1
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Dong L, Yang JH. Rh(III)-Catalyzed Tandem [4+2] Annulation To Construct Functional Dihydroisoquinolinones. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1787-3958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractA highly efficient Rh(III)-catalyzed tandem [4+2] annulation to construct functional dihydroisoquinolinone derivatives with an alkenyl side chain by insertion into an N–O bond as an internal oxidation process has been achieved. A wide range of 1,3-dienes as the coupling partners makes this simple methodology even more useful.
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2
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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3
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Fuglestad B, Kerstetter NE, Bédard S, Wand AJ. Extending the Detection Limit in Fragment Screening of Proteins Using Reverse Micelle Encapsulation. ACS Chem Biol 2019; 14:2224-2232. [PMID: 31550881 DOI: 10.1021/acschembio.9b00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of very weak (Kd > 10 mM) interactions of proteins with small molecules has been elusive. This is particularly important for fragment-based drug discovery, where it is suspected that the majority of potentially useful fragments will be invisible to current screening methodologies. We describe an NMR approach that permits detection of protein-fragment interactions in the very low affinity range and extends the current detection limit of ∼10 mM up to ∼200 mM and beyond. Reverse micelle encapsulation is leveraged to effectively reach very high fragment and protein concentrations, a principle that is validated by binding model fragments to E. coli dihydrofolate reductase. The method is illustrated by target-detected screening of a small polar fragment library against interleukin-1β, which lacks a known ligand-binding pocket. Evaluation of binding by titration and structural context allows for validation of observed hits using rigorous structural and statistical criteria. The 21 curated hit molecules represent a remarkable hit rate of nearly 10% of the library. Analysis shows that fragment binding involves residues comprising two-thirds of the protein's surface. Current fragment screening methods rely on detection of relatively tight binding to ligand binding pockets. The method presented here illustrates a potential to faithfully discover starting points for development of small molecules that bind to a desired region of the protein, even if the targeted region is defined by a relatively flat surface.
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Affiliation(s)
- Brian Fuglestad
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Nicole E. Kerstetter
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sabrina Bédard
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - A. Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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4
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Sommer K, Flachsenberg F, Rarey M. NAOMInext – Synthetically feasible fragment growing in a structure-based design context. Eur J Med Chem 2019; 163:747-762. [DOI: 10.1016/j.ejmech.2018.11.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022]
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5
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De Vita E, Schüler P, Lovell S, Lohbeck J, Kullmann S, Rabinovich E, Sananes A, Heßling B, Hamon V, Papo N, Hess J, Tate EW, Gunkel N, Miller AK. Depsipeptides Featuring a Neutral P1 Are Potent Inhibitors of Kallikrein-Related Peptidase 6 with On-Target Cellular Activity. J Med Chem 2018; 61:8859-8874. [DOI: 10.1021/acs.jmedchem.8b01106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elena De Vita
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Biosciences Faculty, University of Heidelberg, Heidelberg 69120, Germany
| | - Peter Schüler
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Scott Lovell
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Jasmin Lohbeck
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Sven Kullmann
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Eitan Rabinovich
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Amiram Sananes
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bernd Heßling
- Center for Molecular Biology, University of Heidelberg, Heidelberg 69120, Germany
| | - Veronique Hamon
- European Screening Centre, Biocity Scotland, University of Dundee, Newhouse ML1 5UH, U.K
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg 69120, Germany
- Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Nikolas Gunkel
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Aubry K. Miller
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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6
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Lin FY, MacKerell AD. Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding? J Phys Chem B 2017; 121:6813-6821. [PMID: 28657759 PMCID: PMC5523114 DOI: 10.1021/acs.jpcb.7b04198] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halogens are present in a significant number of drugs, contributing favorably to ligand-protein binding. Currently, the contribution of halogens, most notably chlorine and bromine, is largely attributed to halogen bonds involving favorable interactions with hydrogen bond acceptors. However, we show that halogens acting as hydrogen bond acceptors potentially make a more favorable contribution to ligand binding than halogen bonds based on quantum mechanical calculations. In addition, bioinformatics analysis of ligand-protein crystal structures shows the presence of significant numbers of such interactions. It is shown that interactions between halogens and hydrogen bond donors (HBDs) are dominated by perpendicular C-X···HBD orientations. Notably, the orientation dependence of the halogen-HBD (X-HBD) interactions is minimal over greater than 100° with favorable interaction energies ranging from -2 to -14 kcal/mol. This contrasts halogen bonds in that X-HBD interactions are substantially more favorable, being comparable to canonical hydrogen bonds, with a smaller orientation dependence, such that they make significant, favorable contributions to ligand-protein binding and, therefore, should be actively considered during rational ligand design.
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Affiliation(s)
- Fang-Yu Lin
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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7
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Güssregen S, Matter H, Hessler G, Lionta E, Heil J, Kast SM. Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series. J Chem Inf Model 2017; 57:1652-1666. [DOI: 10.1021/acs.jcim.6b00765] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Güssregen
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Hans Matter
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Evanthia Lionta
- R&D, IDD, Structural Design and Informatics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Building G877, 65926 Frankfurt am Main, Germany
| | - Jochen Heil
- Physikalische
Chemie III, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Stefan M. Kast
- Physikalische
Chemie III, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
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8
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Wurtz NR, Parkhurst BL, Jiang W, DeLucca I, Zhang X, Ladziata V, Cheney DL, Bozarth JR, Rendina AR, Wei A, Luettgen JM, Wu Y, Wong PC, Seiffert DA, Wexler RR, Priestley ES. Discovery of Phenylglycine Lactams as Potent Neutral Factor VIIa Inhibitors. ACS Med Chem Lett 2016; 7:1077-1081. [PMID: 27994741 DOI: 10.1021/acsmedchemlett.6b00282] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/16/2016] [Indexed: 11/29/2022] Open
Abstract
Inhibitors of Factor VIIa (FVIIa), a serine protease in the clotting cascade, have shown strong antithrombotic efficacy in preclinical thrombosis models with minimal bleeding liabilities. Discovery of potent, orally active FVIIa inhibitors has been largely unsuccessful because known chemotypes have required a highly basic group in the S1 binding pocket for high affinity. A recently reported fragment screening effort resulted in the discovery of a neutral heterocycle, 7-chloro-3,4-dihydroisoquinolin-1(2H)-one, that binds in the S1 pocket of FVIIa and can be incorporated into a phenylglycine FVIIa inhibitor. Optimization of this P1 binding group led to the first series of neutral, permeable FVIIa inhibitors with low nanomolar potency.
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Affiliation(s)
- Nicholas R. Wurtz
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Brandon L. Parkhurst
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Wen Jiang
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Indawati DeLucca
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Xiaojun Zhang
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Vladimir Ladziata
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Daniel L. Cheney
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - Jeffrey R. Bozarth
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Alan R. Rendina
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Anzhi Wei
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Joseph M. Luettgen
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Yiming Wu
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Pancras C. Wong
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Dietmar A. Seiffert
- Bristol-Myers Squibb R&D, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Ruth R. Wexler
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
| | - E. Scott Priestley
- Bristol-Myers Squibb R&D, 350 Carter Road, Hopewell Township, New Jersey 08540, United States
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9
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Johnson CN, Erlanson DA, Murray CW, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2015. J Med Chem 2016; 60:89-99. [PMID: 27739691 DOI: 10.1021/acs.jmedchem.6b01123] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based drug discovery (FBDD) is now well-established as a technology for generating new chemical leads and drugs. This Miniperspective provides a tabulated overview of the fragment-to-lead literature published in the year 2015, together with a commentary on trends observed across the FBDD field during this time. It is hoped that this tabulated summary will provide a useful point of reference for both FBDD practitioners and the wider medicinal chemistry community.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 409 Illinois Street, San Francisco, California 94158, United States
| | - Christopher W Murray
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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10
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Ladziata V(U, Glunz PW, Zou Y, Zhang X, Jiang W, Jacutin-Porte S, Cheney DL, Wei A, Luettgen JM, Harper TM, Wong PC, Seiffert D, Wexler RR, Priestley ES. Synthesis and P1′ SAR exploration of potent macrocyclic tissue factor-factor VIIa inhibitors. Bioorg Med Chem Lett 2016; 26:5051-5057. [DOI: 10.1016/j.bmcl.2016.08.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
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11
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Zhang X, Glunz PW, Johnson JA, Jiang W, Jacutin-Porte S, Ladziata V, Zou Y, Phillips MS, Wurtz NR, Parkhurst B, Rendina AR, Harper TM, Cheney DL, Luettgen JM, Wong PC, Seiffert D, Wexler RR, Priestley ES. Discovery of a Highly Potent, Selective, and Orally Bioavailable Macrocyclic Inhibitor of Blood Coagulation Factor VIIa-Tissue Factor Complex. J Med Chem 2016; 59:7125-37. [PMID: 27455395 DOI: 10.1021/acs.jmedchem.6b00469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Inhibitors of the tissue factor (TF)/factor VIIa complex (TF-FVIIa) are promising novel anticoagulants which show excellent efficacy and minimal bleeding in preclinical models. Starting with an aminoisoquinoline P1-based macrocyclic inhibitor, optimization of the P' groups led to a series of highly potent and selective TF-FVIIa inhibitors which displayed poor permeability. Fluorination of the aminoisoquinoline reduced the basicity of the P1 group and significantly improved permeability. The resulting lead compound was highly potent, selective, and achieved good pharmacokinetics in dogs with oral dosing. Moreover, it demonstrated robust antithrombotic activity in a rabbit model of arterial thrombosis.
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Affiliation(s)
- Xiaojun Zhang
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Peter W Glunz
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - James A Johnson
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Wen Jiang
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Swanee Jacutin-Porte
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Vladimir Ladziata
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Yan Zou
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Monique S Phillips
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Nicholas R Wurtz
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Brandon Parkhurst
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Alan R Rendina
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Timothy M Harper
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Daniel L Cheney
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Joseph M Luettgen
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Pancras C Wong
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Dietmar Seiffert
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Ruth R Wexler
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - E Scott Priestley
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
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12
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Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
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Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
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13
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Zimmermann MO, Boeckler FM. Targeting the protein backbone with aryl halides: systematic comparison of halogen bonding and π⋯π interactions using N-methylacetamide. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00499c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Systematic plane scans reveal a seamless transition from σ-hole interactions with the carbonyl oxygen to interactions with the amide π-electrons at increasing distances.
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Affiliation(s)
- M. O. Zimmermann
- Department of Pharmaceutical and Medicinal Chemistry
- Institute of Pharmaceutical Sciences
- Eberhard Karls Universität Tübingen
- 72076 Tübingen
- Germany
| | - F. M. Boeckler
- Department of Pharmaceutical and Medicinal Chemistry
- Institute of Pharmaceutical Sciences
- Eberhard Karls Universität Tübingen
- 72076 Tübingen
- Germany
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14
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Varnes JG, Geschwindner S, Holmquist CR, Forst J, Wang X, Dekker N, Scott CW, Tian G, Wood MW, Albert JS. Fragment-assisted hit investigation involving integrated HTS and fragment screening: Application to the identification of phosphodiesterase 10A (PDE10A) inhibitors. Bioorg Med Chem Lett 2015; 26:197-202. [PMID: 26597534 DOI: 10.1016/j.bmcl.2015.10.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/26/2015] [Accepted: 10/30/2015] [Indexed: 12/29/2022]
Abstract
Fragment-based drug design (FBDD) relies on direct elaboration of fragment hits and typically requires high resolution structural information to guide optimization. In fragment-assisted drug discovery (FADD), fragments provide information to guide selection and design but do not serve as starting points for elaboration. We describe FADD and high-throughput screening (HTS) campaign strategies conducted in parallel against PDE10A where fragment hit co-crystallography was not available. The fragment screen led to prioritized fragment hits (IC50's ∼500μM), which were used to generate a hypothetical core scaffold. Application of this scaffold as a filter to HTS output afforded a 4μM hit, which, after preparation of a small number of analogs, was elaborated into a 16nM lead. This approach highlights the strength of FADD, as fragment methods were applied despite the absence of co-crystallographical information to efficiently identify a lead compound for further optimization.
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Affiliation(s)
- Jeffrey G Varnes
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA.
| | | | - Christopher R Holmquist
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Janet Forst
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Xia Wang
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Niek Dekker
- Discovery Sciences, AstraZeneca R&D, SE-431 83 Mölndal, Sweden
| | - Clay W Scott
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Gaochao Tian
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Michael W Wood
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Jeffrey S Albert
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA.
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15
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Priestley ES, Cheney DL, DeLucca I, Wei A, Luettgen JM, Rendina AR, Wong PC, Wexler RR. Structure-Based Design of Macrocyclic Coagulation Factor VIIa Inhibitors. J Med Chem 2015; 58:6225-36. [PMID: 26151189 DOI: 10.1021/acs.jmedchem.5b00788] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.
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