley M. Deacon
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | - David M. Wilson
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Biomedical Research Institute, Hasselt University, 3500 Diepenbeek, Belgium
- Belgium & Boost Scientific, 3550 Heusden-Zolder, Belgium
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Fisher N, Edwards MG, Hemming R, Allin SM, Wallis JD, Bulman Page PC, Mckenzie MJ, Jones SM, Elsegood MRJ, King-Underwood J, Richardson A. Synthesis and Activity of a Novel Autotaxin Inhibitor-Icodextrin Conjugate. J Med Chem 2018; 61:7942-7951. [PMID: 30059212 DOI: 10.1021/acs.jmedchem.8b00935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Autotaxin is an extracellular phospholipase D that catalyzes the hydrolysis of lysophosphatidyl choline (LPC) to generate the bioactive lipid lysophosphatidic acid (LPA). Autotaxin has been implicated in many pathological processes relevant to cancer. Intraperitoneal administration of an autotaxin inhibitor may benefit patients with ovarian cancer; however, low molecular mass compounds are known to be rapidly cleared from the peritoneal cavity. Icodextrin is a polymer that is already in clinical use because it is slowly eliminated from the peritoneal cavity. Herein we report conjugation of the autotaxin inhibitor HA155 to icodextrin. The conjugate inhibits autotaxin activity (IC50 = 0.86 ± 0.13 μg mL-1) and reduces cell migration. Conjugation of the inhibitor increased its solubility, decreased its membrane permeability, and improved its intraperitoneal retention in mice. These observations demonstrate the first application of icodextrin as a covalently-bonded drug delivery platform with potential use in the treatment of ovarian cancer.
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Affiliation(s)
- Natalie Fisher
- School of Pharmacy and Institute for Science and Technology in Medicine , Keele University , Keele ST5 5BG , U.K.,Keele Molecular Chemistry Group, Lennard-Jones Laboratories, School of Chemical and Physical Sciences , Keele University , Keele ST5 5BG , U.K
| | - Michael G Edwards
- Keele Molecular Chemistry Group, Lennard-Jones Laboratories, School of Chemical and Physical Sciences , Keele University , Keele ST5 5BG , U.K
| | - Ryan Hemming
- School of Science and Technology , Nottingham Trent University , Nottingham NG11 8NS , U.K
| | - Steven M Allin
- School of Science and Technology , Nottingham Trent University , Nottingham NG11 8NS , U.K
| | - John D Wallis
- School of Science and Technology , Nottingham Trent University , Nottingham NG11 8NS , U.K
| | | | - Michael J Mckenzie
- Charnwood Molecular Ltd. , The Heritage Building, Prince William Road , Loughborough LE11 5DA , U.K
| | - Stefanie M Jones
- School of Pharmacy and Institute for Science and Technology in Medicine , Keele University , Keele ST5 5BG , U.K
| | - Mark R J Elsegood
- Department of Chemistry , Loughborough University , Loughborough LE11 3TU , U.K
| | - John King-Underwood
- Computational Chemistry Resource , Old Cottage Hospital , Ledbury HR8 1ED , U.K
| | - Alan Richardson
- School of Pharmacy and Institute for Science and Technology in Medicine , Keele University , Keele ST5 5BG , U.K
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Fordyce EAF, Fraser Hunt S, Crepin D, Onions ST, Parra GF, Sleigh CJ, King-Underwood J, Finch H, Murray J. Conformationally restricted benzothienoazepine respiratory syncytial virus inhibitors: their synthesis, structural analysis and biological activities. Medchemcomm 2018; 9:583-589. [PMID: 30108949 DOI: 10.1039/c8md00033f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/16/2018] [Indexed: 11/21/2022]
Abstract
Atropisomeric drug substances are known to have different biological properties. Compounds containing the N-benzoylbenzazepine motif have been shown to exhibit energetically restricted rotation around the Ar(CO)N axis. Herein we report, for the first time, the synthesis, physical characterisation and anti-viral profiles of a series of C-4 and C-5 methylated thieno-benzazepines. NMR analysis reveals that incorporation of a single additional substituent at either of these loci influences the conformational dynamics of the azepine ring system. In the case of the C-5 alkyl analogues, the influence of the new stereocentre is so pronounced that its absolute configuration determines which unique atropisomer is obtained following the generation of the benzazepine nucleus. Screening of the alkylated derivatives for their anti-respiratory syncytial virus (RSV) activity indicates that the desired viral pathogenicity is strongly associated with the conformation adopted by the modified tricyclic scaffolds. This is particularly evident in the case of the C-5 homologues in which one atropisomer was found to be potently active and the other essentially inert. These results provide compelling evidence that we have determined the bioactive conformation shared by RSV inhibitors that employ the thienobenazapine nucleus as their core molecular architecture. Furthermore, the understanding obtained from these studies may make it possible to design improved agents against RSV infection in the future.
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Affiliation(s)
- Euan A F Fordyce
- Sygnature Discovery Ltd. , BioCity , Nottingham , NG1 1GF , UK . ; Tel: +44 (0)1159415401
| | - S Fraser Hunt
- Sygnature Discovery Ltd. , BioCity , Nottingham , NG1 1GF , UK . ; Tel: +44 (0)1159415401
| | - Damien Crepin
- Sygnature Discovery Ltd. , BioCity , Nottingham , NG1 1GF , UK . ; Tel: +44 (0)1159415401
| | - Stuart T Onions
- Sygnature Discovery Ltd. , BioCity , Nottingham , NG1 1GF , UK . ; Tel: +44 (0)1159415401
| | - Guillaume F Parra
- Sygnature Discovery Ltd. , BioCity , Nottingham , NG1 1GF , UK . ; Tel: +44 (0)1159415401
| | - Chris J Sleigh
- Sygnature Discovery Ltd. , BioCity , Nottingham , NG1 1GF , UK . ; Tel: +44 (0)1159415401
| | - John King-Underwood
- CompChem Resource , Old Cottage Hospital , Homend , Ledbury , Herefordshire HR8 1ED , UK
| | - Harry Finch
- Pulmocide Ltd. , 52 Princes Gate, Exhibition Road, South Kensington , London , SW7 2PG , UK . ; Tel: +44 (0)2037639484
| | - John Murray
- Pulmocide Ltd. , 52 Princes Gate, Exhibition Road, South Kensington , London , SW7 2PG , UK . ; Tel: +44 (0)2037639484
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Fordyce EAF, Fraser Hunt S, Crepin D, Onions ST, Parra GF, Sleigh CJ, King-Underwood J, Finch H, Murray J. Correction: Conformationally restricted benzothienoazepine respiratory syncytial virus inhibitors: their synthesis, structural analysis and biological activities. Med Chem Commun 2018; 9:746. [PMID: 30288214 PMCID: PMC6146609 DOI: 10.1039/c8md90016g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 11/26/2022]
Abstract
Correction for ‘Conformationally restricted benzothienoazepine respiratory syncytial virus inhibitors: their synthesis, structural analysis and biological activities’ by Euan A. F. Fordyce et al., Med. Chem. Commun., 2018, DOI: ; 10.1039/c8md00033f.
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Onions ST, Ito K, Charron CE, Brown RJ, Colucci M, Frickel F, Hardy G, Joly K, King-Underwood J, Kizawa Y, Knowles I, Murray PJ, Novak A, Rani A, Rapeport G, Smith A, Strong P, Taddei DM, Williams JG. Discovery of Narrow Spectrum Kinase Inhibitors: New Therapeutic Agents for the Treatment of COPD and Steroid-Resistant Asthma. J Med Chem 2016; 59:1727-46. [PMID: 26800309 DOI: 10.1021/acs.jmedchem.5b01029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The discovery of a novel series of therapeutic agents that has been designed and optimized for treating chronic obstructive pulmonary disease is reported. The pharmacological strategy was based on the identification of compounds that inhibit a defined subset of kinase enzymes modulating inflammatory processes that would be effective against steroid refractory disease and exhibit a sustained duration of action after inhaled delivery.
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Affiliation(s)
- Stuart T Onions
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - Kazuhiro Ito
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - Catherine E Charron
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - Richard J Brown
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - Marie Colucci
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - Fritz Frickel
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - George Hardy
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - Kevin Joly
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - John King-Underwood
- CompChem Resource , Old Cottage Hospital, Homend, Ledbury, Herefordshire HR8 1ED, United Kingdom
| | - Yasuo Kizawa
- Department of Physiology and Anatomy, Nihon University School of Pharmacy , 7-7-1, Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Ian Knowles
- Pneumolabs UK Limited , Harrow, Middlesex HA1 3UJ, United Kingdom
| | - P John Murray
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - Andrew Novak
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - Anjna Rani
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - Garth Rapeport
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - Alun Smith
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
| | - Peter Strong
- RespiVert Limited , 2 Royal College Street, The London Bioscience Innovation Centre, London NW1 0NH, United Kingdom
| | - David M Taddei
- Sygnature Discovery Limited, Biocity , Nottingham NG1 1GF, United Kingdom
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Farinha CM, King-Underwood J, Sousa M, Correia AR, Henriques BJ, Roxo-Rosa M, Da Paula AC, Williams J, Hirst S, Gomes CM, Amaral MD. Revertants, low temperature, and correctors reveal the mechanism of F508del-CFTR rescue by VX-809 and suggest multiple agents for full correction. ACTA ACUST UNITED AC 2014; 20:943-55. [PMID: 23890012 DOI: 10.1016/j.chembiol.2013.06.004] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 05/10/2013] [Accepted: 06/09/2013] [Indexed: 11/30/2022]
Abstract
Cystic fibrosis is mostly caused by the F508del mutation, which impairs CFTR protein from exiting the endoplasmic reticulum due to misfolding. VX-809 is a small molecule that rescues F508del-CFTR localization, which recently went into clinical trial but with unknown mechanism of action (MoA). Herein, we assessed if VX-809 is additive or synergistic with genetic revertants of F508del-CFTR, other correctors, and low temperature to determine its MoA. We explored and integrated those various agents in combined treatments, showing how they add to each other to identify their complementary MoA upon correction of F508del-CFTR. Our experimental and modeling data, while compatible with putative binding of VX-809 to NBD1:ICL4 interface, also indicate scope for further synergistic F508del-CFTR correction by other compounds at distinct conformational sites/cellular checkpoints, thus suggesting requirement of combined therapies to fully rescue F508del-CFTR.
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Affiliation(s)
- Carlos M Farinha
- Faculty of Sciences, Center for Biodiversity, Functional, and Integrative Genomics, University of Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Dahimène S, Romão A, Botelho H, Palma M, Correia A, Farinha C, King-Underwood J, Williams J, Hirst S, Gomes C, Amaral M. WS21.9 Screening for novel F508del-CFTR correctors identified by pharmacophore modelling through automated microscopy and NBD1 folding assays. J Cyst Fibros 2013. [DOI: 10.1016/s1569-1993(13)60137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bennett JM, Campbell AD, Campbell AJ, Carr MG, Dunsdon RM, Greening JR, Hurst DN, Jennings NS, Jones PS, Jordan S, Kay PB, O'Brien MA, King-Underwood J, Raynham TM, Wilkinson CS, Wilkinson TC, Wilson FX. The identification of alpha-ketoamides as potent inhibitors of hepatitis C virus NS3-4A proteinase. Bioorg Med Chem Lett 2001; 11:355-7. [PMID: 11212109 DOI: 10.1016/s0960-894x(00)00654-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Peptides based upon the non-prime side residues of the NS4A-4B cleavage site of hepatitis C virus (HCV) NS3-4A proteinase containing an alpha-ketoamide moiety in place of the scissile amide bond are potent inhibitors of this enzyme.
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Affiliation(s)
- J M Bennett
- Department of Chemistry, Roche Discover Welwyn, Welwyn Garden City, Hertfordshire, UK
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Attwood MR, Bennett JM, Campbell AD, Canning GG, Carr MG, Conway E, Dunsdon RM, Greening JR, Jones PS, Kay PB, Handa BK, Hurst DN, Jennings NS, Jordan S, Keech E, O'Brien MA, Overton HA, King-Underwood J, Raynham TM, Stenson KP, Wilkinson CS, Wilkinson TC, Wilson FX. The design and synthesis of potent inhibitors of hepatitis C virus NS3-4A proteinase. Antivir Chem Chemother 1999; 10:259-73. [PMID: 10574181 DOI: 10.1177/095632029901000505] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Hepatitis C virus (HCV) is the cause of the majority of transfusion-associated hepatitis and a significant proportion of community-acquired hepatitis worldwide. Infection by HCV frequently leads to persistent infections that result in a range of clinical conditions including an asymptomatic carrier state, severe chronic active hepatitis, cirrhosis and, in some cases, hepatocellular carcinoma. The HCV genome consists of a single-stranded, positive sense RNA containing an open reading frame of approximately 9060 nucleotides. This is translated into a single polyprotein of approximately 3020 amino acids (C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B), which in turn is processed by a series of host and viral proteinases into at least 10 cleavage products. The N-terminal portion of the NS3 protein encodes a serine proteinase that is responsible for the cleavage at the NS3-4A, NS4A-4B, NS4B-5A and NS5A-5B junctions. The 54 amino acid NS4A protein is a cofactor that binds to the NS3 protein and enhances its proteolytic activity. This report describes the expression of a recombinant NS3-4A proteinase fusion protein in Escherichia coli and the in vitro characterization of the enzyme activity using synthetic peptide substrates. It then demonstrates how these results were employed to guide the design of potent inhibitors of this enzyme.
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Affiliation(s)
- M R Attwood
- Department of Chemistry, Roche Discovery Welwyn, Welwyn Garden City, Hertfordshire, UK
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