1
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Kleiner VA, O Fischmann T, Howe JA, Beshore DC, Eddins MJ, Hou Y, Mayhood T, Klein D, Nahas DD, Lucas BJ, Xi H, Murray E, Ma DY, Getty K, Fearns R. Conserved allosteric inhibitory site on the respiratory syncytial virus and human metapneumovirus RNA-dependent RNA polymerases. Commun Biol 2023; 6:649. [PMID: 37337079 DOI: 10.1038/s42003-023-04990-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023] Open
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults1-3. Therapeutic small molecule inhibitors that bind to the RSV polymerase and inhibit viral replication are being developed, but their binding sites and molecular mechanisms of action remain largely unknown4. Here we report a conserved allosteric inhibitory site identified on the L polymerase proteins of RSV and HMPV that can be targeted by a dual-specificity, non-nucleoside inhibitor, termed MRK-1. Cryo-EM structures of the inhibitor in complexes with truncated RSV and full-length HMPV polymerase proteins provide a structural understanding of how MRK-1 is active against both viruses. Functional analyses indicate that MRK-1 inhibits conformational changes necessary for the polymerase to engage in RNA synthesis initiation and to transition into an elongation mode. Competition studies reveal that the MRK-1 binding pocket is distinct from that of a capping inhibitor with an overlapping resistance profile, suggesting that the polymerase conformation bound by MRK-1 may be distinct from that involved in mRNA capping. These findings should facilitate optimization of dual RSV and HMPV replication inhibitors and provide insights into the molecular mechanisms underlying their polymerase activities.
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Affiliation(s)
- Victoria A Kleiner
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | | | | | | | | | - Yan Hou
- MRL, Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | | | - He Xi
- MRL, Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
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2
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Moore KP, Schwaid AG, Tudor M, Park S, Beshore DC, Converso A, Shipe WD, Anand R, Lan P, Moningka R, Rothman DM, Sun W, Chi A, Cornella-Taracido I, Adam GC, Bahnck-Teets C, Carroll SS, Fay JF, Goh SL, Lusen J, Quan S, Rodriguez S, Xu M, Andrews CL, Song C, Filzen T, Li J, Hollenstein K, Klein DJ, Lammens A, Lim UM, Fang Z, McHale C, Li Y, Lu M, Diamond TL, Howell BJ, Zuck P, Balibar CJ. A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells. ACS Chem Biol 2022; 17:2595-2604. [PMID: 36044633 DOI: 10.1021/acschembio.2c00515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Although current antiretroviral therapy can control HIV-1 replication and prevent disease progression, it is not curative. Identifying mechanisms that can lead to eradication of persistent viral reservoirs in people living with HIV-1 (PLWH) remains an outstanding challenge to achieving cure. Utilizing a phenotypic screen, we identified a novel chemical class capable of killing HIV-1 infected peripheral blood mononuclear cells. Tool compounds ICeD-1 and ICeD-2 ("inducer of cell death-1 and 2"), optimized for potency and selectivity from screening hits, were used to deconvolute the mechanism of action using a combination of chemoproteomic, biochemical, pharmacological, and genetic approaches. We determined that these compounds function by modulating dipeptidyl peptidase 9 (DPP9) and activating the caspase recruitment domain family member 8 (CARD8) inflammasome. Efficacy of ICeD-1 and ICeD-2 was dependent on HIV-1 protease activity and synergistic with efavirenz, which promotes premature activation of HIV-1 protease at high concentrations in infected cells. This in vitro synergy lowers the efficacious cell kill concentration of efavirenz to a clinically relevant dose at concentrations of ICeD-1 or ICeD-2 that do not result in complete DPP9 inhibition. These results suggest engagement of the pyroptotic pathway as a potential approach to eliminate HIV-1 infected cells.
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Affiliation(s)
- Keith P Moore
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Adam G Schwaid
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew Tudor
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sangho Park
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Douglas C Beshore
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Antonella Converso
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - William D Shipe
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Rajan Anand
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ping Lan
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Remond Moningka
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Deborah M Rothman
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Wanying Sun
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - An Chi
- Chemical Biology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Gregory C Adam
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carolyn Bahnck-Teets
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Steven S Carroll
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - John F Fay
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shih Lin Goh
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey Lusen
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shuo Quan
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Silveria Rodriguez
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Min Xu
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Christine L Andrews
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Cheng Song
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tracey Filzen
- Screening and Protein Sciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jing Li
- Screening and Protein Sciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Kaspar Hollenstein
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Daniel J Klein
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Alfred Lammens
- Proteros Biostructures GmbH, Bunsenstr, Martinsried 82152, Germany
| | - U-Ming Lim
- Genome and Biomarker Sciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhiyu Fang
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carolyn McHale
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuan Li
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Meiqing Lu
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tracy L Diamond
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Bonnie J Howell
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Paul Zuck
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carl J Balibar
- Infectious Disease and Vaccines, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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3
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Beshore DC, Haidle AM, Arasappan A, Lim YH, Raheem I, Roecker AJ, Shockley SE, Simov V. Building a Culture of Medicinal Chemistry Knowledge Sharing. J Med Chem 2022; 65:3776-3785. [PMID: 35192762 DOI: 10.1021/acs.jmedchem.1c02144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Increasing the efficiency of the drug discovery process is a challenge faced by drug hunters everywhere. One strategy medicinal chemists employ to meet this challenge is learning from knowledge sources within and beyond their organization. In this Perspective, we discuss the evolution of mechanisms for medicinal chemistry knowledge capture and sharing at Merck & Co. over the past 15 years. We describe our approach to knowledge management and report on the multiple enduring and complementary teams and initiatives we have created to capture and share knowledge within a geographically diverse medicinal chemistry community. In addition, this Perspective will share the benefits we have observed and also reflect on what has allowed our efforts to be both successful and sustainable.
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Affiliation(s)
- Douglas C Beshore
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Andrew M Haidle
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ashok Arasappan
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yeon-Hee Lim
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Izzat Raheem
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Anthony J Roecker
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samantha E Shockley
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Vladimir Simov
- Department of Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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4
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Beshore DC, Adam GC, Barnard RJO, Burlein C, Gallicchio SN, Holloway MK, Krosky D, Lemaire W, Myers RW, Patel S, Plotkin MA, Powell DA, Rada V, Cox CD, Coleman PJ, Klein DJ, Wolkenberg SE. Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction. ACS Med Chem Lett 2021; 12:540-547. [PMID: 33854701 PMCID: PMC8040053 DOI: 10.1021/acsmedchemlett.1c00074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023] Open
Abstract
A novel series of histone deacetylase (HDAC) inhibitors lacking a zinc-binding moiety has been developed and described herein. HDAC isozyme profiling and kinetic studies indicate that these inhibitors display a selectivity preference for HDACs 1, 2, 3, 10, and 11 via a rapid equilibrium mechanism, and crystal structures with HDAC2 confirm that these inhibitors do not interact with the catalytic zinc. The compounds are nonmutagenic and devoid of electrophilic and mutagenic structural elements and exhibit off-target profiles that are promising for further optimization. The efficacy of this new class in biochemical and cell-based assays is comparable to the marketed HDAC inhibitors belinostat and vorinostat. These results demonstrate that the long-standing pharmacophore model of HDAC inhibitors requiring a metal binding motif should be revised and offers a distinct class of HDAC inhibitors.
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Affiliation(s)
| | - Gregory C. Adam
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | | | | | | | - Daniel Krosky
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Lemaire
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Robert W. Myers
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Sangita Patel
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - David A. Powell
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Vanessa Rada
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Paul J. Coleman
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daniel J. Klein
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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5
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Salter R, Beshore DC, Colletti SL, Evans L, Gong Y, Helmy R, Liu Y, Maciolek CM, Martin G, Pajkovic N, Phipps R, Small J, Steele J, de Vries R, Williams H, Martin IJ. Microbial biotransformation – an important tool for the study of drug metabolism. Xenobiotica 2018; 49:877-886. [DOI: 10.1080/00498254.2018.1512018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rhys Salter
- Department of Preclinical Development and Safety, Janssen Research and Development LLC, Spring House, PA, USA
| | | | | | | | - Yong Gong
- Department of Preclinical Development and Safety, Janssen Research and Development LLC, Spring House, PA, USA
| | - Roy Helmy
- Department of Pharmacokinetics, Pharmacokinetics and Drug Metabolism, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yong Liu
- Department of Preclinical Development, Merck & Co., Inc., West Point, PA, USA
| | - Cheri M. Maciolek
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA
| | - Gary Martin
- Department of Global Chemistry, Merck & Co., Inc., Rahway, NJ, USA
| | - Natasa Pajkovic
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA
| | | | - James Small
- Department of Global Chemistry, Merck & Co., Inc., West Point, PA, USA
| | | | - Ronald de Vries
- Department of Preclinical Development and Safety, Janssen Pharmaceutica, Beerse, Belgium
| | | | - Iain J. Martin
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Boston, MA, USA
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6
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Beshore DC, N. Di Marco C, Chang RK, Greshock TJ, Ma L, Wittmann M, Seager MA, Koeplinger KA, Thompson CD, Fuerst J, Hartman GD, Bilodeau MT, Ray WJ, Kuduk SD. MK-7622: A First-in-Class M 1 Positive Allosteric Modulator Development Candidate. ACS Med Chem Lett 2018; 9:652-656. [PMID: 30034595 DOI: 10.1021/acsmedchemlett.8b00095] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Identification of ligands that selectively activate the M1 muscarinic signaling pathway has been sought for decades to treat a range of neurological and cognitive disorders. Herein, we describe the optimization efforts focused on addressing key physicochemical and safety properties, ultimately leading to the clinical candidate MK-7622, a highly selective positive allosteric modulator of the M1 muscarinic receptor that has entered Phase II studies in patients with Alzheimer's disease.
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Affiliation(s)
| | | | - Ronald K. Chang
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Lei Ma
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Marion Wittmann
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | | | | | - Joy Fuerst
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Mark T. Bilodeau
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - William J. Ray
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Scott D. Kuduk
- MRL, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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7
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Uslaner JM, Kuduk SD, Wittmann M, Lange HS, Fox SV, Min C, Pajkovic N, Harris D, Cilissen C, Mahon C, Mostoller K, Warrington S, Beshore DC. Preclinical to Human Translational Pharmacology of the Novel M1 Positive Allosteric Modulator MK-7622. J Pharmacol Exp Ther 2018; 365:556-566. [DOI: 10.1124/jpet.117.245894] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/16/2018] [Indexed: 11/22/2022] Open
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8
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Sanders JM, Beshore DC, Culberson JC, Fells JI, Imbriglio JE, Gunaydin H, Haidle AM, Labroli M, Mattioni BE, Sciammetta N, Shipe WD, Sheridan RP, Suen LM, Verras A, Walji A, Joshi EM, Bueters T. Informing the Selection of Screening Hit Series with in Silico Absorption, Distribution, Metabolism, Excretion, and Toxicity Profiles. J Med Chem 2017; 60:6771-6780. [DOI: 10.1021/acs.jmedchem.6b01577] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- John M. Sanders
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Douglas C. Beshore
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - J. Christopher Culberson
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - James I. Fells
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Jason E. Imbriglio
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Hakan Gunaydin
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Andrew M. Haidle
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Marc Labroli
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Brian E. Mattioni
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Nunzio Sciammetta
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - William D. Shipe
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Robert P. Sheridan
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Linda M. Suen
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Andreas Verras
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Abbas Walji
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Elizabeth M. Joshi
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
| | - Tjerk Bueters
- Modeling & Informatics, ‡Discovery Chemistry, and §Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07065, United States
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9
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Homsher MF, Beshore DC, Cassaday J, Squadroni B, Mohammed E, Hartnett M, Day S, Ma L, Pechter D, Smith MD, Monsma F, Zuck P, Finley MF, Uebele VN, Hermes JD. High-Throughput Agonist Shift Assay Development for the Analysis of M 1-Positive Allosteric Modulators. SLAS Discov 2017; 22:1060-1066. [PMID: 28426939 DOI: 10.1177/2472555217705373] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Agonist shift assays feature cross-titrations of allosteric modulators and orthosteric ligands. Information generated in agonist shift assays can include a modulator's effect on the orthosteric agonist's potency (alpha) and efficacy (beta), as well as direct agonist activity of the allosteric ligand (tauB) and the intrinsic binding affinity of the modulator to the unoccupied receptor (KB). Because of the heavy resource demand and complex data handling, these allosteric parameters are determined infrequently during the course of a drug discovery program and on a relatively small subset of compounds. Automation of agonist shift assays enables this data-rich analysis to evaluate a larger number of compounds, offering the potential to differentiate compound classes earlier and prospectively prioritize based on desired molecular pharmacology. A high-throughput calcium-imaging agonist shift assay was pursued to determine the allosteric parameters of over 1000 positive allosteric modulator (PAM) molecules for the human muscarinic acetylcholine receptor 1 (M1). Control compounds were run repeatedly to demonstrate internal consistency. Comparisons between potency measurements and the allosteric parameter results demonstrate that these different types of measurements do not necessarily correlate, highlighting the importance of fully characterizing and understanding the allosteric properties of leads.
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Affiliation(s)
| | | | - Jason Cassaday
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
| | - Brian Squadroni
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
| | | | - Michelle Hartnett
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
| | - Stephen Day
- 3 MRL Pipeline Support, Merck and Co, Montreal, Canada
| | - Lei Ma
- 4 Neuroscience, Merck Research Labs, West Point, PA, USA
| | - David Pechter
- 5 Assay Operations, Merck Research Labs, Kenilworth, NJ, USA
| | | | | | - Paul Zuck
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
| | - Michael F Finley
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
| | - Victor N Uebele
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
| | - Jeffrey D Hermes
- 1 Screening and Protein Sciences, Merck and Co, North Wales, PA, USA
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10
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Affiliation(s)
- Douglas C. Beshore
- Department of Medicinal Chemistry; Merck Research Laboratories; West Point PA 19486 USA
| | - Adam W. Johnson
- Department of Medicinal Chemistry; Merck Research Laboratories; West Point PA 19486 USA
| | - Robert M. DiPardo
- Department of Medicinal Chemistry; Merck Research Laboratories; West Point PA 19486 USA
| | - Daniel R. Pitts
- Department of Medicinal Chemistry; Merck Research Laboratories; West Point PA 19486 USA
| | - Victoria Cofre
- Department of Medicinal Chemistry; Merck Research Laboratories; West Point PA 19486 USA
| | - Scott D. Kuduk
- Department of Medicinal Chemistry; Merck Research Laboratories; West Point PA 19486 USA
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11
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Kuduk SD, Di Marco CN, Saffold JR, Ray WJ, Ma L, Wittmann M, Koeplinger KA, Thompson CD, Hartman GD, Bilodeau MT, Beshore DC. Identification of a methoxynaphthalene scaffold as a core replacement in quinolizidinone amide M(1) positive allosteric modulators. Bioorg Med Chem Lett 2014; 24:1417-20. [PMID: 24485781 DOI: 10.1016/j.bmcl.2014.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/02/2014] [Accepted: 01/06/2014] [Indexed: 11/28/2022]
Abstract
A series of methoxynaphthalene amides were prepared and evaluated as alternatives to quinolizidinone amide M1 positive allosteric modulators. A methoxy group was optimal for M1 activity and addressed key P-gp issues present in the aforementioned quinolizidinone amide series.
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Affiliation(s)
- Scott D Kuduk
- Department of Medicinal Chemistry, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA.
| | - Christina N Di Marco
- Department of Medicinal Chemistry, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Jonathan R Saffold
- Department of Medicinal Chemistry, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - William J Ray
- Department of Alzheimer's Research, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Lei Ma
- Department of Alzheimer's Research, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Marion Wittmann
- Department of Alzheimer's Research, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Kenneth A Koeplinger
- Department of Drug Metabolism, Merck Research Laboratories, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Charles D Thompson
- Department of Drug Metabolism, Merck Research Laboratories, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - George D Hartman
- Department of Medicinal Chemistry, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Mark T Bilodeau
- Department of Medicinal Chemistry, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
| | - Douglas C Beshore
- Department of Medicinal Chemistry, Sumneytown Pike, PO Box 4, West Point, PA 19486, USA
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12
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Abstract
INTRODUCTION There is substantial evidence from preclinical and early proof-of-concept studies suggesting that selective modulation of the M(1) muscarinic receptor is efficacious in cognitive models of Alzheimer's disease (AD) and antipsychotic models of schizophrenia. For example, a number of nonselective M(1) muscarinic agonists have previously shown positive effects on cognitive function in AD patients, but were limited due to cholinergic adverse events thought to be mediated by pan activation of the M(2) to M(5) subtypes. Thus, there is a need to identify selective activators of the M(1) receptor to evaluate their potential in cognitive disorders. One strategy to confer selectivity for M(1) is the identification of allosteric agonists or positive allosteric modulators, which would target an allosteric site on the M(1) receptor rather than the highly conserved orthosteric acetylcholine binding site. AREAS COVERED This review discusses the M(1) muscarinic receptor and its potential therapeutic value in the treatment of CNS disorders such as AD and schizophrenia. Specifically, novel allosteric ligands that activate or positively modulate the M(1) receptor are examined and peer-reviewed articles associated with these patents publications are also described. EXPERT OPINION There is substantial evidence supporting activation of the M(1) receptor might be effective in treating symptoms of AD and schizophrenia, but therapeutic success has been elusive and is hypothesized to be due to the lack of selectivity among orthosteric agonists. During the past decade, allosteric modulation of GPCRs has evolved as a viable strategy toward generating subtype selective molecules. A number of novel, selective ligands in the form of allosteric agonists and positive allosteric modulators of the M(1) receptor have been identified offering the potential for clinical evaluation of M(1)-specific receptor activation.
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Affiliation(s)
- Scott D Kuduk
- Department of Medicinal Chemistry, Merck Research Laboratories , Sumneytown Pike, PO Box 4, West Point, PA 19486, USA.
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13
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Beshore DC, Liverton NJ, McIntyre CJ, Claiborne CF, Libby B, Culberson JC, Salata JJ, Regan CP, Lynch JJ, Kiss L, Spencer RH, Kane SA, White RB, Yeh S, Hartman GD, Dinsmore CJ. Discovery of triarylethanolamine inhibitors of the Kv1.5 potassium channel. Bioorg Med Chem Lett 2010; 20:2493-6. [DOI: 10.1016/j.bmcl.2010.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/26/2010] [Accepted: 03/01/2010] [Indexed: 02/02/2023]
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14
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Kuduk SD, DiPardo RM, Beshore DC, Ray WJ, Ma L, Wittmann M, Seager MA, Koeplinger KA, Thompson CD, Hartman GD, Bilodeau MT. Hydroxy cycloalkyl fused pyridone carboxylic acid M1 positive allosteric modulators. Bioorg Med Chem Lett 2010; 20:2538-41. [DOI: 10.1016/j.bmcl.2010.02.095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 02/24/2010] [Accepted: 02/25/2010] [Indexed: 10/19/2022]
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15
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Abstract
An efficient protocol for elaboration of the 5,6-fused 2-pyridone ring system, exploiting the tandem condensation of propiolamide and cyclic β-ketomethyl esters in water, followed by acid or base promoted intramolecular ring closure and decarboxylation, has been developed.
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Affiliation(s)
- Amos B Smith
- Department of Chemistry, Monell Chemical Senses Center and Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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16
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Affiliation(s)
- Christopher J. Dinsmore
- a Department of Medicinal Chemistry , Merck Research Laboratories , West Point, PA, 19486, USA
| | - Douglas C. Beshore
- a Department of Medicinal Chemistry , Merck Research Laboratories , West Point, PA, 19486, USA
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17
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Abstract
A full account of the enantioselective total syntheses of (+)-lyconadin A (1) and (-)-lyconadin B (2) is presented. Central to this venture was recognition and deployment of a key strategy-level intramolecular aldol/conjugate addition cascade that led, in a single operation, to two new carbon-carbon sigma-bonds, three new stereogenic centers, and two new rings, albeit with the incorrect stereogenicity at C(12) for the lyconadins. Correction of the C(12) stereogenicity was achieved via innovative use of a protonated intramolecular aminal. An aminoiodo olefin cyclization, in conjunction with alpha-pyridinone and 3,4-dihydropyridinone annulation protocols, permitted completion of the syntheses of (+)-lyconadin A (1) and (-)-lyconadin B (2), respectively.
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Affiliation(s)
| | - Amos B. Smith
- Department of Chemistry, Laboratory for Research on the Structure of Matter, and Monell Chemical Senses Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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18
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Regan CP, Kiss L, Stump GL, McIntyre CJ, Beshore DC, Liverton NJ, Dinsmore CJ, Lynch JJ. Atrial antifibrillatory effects of structurally distinct IKur blockers 3-[(dimethylamino)methyl]-6-methoxy-2-methyl-4-phenylisoquinolin-1(2H)-one and 2-phenyl-1,1-dipyridin-3-yl-2-pyrrolidin-1-yl-ethanol in dogs with underlying heart failure. J Pharmacol Exp Ther 2007; 324:322-30. [PMID: 17967939 DOI: 10.1124/jpet.107.127654] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Drug discovery efforts have focused recently on atrial-selective targets, including the Kv1.5 channel, which underlies the ultrarapid delayed rectifier current, I(Kur), to develop novel treatments for atrial fibrillation (AF). Two structurally distinct compounds, a triarylethanolamine TAEA and an isoquinolinone 3-[(dimethylamino)-methyl]-6-methoxy-2-methyl-4-phenylisoquinolin-1(2H)-one (ISQ-1), blocked I(Kur) in Chinese hamster ovary cells expressing human Kv1.5 with IC(50) values of 238 and 324 nM, respectively. In anesthetized dogs, i.v. infusions of TAEA and ISQ-1 elicited comparable 16% increases in atrial refractory period, with no effect on ventricular refractory period or QTc interval. Plasma concentrations at end infusion for TAEA and ISQ-1 were 58.5 +/- 23.6 and 330.3 +/- 43.5 nM, respectively. The abilities of TAEA and ISQ-1 to terminate AF, with comparison to the rapidly activating component of delayed rectifier potassium current blocker (+)-N-[1'-(6-cyano-1,2,3,4-tetrahydro-2(R)-naphthalenyl)-3,4-dihydro-4(R)-hydroxyspiro(2H-1-benzopyran-2,4'-piperidin)-6-yl]methanesulfonamide] monohydrochloride (MK-499) and the class IC 1-[2-[2-hydroxy-3-(propylamino)-propoxy]phenyl]-3-phenyl-1-propanone (propafenone), were assessed in conscious dogs with heart failure and inducible AF (entry criterion). All test agents administered in i.v. bolus regimens terminated AF in at least half of animals tested; conversely no agent was universally effective. MK-499, ISQ-1, TAEA, and propafenone terminated AF in five of six, four of seven, four of six, and five of six animals at plasma concentrations of 32.6 +/- 18.7, 817 +/- 274, 714 +/- 622, and 816 +/- 240 nM, respectively. Directed cardiac electrophysiologic studies in anesthetized dogs using i.v. bolus (consistent with AF studies) plus infusion regimens with TAEA and ISQ-1 demonstrated significant increases in atrial refractory period (12-15%), A-H and P-A intervals, but no effects on ventricular refractory period, H-V, and HEG intervals. The demonstration of AF termination with TAEA and ISQ-1 in the dog heart failure model extends the profile of antiarrhythmic efficacy of Kv1.5 blockade.
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Affiliation(s)
- Christopher P Regan
- Departments of Stroke and Neurodegeneration, Merck Research Laboratories, West Point, PA 19486, USA
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Affiliation(s)
- Douglas C Beshore
- Department of Chemistry, Laboratory for Research on the Structure of Matter, and Monell Chemical Senses Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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20
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Trotter BW, Nanda KK, Kett NR, Regan CP, Lynch JJ, Stump GL, Kiss L, Wang J, Spencer RH, Kane SA, White RB, Zhang R, Anderson KD, Liverton NJ, McIntyre CJ, Beshore DC, Hartman GD, Dinsmore CJ. Design and synthesis of novel isoquinoline-3-nitriles as orally bioavailable Kv1.5 antagonists for the treatment of atrial fibrillation. J Med Chem 2007; 49:6954-7. [PMID: 17125248 DOI: 10.1021/jm060927v] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [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: 11/28/2022]
Abstract
Novel 3-cyanoisoquinoline Kv1.5 antagonists have been prepared and evaluated in in vitro and in vivo assays for inhibition of the Kv1.5 potassium channel and its associated cardiac potassium current, IKur. Structural modifications of isoquinolinone lead 1 afforded compounds with excellent potency, selectivity, and oral bioavailability.
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Affiliation(s)
- B Wesley Trotter
- Department of Medicinal Chemistry, Merck Research Laboratories, WP14-2, P.O. Box 4, Sumneytown Pike, West Point, Pennsylvania 19486, USA.
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Affiliation(s)
- Douglas C. Beshore
- a Merck Research Laboratories, Department of Medicinal Chemistry , West Point, Pennsylvania, USA
| | - Christopher J. Dinsmore
- a Merck Research Laboratories, Department of Medicinal Chemistry , West Point, Pennsylvania, USA
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Bell IM, Gallicchio SN, Abrams M, Beese LS, Beshore DC, Bhimnathwala H, Bogusky MJ, Buser CA, Culberson JC, Davide J, Ellis-Hutchings M, Fernandes C, Gibbs JB, Graham SL, Hamilton KA, Hartman GD, Heimbrook DC, Homnick CF, Huber HE, Huff JR, Kassahun K, Koblan KS, Kohl NE, Lobell RB, Lynch JJ, Robinson R, Rodrigues AD, Taylor JS, Walsh ES, Williams TM, Zartman CB. 3-Aminopyrrolidinone farnesyltransferase inhibitors: design of macrocyclic compounds with improved pharmacokinetics and excellent cell potency. J Med Chem 2002; 45:2388-409. [PMID: 12036349 DOI: 10.1021/jm010531d] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [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: 11/28/2022]
Abstract
A series of macrocyclic 3-aminopyrrolidinone farnesyltransferase inhibitors (FTIs) has been synthesized. Compared with previously described linear 3-aminopyrrolidinone FTIs such as compound 1, macrocycles such as 49 combined improved pharmacokinetic properties with a reduced potential for side effects. In dogs, oral bioavailability was good to excellent, and increases in plasma half-life were due to attenuated clearance. It was observed that in vivo clearance correlated with the flexibility of the molecules and this concept proved useful in the design of FTIs that exhibited low clearance, such as FTI 78. X-ray crystal structures of compounds 49 and 66 complexed with farnesyltransferase (FTase)-farnesyl diphosphate (FPP) were determined, and they provide details of the key interactions in such ternary complexes. Optimization of this 3-aminopyrrolidinone series of compounds led to significant increases in potency, providing 83 and 85, the most potent inhibitors of FTase in cells described to date.
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Affiliation(s)
- Ian M Bell
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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Abstract
[reaction: see text] A one-pot, tandem reductive amination-transamidation-cyclization reaction was employed to produce substituted piperazin-2-ones in good yields. Various amino acid methyl esters and transferable acyl groups were examined to establish the reaction's scope.
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Affiliation(s)
- Douglas C Beshore
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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Bell IM, Gallicchio SN, Abrams M, Beshore DC, Buser CA, Culberson JC, Davide J, Ellis-Hutchings M, Fernandes C, Gibbs JB, Graham SL, Hartman GD, Heimbrook DC, Homnick CF, Huff JR, Kassahun K, Koblan KS, Kohl NE, Lobell RB, Lynch JJ, Miller PA, Omer CA, Rodrigues AD, Walsh ES, Williams TM. Design and biological activity of (S)-4-(5-([1-(3-chlorobenzyl)-2-oxopyrrolidin-3-ylamino]methyl)imidazol-1-ylmethyl)benzonitrile, a 3-aminopyrrolidinone farnesyltransferase inhibitor with excellent cell potency. J Med Chem 2001; 44:2933-49. [PMID: 11520202 DOI: 10.1021/jm010156p] [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: 11/28/2022]
Abstract
The synthesis, structure-activity relationships, and biological properties of a novel series of imidazole-containing inhibitors of farnesyltransferase are described. Starting from a 3-aminopyrrolidinone core, a systematic series of modifications provided 5h, a non-thiol, non-peptide farnesyltransferase inhibitor with excellent bioavailability in dogs. Compound 5h was found to have an unusually favorable ratio of cell potency to intrinsic potency, compared with other known FTIs. It exhibited excellent potency against a range of tumor cell lines in vitro and showed full efficacy in the K-rasB transgenic mouse model.
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Affiliation(s)
- I M Bell
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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Beshore DC, Bell IM, Dinsmore CJ, Homnick CF, Culberson JC, Robinson RG, Fernandes C, Walsh ES, Abrams MT, Bhimnathwala HG, Davide JP, Ellis-Hutchings MS, Huber HA, Koblan KS, Buser CA, Kohl NE, Lobell RB, Chen IW, McLoughlin DA, Olah TV, Graham SL, Hartman GD, Williams TM. Evaluation of amino acid-based linkers in potent macrocyclic inhibitors of farnesyl-protein transferase. Bioorg Med Chem Lett 2001; 11:1817-21. [PMID: 11459639 DOI: 10.1016/s0960-894x(01)00340-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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
A series of amino acid-based linkers was used to investigate the effects of various substituents upon the potency, pharmacokinetic properties, and conformation of macrocyclic farnesyl-protein transferase inhibitors (FTIs). As a result of the studies described herein, highly potent FTIs with improved pharmacokinetic profiles have been identified.
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Affiliation(s)
- D C Beshore
- Department of Medicinal Chemistry, Merck Research Laboratories, PA 19486, West Point, USA.
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Beshore DC, Dinsmore CJ. Efficient synthesis of unsymmetrical 1,4-disubstituted-2,3-diketopiperazines via tandem reductive amination–cyclization. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01565-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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