1
|
Taylor AM, Bailey C, Belmont LD, Campbell R, Cantone N, Côté A, Crawford TD, Cummings R, DeMent K, Duplessis M, Flynn M, Good AC, Huang HR, Joshi S, Leblanc Y, Murray J, Nasveschuk CG, Neiss A, Poy F, Romero FA, Sandy P, Tang Y, Tsui V, Zawadzke L, Sims RJ, Audia JE, Bellon SF, Magnuson SR, Albrecht BK, Cochran AG. GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1. J Med Chem 2022; 65:11177-11186. [PMID: 35930799 DOI: 10.1021/acs.jmedchem.2c00662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bromodomains are acetyllysine recognition domains present in a variety of human proteins. Bromodomains also bind small molecules that compete with acetyllysine, and therefore bromodomains have been targets for drug discovery efforts. Highly potent and selective ligands with good cellular permeability have been proposed as chemical probes for use in exploring the functions of many of the bromodomain proteins. We report here the discovery of a class of such inhibitors targeting the family VIII bromodomains of SMARCA2 (BRM) and SMARCA4 (BRG1), and PBRM1 (polybromo-1) bromodomain 5. We propose one example from this series, GNE-064, as a chemical probe for the bromodomains SMARCA2, SMARCA4, and PBRM1(5) with the potential for in vivo use.
Collapse
Affiliation(s)
- Alexander M Taylor
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Chris Bailey
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Lisa D Belmont
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Campbell
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Nico Cantone
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Terry D Crawford
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Cummings
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Kevin DeMent
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Martin Duplessis
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Megan Flynn
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Andrew C Good
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Shivangi Joshi
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yves Leblanc
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy Murray
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G Nasveschuk
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Adrianne Neiss
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F Anthony Romero
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Sandy
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yong Tang
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Vickie Tsui
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laura Zawadzke
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Robert J Sims
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven F Bellon
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R Magnuson
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Brian K Albrecht
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G Cochran
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
2
|
Gehling VS, McGrath JP, Duplessis M, Khanna A, Brucelle F, Vaswani RG, Côté A, Stuckey J, Watson V, Cummings RT, Balasubramanian S, Iyer P, Sawant P, Good AC, Albrecht BK, Harmange JC, Audia JE, Bellon SF, Trojer P, Levell JR. Design and Synthesis of Styrenylcyclopropylamine LSD1 Inhibitors. ACS Med Chem Lett 2020; 11:1213-1220. [PMID: 32551003 PMCID: PMC7294731 DOI: 10.1021/acsmedchemlett.0c00060] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/03/2020] [Accepted: 05/06/2020] [Indexed: 02/03/2023] Open
Abstract
Leveraging the catalytic machinery of LSD1 (KDM1A), a series of covalent styrenylcyclopropane LSD1 inhibitors were identified. These inhibitors represent a new class of mechanism-based inhibitors that target and covalently label the FAD cofactor of LSD1. The series was rapidly progressed to potent biochemical and cellular LSD1 inhibitors with good physical properties. This effort resulted in the identification of 34, a highly potent (<4 nM biochemical, 2 nM cell, and 1 nM GI50), and selective LSD1 inhibitor. In-depth kinetic profiling of 34 confirmed its covalent mechanism of action, validated the styrenylcyclopropane as an FAD-directed warhead, and demonstrated that the potency of this inhibitor is driven by improved non-covalent binding (K I). 34 demonstrated robust cell-killing activity in a panel of AML cell lines and robust antitumor activity in a Kasumi-1 xenograft model of AML when dosed orally at 1.5 mg/kg once daily.
Collapse
Affiliation(s)
- Victor S. Gehling
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - John P. McGrath
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | | | - Avinash Khanna
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | | | - Rishi G. Vaswani
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | | | - Jacob Stuckey
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | | | - Richard T. Cummings
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | | | | | | | | | | | | | | | | | - Patrick Trojer
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Julian R. Levell
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
3
|
Venables BL, Sin N, Wang AX, Sun LQ, Tu Y, Hernandez D, Sheaffer A, Lee M, Dunaj C, Zhai G, Barry D, Friborg J, Yu F, Knipe J, Sandquist J, Falk P, Parker D, Good AC, Rajamani R, McPhee F, Meanwell NA, Scola PM. P3-P4 ureas and reverse carbamates as potent HCV NS3 protease inhibitors: Effective transposition of the P4 hydrogen bond donor. Bioorg Med Chem Lett 2018; 28:1853-1859. [PMID: 29650290 DOI: 10.1016/j.bmcl.2018.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022]
Abstract
A series of tripeptidic acylsulfonamide inhibitors of HCV NS3 protease were prepared that explored structure-activity relationships (SARs) at the P4 position, and their in vitro and in vivo properties were evaluated. Enhanced potency was observed in a series of P4 ureas; however, the PK profiles of these analogues were less than optimal. In an effort to overcome the PK shortcomings, modifications to the P3-P4 junction were made. This included a strategy in which one of the two urea N-H groups was either N-methylated or replaced with an oxygen atom. The former approach provided a series of regioisomeric N-methylated ureas while the latter gave rise to P4 reverse carbamates, both of which retained potent NS3 inhibitory properties while relying upon an alternative H-bond donor topology. Details of the SARs and PK profiles of these analogues are provided.
Collapse
Affiliation(s)
- Brian L Venables
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States.
| | - Ny Sin
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Alan Xiangdong Wang
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Li-Qiang Sun
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Yong Tu
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Dennis Hernandez
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Amy Sheaffer
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Min Lee
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Cindy Dunaj
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Guangzhi Zhai
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Diana Barry
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Jacques Friborg
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Fei Yu
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Jay Knipe
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Jason Sandquist
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Paul Falk
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Dawn Parker
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Andrew C Good
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Ramkumar Rajamani
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Fiona McPhee
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Nicholas A Meanwell
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| | - Paul M Scola
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, United States
| |
Collapse
|
4
|
D de Araujo A, Lim J, Wu KC, Xiang Y, Good AC, Skerlj R, Fairlie DP. Bicyclic Helical Peptides as Dual Inhibitors Selective for Bcl2A1 and Mcl-1 Proteins. J Med Chem 2018; 61:2962-2972. [PMID: 29584430 DOI: 10.1021/acs.jmedchem.8b00010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A 26-residue peptide BimBH3 binds indiscriminately to multiple oncogenic Bcl2 proteins that regulate apoptosis of cancer cells. Specific inhibition of the BimBH3-Bcl2A1 protein-protein interaction was obtained in vitro and in cancer cells by shortening the peptide to 14 residues, inserting two cyclization constraints to stabilize a water-stable α-helix, and incorporating an N-terminal acrylamide electrophile for selective covalent bonding to Bcl2A1. Mass spectrometry of trypsin-digested bands on electrophoresis gels established covalent bonding of an electrophilic helix to just one of the three cysteines in Bcl2A1, the one (Cys55) at the BimBH3-Bcl2A1 protein-protein interaction interface. Optimizing the helix-inducing constraints and the sequence subsequently enabled electrophile removal without loss of inhibitor potency. The bicyclic helical peptides were potent, cell permeable, plasma-stable, dual inhibitors of Bcl2A1 and Mcl-1 with high selectivity over other Bcl2 proteins. One bicyclic peptide was shown to inhibit the interaction between a pro-apoptotic protein (Bim) and either endogenous Bcl2A1 or Mcl-1, to induce apoptosis of SKMel28 human melanoma cells, and to sensitize them for enhanced cell death by the anticancer drug etoposide. These approaches look promising for chemically silencing intracellular proteins.
Collapse
Affiliation(s)
- Aline D de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yibin Xiang
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - Andrew C Good
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - Renato Skerlj
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - David P Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| |
Collapse
|
5
|
Zheng B, D’Andrea SV, Sun LQ, Wang AX, Chen Y, Hrnciar P, Friborg J, Falk P, Hernandez D, Yu F, Sheaffer AK, Knipe JO, Mosure K, Rajamani R, Good AC, Kish K, Tredup J, Klei HE, Paruchuri M, Ng A, Gao Q, Rampulla RA, Mathur A, Meanwell NA, McPhee F, Scola PM. Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor. ACS Med Chem Lett 2018; 9:143-148. [PMID: 29456803 DOI: 10.1021/acsmedchemlett.7b00503] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/19/2018] [Indexed: 01/07/2023] Open
Abstract
The design and synthesis of potent, tripeptidic acylsulfonamide inhibitors of HCV NS3 protease that contain a difluoromethyl cyclopropyl amino acid at P1 are described. A cocrystal structure of 18 with a NS3/4A protease complex suggests the presence of a H-bond between the polarized C-H of the CHF2 moiety and the backbone carbonyl of Leu135 of the enzyme. Structure-activity relationship studies indicate that this H-bond enhances enzyme inhibitory potency by 13- and 17-fold compared to the CH3 and CF3 analogues, respectively, providing insight into the deployment of this unique amino acid.
Collapse
Affiliation(s)
- Barbara Zheng
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Stanley V. D’Andrea
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Li-Qiang Sun
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Alan Xiangdong Wang
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yan Chen
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Peter Hrnciar
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jacques Friborg
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul Falk
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Dennis Hernandez
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Fei Yu
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Amy K. Sheaffer
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jay O. Knipe
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kathy Mosure
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ramkumar Rajamani
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew C. Good
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kevin Kish
- Research
and Development, Bristol-Myers Squibb, PO Box 5400, Princeton, New Jersey 08543, United States
| | - Jeffrey Tredup
- Research
and Development, Bristol-Myers Squibb, PO Box 5400, Princeton, New Jersey 08543, United States
| | - Herbert E. Klei
- Research
and Development, Bristol-Myers Squibb, PO Box 5400, Princeton, New Jersey 08543, United States
| | - Manjula Paruchuri
- Biologics
Process Development, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, New Jersey 08534, United States
| | - Alicia Ng
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Qi Gao
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Richard A. Rampulla
- Discovery
Synthesis, Research and Development, Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Arvind Mathur
- Discovery
Synthesis, Research and Development, Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Nicholas A. Meanwell
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Fiona McPhee
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul M. Scola
- Research
and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| |
Collapse
|
6
|
de Araujo AD, Lim J, Good AC, Skerlj RT, Fairlie DP. Electrophilic Helical Peptides That Bond Covalently, Irreversibly, and Selectively in a Protein-Protein Interaction Site. ACS Med Chem Lett 2017; 8:22-26. [PMID: 28105269 DOI: 10.1021/acsmedchemlett.6b00395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 10/07/2016] [Accepted: 11/15/2016] [Indexed: 12/28/2022] Open
Abstract
Protein-protein interactions mediate most physiological and disease processes. Helix-constrained peptides potently mimic or inhibit these interactions by making multiple contacts over large surface areas. However, despite high affinities, they typically have short lifetimes bound to the protein. Here we insert both a helix-inducing constraint and an adjacent electrophile into the native peptide ligand BIM to target the oncogenic protein Bcl2A1. The modified BIM peptide bonds covalently and irreversibly to one cysteine within the helix-binding groove of Bcl2A1, but not to two other exposed cysteines on its surface, and shows no covalent bonding to other Bcl2 proteins. It also penetrates cell membranes and bonds covalently to Bcl2A1 inside cells. This innovative approach to increasing receptor residence time of helical peptides demonstrates the potential to selectively silence a PPI inside cells, with selectivity over other nucleophilic sites on proteins.
Collapse
Affiliation(s)
- Aline Dantas de Araujo
- Division of Chemistry
and Structural Biology, Centre for Inflammation and Disease Research
and ARC Centre of Excellence in Advanced Molecular Imaging, Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junxian Lim
- Division of Chemistry
and Structural Biology, Centre for Inflammation and Disease Research
and ARC Centre of Excellence in Advanced Molecular Imaging, Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew C. Good
- Noliva Therapeutics, Newton, Massachusetts 02465, United States
| | | | - David P. Fairlie
- Division of Chemistry
and Structural Biology, Centre for Inflammation and Disease Research
and ARC Centre of Excellence in Advanced Molecular Imaging, Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
7
|
Vaswani RG, Gehling VS, Dakin LA, Cook AS, Nasveschuk CG, Duplessis M, Iyer P, Balasubramanian S, Zhao F, Good AC, Campbell R, Lee C, Cantone N, Cummings RT, Normant E, Bellon SF, Albrecht BK, Harmange JC, Trojer P, Audia JE, Zhang Y, Justin N, Chen S, Wilson JR, Gamblin SJ. Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas. J Med Chem 2016; 59:9928-9941. [PMID: 27739677 PMCID: PMC5451150 DOI: 10.1021/acs.jmedchem.6b01315] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [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] [Indexed: 12/16/2022]
Abstract
![]()
Polycomb
repressive complex 2 (PRC2) has been shown to play a major
role in transcriptional silencing in part by installing methylation
marks on lysine 27 of histone 3. Dysregulation of PRC2 function correlates
with certain malignancies and poor prognosis. EZH2 is the catalytic
engine of the PRC2 complex and thus represents a key candidate oncology
target for pharmacological intervention. Here we report the optimization
of our indole-based EZH2 inhibitor series that led to the identification
of CPI-1205, a highly potent (biochemical IC50 = 0.002
μM, cellular EC50 = 0.032 μM) and selective
inhibitor of EZH2. This compound demonstrates robust antitumor effects
in a Karpas-422 xenograft model when dosed at 160 mg/kg BID and is
currently in Phase I clinical trials. Additionally, we disclose the
co-crystal structure of our inhibitor series bound to the human PRC2
complex.
Collapse
Affiliation(s)
- Rishi G Vaswani
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Victor S Gehling
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Les A Dakin
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrew S Cook
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Christopher G Nasveschuk
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Priyadarshini Iyer
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Srividya Balasubramanian
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Feng Zhao
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrew C Good
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Robert Campbell
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Christina Lee
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Nico Cantone
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Richard T Cummings
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Emmanuel Normant
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven F Bellon
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Brian K Albrecht
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jean-Christophe Harmange
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Patrick Trojer
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Neil Justin
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Shuyang Chen
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jon R Wilson
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven J Gamblin
- Constellation Pharmaceuticals, Inc., 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
8
|
Affiliation(s)
- Andrew C. Good
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California
| | | |
Collapse
|
9
|
Crawford TD, Tsui V, Flynn EM, Wang S, Taylor AM, Côté A, Audia JE, Beresini MH, Burdick DJ, Cummings R, Dakin LA, Duplessis M, Good AC, Hewitt MC, Huang HR, Jayaram H, Kiefer JR, Jiang Y, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG. Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. J Med Chem 2016; 59:5391-402. [PMID: 27219867 DOI: 10.1021/acs.jmedchem.6b00264] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.
Collapse
Affiliation(s)
- Terry D Crawford
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - E Megan Flynn
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Shumei Wang
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Maureen H Beresini
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Cummings
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Les A Dakin
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrew C Good
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Michael C Hewitt
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Ying Jiang
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jeremy Murray
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G Nasveschuk
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F Anthony Romero
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Yong Tang
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jian Wang
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Zhaowu Xu
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Laura E Zawadzke
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoyu Zhu
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Brian K Albrecht
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R Magnuson
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G Cochran
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
10
|
Boy KM, Guernon JM, Wu YJ, Zhang Y, Shi J, Zhai W, Zhu S, Gerritz SW, Toyn JH, Meredith JE, Barten DM, Burton CR, Albright CF, Good AC, Grace JE, Lentz KA, Olson RE, Macor JE, Thompson LA. Macrocyclic prolinyl acyl guanidines as inhibitors of β-secretase (BACE). Bioorg Med Chem Lett 2015; 25:5040-7. [DOI: 10.1016/j.bmcl.2015.10.031] [Citation(s) in RCA: 7] [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: 06/30/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 02/02/2023]
|
11
|
Gehling VS, Vaswani RG, Nasveschuk CG, Duplessis M, Iyer P, Balasubramanian S, Zhao F, Good AC, Campbell R, Lee C, Dakin LA, Cook AS, Gagnon A, Harmange JC, Audia JE, Cummings RT, Normant E, Trojer P, Albrecht BK. Discovery, design, and synthesis of indole-based EZH2 inhibitors. Bioorg Med Chem Lett 2015; 25:3644-9. [PMID: 26189078 DOI: 10.1016/j.bmcl.2015.06.056] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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: 05/04/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022]
Abstract
The discovery and optimization of a series of small molecule EZH2 inhibitors is described. Starting from dimethylpyridone HTS hit (2), a series of indole-based EZH2 inhibitors were identified. Biochemical potency and microsomal stability were optimized during these studies and afforded compound 22. This compound demonstrates nanomolar levels of biochemical potency (IC50=0.002 μM), cellular potency (EC50=0.080 μM), and afforded tumor regression when dosed (200 mpk SC BID) in an EZH2 dependent tumor xenograft model.
Collapse
Affiliation(s)
- Victor S Gehling
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA.
| | - Rishi G Vaswani
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | | | - Martin Duplessis
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Priyadarshini Iyer
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | | | - Feng Zhao
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Andrew C Good
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Robert Campbell
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Christina Lee
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Les A Dakin
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Andrew S Cook
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Alexandre Gagnon
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | | | - James E Audia
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Richard T Cummings
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Emmanuel Normant
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| | - Brian K Albrecht
- Constellation Pharmaceuticals, Inc., 215 First Street, Cambridge, MA 02142, USA
| |
Collapse
|
12
|
Scola PM, Sun LQ, Wang AX, Chen J, Sin N, Venables BL, Sit SY, Chen Y, Cocuzza A, Bilder DM, D'Andrea SV, Zheng B, Hewawasam P, Tu Y, Friborg J, Falk P, Hernandez D, Levine S, Chen C, Yu F, Sheaffer AK, Zhai G, Barry D, Knipe JO, Han YH, Schartman R, Donoso M, Mosure K, Sinz MW, Zvyaga T, Good AC, Rajamani R, Kish K, Tredup J, Klei HE, Gao Q, Mueller L, Colonno RJ, Grasela DM, Adams SP, Loy J, Levesque PC, Sun H, Shi H, Sun L, Warner W, Li D, Zhu J, Meanwell NA, McPhee F. The discovery of asunaprevir (BMS-650032), an orally efficacious NS3 protease inhibitor for the treatment of hepatitis C virus infection. J Med Chem 2014; 57:1730-52. [PMID: 24564672 DOI: 10.1021/jm500297k] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of asunaprevir (BMS-650032, 24) is described. This tripeptidic acylsulfonamide inhibitor of the NS3/4A enzyme is currently in phase III clinical trials for the treatment of hepatitis C virus infection. The discovery of 24 was enabled by employing an isolated rabbit heart model to screen for the cardiovascular (CV) liabilities (changes to HR and SNRT) that were responsible for the discontinuation of an earlier lead from this chemical series, BMS-605339 (1), from clinical trials. The structure-activity relationships (SARs) developed with respect to CV effects established that small structural changes to the P2* subsite of the molecule had a significant impact on the CV profile of a given compound. The antiviral activity, preclincial PK profile, and toxicology studies in rat and dog supported clinical development of BMS-650032 (24).
Collapse
Affiliation(s)
- Paul M Scola
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut, 06492, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Scola PM, Wang AX, Good AC, Sun LQ, Combrink KD, Campbell JA, Chen J, Tu Y, Sin N, Venables BL, Sit SY, Chen Y, Cocuzza A, Bilder DM, D’Andrea S, Zheng B, Hewawasam P, Ding M, Thuring J, Li J, Hernandez D, Yu F, Falk P, Zhai G, Sheaffer AK, Chen C, Lee MS, Barry D, Knipe JO, Li W, Han YH, Jenkins S, Gesenberg C, Gao Q, Sinz MW, Santone KS, Zvyaga T, Rajamani R, Klei HE, Colonno RJ, Grasela DM, Hughes E, Chien C, Adams S, Levesque PC, Li D, Zhu J, Meanwell NA, McPhee F. Discovery and Early Clinical Evaluation of BMS-605339, a Potent and Orally Efficacious Tripeptidic Acylsulfonamide NS3 Protease Inhibitor for the Treatment of Hepatitis C Virus Infection. J Med Chem 2014; 57:1708-29. [DOI: 10.1021/jm401840s] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paul M. Scola
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Alan Xiangdong Wang
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew C. Good
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Li-Qiang Sun
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Keith D. Combrink
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jeffrey A. Campbell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jie Chen
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yong Tu
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ny Sin
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Brian L. Venables
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Sing-Yuen Sit
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yan Chen
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Anthony Cocuzza
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Donna M. Bilder
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Stanley D’Andrea
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Barbara Zheng
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Piyasena Hewawasam
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Min Ding
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jan Thuring
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jianqing Li
- Department
of Discovery Chemical Synthesis, Bristol-Myers Squibb Research and Development, P.O.
Box 4000, Princeton, New Jersey 08543, United States
| | - Dennis Hernandez
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Fei Yu
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul Falk
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Guangzhi Zhai
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Amy K. Sheaffer
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Chaoqun Chen
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Min S. Lee
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Diana Barry
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jay O. Knipe
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Wenying Li
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yong-Hae Han
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Susan Jenkins
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Christoph Gesenberg
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Qi Gao
- Department of Pharmaceutical Development, Bristol-Myers Squibb Research and Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael W. Sinz
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kenneth S. Santone
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Tatyana Zvyaga
- Department of
Lead Discovery and Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ramkumar Rajamani
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Herbert E. Klei
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Richard J. Colonno
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Dennis M. Grasela
- Department of Early Clinical and Translational
Research, Discovery Medicine—Virology, Bristol-Myers Squibb Research and Development, Hopewell, New Jersey 08543, United States
| | - Eric Hughes
- Department of Early Clinical and Translational
Research, Discovery Medicine—Virology, Bristol-Myers Squibb Research and Development, Hopewell, New Jersey 08543, United States
| | - Caly Chien
- Department of Early Clinical and Translational
Research, Discovery Medicine—Virology, Bristol-Myers Squibb Research and Development, Hopewell, New Jersey 08543, United States
| | - Stephen Adams
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul C. Levesque
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Danshi Li
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jialong Zhu
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Fiona McPhee
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| |
Collapse
|
14
|
Belema M, Nguyen VN, Romine JL, St. Laurent DR, Lopez OD, Goodrich JT, Nower PT, O’Boyle DR, Lemm JA, Fridell RA, Gao M, Fang H, Krause RG, Wang YK, Oliver AJ, Good AC, Knipe JO, Meanwell NA, Snyder LB. Hepatitis C Virus NS5A Replication Complex Inhibitors. Part 6: Discovery of a Novel and Highly Potent Biarylimidazole Chemotype with Inhibitory Activity Toward Genotypes 1a and 1b Replicons. J Med Chem 2014; 57:1995-2012. [DOI: 10.1021/jm4016203] [Citation(s) in RCA: 21] [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: 12/14/2022]
Affiliation(s)
- Makonen Belema
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Van N. Nguyen
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jeffrey L. Romine
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Denis R. St. Laurent
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Omar D. Lopez
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jason T. Goodrich
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Peter T. Nower
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Donald R. O’Boyle
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Julie A. Lemm
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Robert A. Fridell
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Min Gao
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Hua Fang
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Rudolph G. Krause
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ying-Kai Wang
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - A. Jayne Oliver
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew C. Good
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jay O. Knipe
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A. Meanwell
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Lawrence B. Snyder
- Departments of Discovery Chemistry, ‡Virology, §Lead Discovery and Optimization, ∥Computer-Assisted
Drug Design, and ⊥Metabolism and Pharmacokinetics, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| |
Collapse
|
15
|
Lopez OD, Nguyen VN, St. Laurent DR, Belema M, Serrano-Wu MH, Goodrich JT, Yang F, Qiu Y, Ripka AS, Nower PT, Valera L, Liu M, O’Boyle DR, Sun JH, Fridell RA, Lemm JA, Gao M, Good AC, Meanwell NA, Snyder LB. HCV NS5A replication complex inhibitors. Part 3: discovery of potent analogs with distinct core topologies. Bioorg Med Chem Lett 2013; 23:779-84. [DOI: 10.1016/j.bmcl.2012.11.086] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/14/2012] [Accepted: 11/20/2012] [Indexed: 12/23/2022]
|
16
|
Gerritz SW, Zhai W, Shi S, Zhu S, Toyn JH, Meredith JE, Iben LG, Burton CR, Albright CF, Good AC, Tebben AJ, Muckelbauer JK, Camac DM, Metzler W, Cook LS, Padmanabha R, Lentz KA, Sofia MJ, Poss MA, Macor JE, Thompson LA. Acyl Guanidine Inhibitors of β-Secretase (BACE-1): Optimization of a Micromolar Hit to a Nanomolar Lead via Iterative Solid- and Solution-Phase Library Synthesis. J Med Chem 2012; 55:9208-23. [DOI: 10.1021/jm300931y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samuel W. Gerritz
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Weixu Zhai
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shuhao Shi
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shirong Zhu
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jeremy H. Toyn
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jere E. Meredith
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Lawrence G. Iben
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Catherine R. Burton
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Charles F. Albright
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew C. Good
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew J. Tebben
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Jodi K. Muckelbauer
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Daniel M. Camac
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - William Metzler
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Lynda S. Cook
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ramesh Padmanabha
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kimberley A. Lentz
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Michael J. Sofia
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Michael A. Poss
- Bristol-Myers Squibb Research,
P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - John E. Macor
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Lorin A. Thompson
- Bristol-Myers Squibb Research,
5 Research Parkway, Wallingford, Connecticut 06492, United States
| |
Collapse
|
17
|
Good AC, Liu J, Hirth B, Asmussen G, Xiang Y, Biemann HP, Bishop KA, Fremgen T, Fitzgerald M, Gladysheva T, Jain A, Jancsics K, Metz M, Papoulis A, Skerlj R, Stepp JD, Wei RR. Implications of Promiscuous Pim-1 Kinase Fragment Inhibitor Hydrophobic Interactions for Fragment-Based Drug Design. J Med Chem 2012; 55:2641-8. [DOI: 10.1021/jm2014698] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Kimberly A. Bishop
- Department of Therapeutic Protein Discovery, Genzyme Corp., 49 New York Ave., Framingham, Massachusetts
01701, United States
| | | | | | | | - Annuradha Jain
- Department of Therapeutic Protein Discovery, Genzyme Corp., 49 New York Ave., Framingham, Massachusetts
01701, United States
| | | | | | | | | | | | - Ronnie R. Wei
- Department of Therapeutic Protein
Research, Genzyme Corp., 1 Mountain Road,
Framingham, Massachusetts 01701, United States
| |
Collapse
|
18
|
Thompson LA, Shi J, Decicco CP, Tebben AJ, Olson RE, Boy KM, Guernon JM, Good AC, Liauw A, Zheng C, Copeland RA, Combs AP, Trainor GL, Camac DM, Muckelbauer JK, Lentz KA, Grace JE, Burton CR, Toyn JH, Barten DM, Marcinkeviciene J, Meredith JE, Albright CF, Macor JE. Synthesis and in vivo evaluation of cyclic diaminopropane BACE-1 inhibitors. Bioorg Med Chem Lett 2011; 21:6909-15. [DOI: 10.1016/j.bmcl.2011.06.116] [Citation(s) in RCA: 10] [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: 03/31/2011] [Revised: 06/24/2011] [Accepted: 06/27/2011] [Indexed: 11/26/2022]
|
19
|
Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. J Med Chem 2010; 53:3862-86. [PMID: 20158188 PMCID: PMC2874267 DOI: 10.1021/jm900818s] [Citation(s) in RCA: 235] [Impact Index Per Article: 16.8] [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] [Indexed: 11/30/2022]
Abstract
The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for "decoration" with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, ligand fitting, pose prediction, or active site description. Computing power has facilitated this evolution by allowing shape to be handled precisely without the need to reduce down to point descriptors or approximate metrics, and the diversity of resultant applications argues for this being an important step forward. Certainly, it is encouraging that as computation has enabled our intuition, molecular shape has consistently surprised us in its usefulness and adaptability. The first Aurelius question, "What is the essence of a thing?", seems well answered, however, the third, "What do molecules do?", only partly so. Are the topics covered here exhaustive, or is there more to come? To date, there has been little published on the use of the volumetric definition of shape described here as a QSAR variable, for instance, in the prediction or classification of activity, although other shape definitions have been successful applied, for instance, as embodied in the Compass program described above in "Shape from Surfaces". Crystal packing is a phenomenon much desired to be understood. Although powerful models have been applied to the problem, to what degree is this dominated purely by the shape of a molecule? The shape comparison described here is typically of a global nature, and yet some importance must surely be placed on partial shape matching, just as the substructure matching of chemical graphs has proved useful. The approach of using surfaces, as described here, offers some flavor of this, as does the use of metrics that penalize volume mismatch less than the Tanimoto, e.g., Tversky measures. As yet, there is little to go on as to how useful a paradigm this will be because there is less software and fewer concrete results.Finally, the distance between molecular shapes, or between any shapes defined as volumes or surfaces, is a metric property in the mathematical sense of the word. As yet, there has been little, if any, application of this observation. We cannot know what new application to the design and discovery of pharmaceuticals may yet arise from the simple concept of molecular shape, but it is fair to say that the progress so far is impressive.
Collapse
Affiliation(s)
- Anthony Nicholls
- OpenEye Scientific Software, Inc., Santa Fe, New Mexico 87508, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Yeung KS, Qiu Z, Farkas ME, Xue Q, Regueiro-Ren A, Yang Z, Bender JA, Good AC, Kadow JF. An efficient one-pot synthesis of 3-glyoxylic acids of electron-deficient substituted azaindoles by ionic liquid imidazolium chloroaluminate-promoted Friedel–Crafts acylation. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.08.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
|
22
|
Good AC, Oprea TI. Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J Comput Aided Mol Des 2008; 22:169-78. [DOI: 10.1007/s10822-007-9167-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 12/19/2007] [Indexed: 11/28/2022]
|
23
|
Good AC. Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: Adding flexibility to the search for ligand kin. J Mol Graph Model 2007; 26:656-66. [PMID: 17482856 DOI: 10.1016/j.jmgm.2007.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 03/28/2007] [Indexed: 10/23/2022]
Abstract
With readily available CPU power and copious disk storage, it is now possible to undertake rapid comparison of 3D properties derived from explicit ligand overlay experiments. With this in mind, shape software tools originally devised in the 1990s are revisited, modified and applied to the problem of ligand database shape comparison. The utility of Connolly surface data is highlighted using the program MAKESITE, which leverages surface normal data to a create ligand shape cast. This cast is applied directly within DOCK, allowing the program to be used unmodified as a shape searching tool. In addition, DOCK has undergone multiple modifications to create a dedicated ligand shape comparison tool KIN. Scoring has been altered to incorporate the original incarnation of Gaussian function derived shape description based on STO-3G atomic electron density. In addition, a tabu-like search refinement has been added to increase search speed by removing redundant starting orientations produced during clique matching. The ability to use exclusion regions, again based on Gaussian shape overlap, has also been integrated into the scoring function. The use of both DOCK with MAKESITE and KIN in database screening mode is illustrated using a published ligand shape virtual screening template. The advantages of using a clique-driven search paradigm are highlighted, including shape optimization within a pharmacophore constrained framework, and easy incorporation of additional scoring function modifications. The potential for further development of such methods is also discussed.
Collapse
Affiliation(s)
- Andrew C Good
- Bristol-Myers Squibb, PO Box 5100, Wallingford, CT 06492, USA.
| |
Collapse
|
24
|
Rajamani R, Good AC. Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development. Curr Opin Drug Discov Devel 2007; 10:308-15. [PMID: 17554857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The ability to accurately predict the potency of ligand binding to its intended target prior to synthesis is of significant value in the drug-discovery paradigm. The protocols designed to this end follow a two-step process. First, ligands are docked into the active site of interest, and then the resulting interactions at the target are scored. Scoring functions form the key component in this process, providing a quantitative measure of fit quality. There is an abundance of new research in the field of scoring function design, from incorporation of novel descriptors (derived from first principles or empirical analysis) to function redesign based on improved data set handling. This article provides a brief overview on the state-of-the-art developments in the field, with particular reference to their performance in relation to expected outcomes.
Collapse
Affiliation(s)
- Ramkumar Rajamani
- Computer-Assisted Drug Design, Bristol-Myers Squibb Co, 5 Research Parkway, Wallingford, CT 06492, USA
| | | |
Collapse
|
25
|
Good AC, Hermsmeier MA. Measuring CAMD Technique Performance. 2. How “Druglike” Are Drugs? Implications of Random Test Set Selection Exemplified Using Druglikeness Classification Models. J Chem Inf Model 2006; 47:110-4. [PMID: 17238255 DOI: 10.1021/ci6003493] [Citation(s) in RCA: 23] [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: 11/28/2022]
Abstract
Research into the advancement of computer-aided molecular design (CAMD) has a tendency to focus on the discipline of algorithm development. Such efforts are often wrought to the detriment of the data set selection and analysis used in said algorithm validation. Here we highlight the potential problems this can cause in the context of druglikeness classification. More rigorous efforts are applied to the selection of decoy (nondruglike) molecules from the ACD. Comparisons are made between model performance using the standard technique of random test set creation with test sets derived from explicit ontological separation by drug class. The dangers of viewing druglike space as sufficiently coherent to permit simple classification are highlighted. In addition the issues inherent in applying unfiltered data and random test set selection to (Q)SAR models utilizing large and supposedly heterogeneous databases are discussed.
Collapse
Affiliation(s)
- Andrew C Good
- Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, USA.
| | | |
Collapse
|
26
|
Abstract
A process for objective identification and filtering of undesirable compounds that contribute to high-throughput screening (HTS) deck promiscuity is described. Two methods of mapping hit promiscuity have been developed linking SMARTS-based structural queries with historical primary HTS data. The first compares an expected assay hit rate to actual hit rates. The second examines the propensity of an individual compound to hit multiple assays. Statistical evaluation of the data indicates a correlation between the resultant functional group filters and compound promiscuity. These data corroborate a number of commonly applied filters as well as producing some unexpected results. Application of these models to HTS collection triage reduced the number of in-house compounds considered for screening by 12%. The implications of these findings are further discussed in the context of the HTS screening set and combinatorial library design as well as compound acquisition.
Collapse
Affiliation(s)
- Bradley C Pearce
- Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, Connecticut 06492, USA.
| | | | | | | | | |
Collapse
|
27
|
Good AC, Hermsmeier MA, Hindle SA. Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments. J Comput Aided Mol Des 2005; 18:529-36. [PMID: 15729852 DOI: 10.1007/s10822-004-4067-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [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: 10/25/2022]
Abstract
The dynamic nature and comparatively young age of computational chemistry is such that novel algorithms continue to be developed at a rapid pace. Such efforts are often wrought at the expense of extensive experimental validations of said techniques, preventing a deeper understanding of their potential utility and limitations. Here we address this issue for ligand-based virtual screening descriptors through design of validation experiments that better reflect the aims of real world application. Applying the newly defined chemotype enrichment approach, a variety of two- and three-dimensional (2D/3D) similarity descriptors have been compared extensively across data sets from four diverse target types. The inhibitors within said data sets contain molecules exhibiting a wide array of substructure functionality, size and flexibility, permitting descriptor comparison in myriad settings. Relative descriptor performance under these conditions is examined, including results obtained using more typical virtual screening validation experiments. Guidelines for optimal application of said descriptors are also discussed in the context of the results obtained, as is the potential utility of fingerprint filtering.
Collapse
Affiliation(s)
- Andrew C Good
- Bristol-Myers Squibb, 5 Research Parkway, Wallingford, CT 06492, USA.
| | | | | |
Collapse
|
28
|
Abstract
The three-dimensional (3D) binary pharmacophore fingerprints find wide application as descriptors in applications ranging from virtual screening through library design. While the 3D content they capture is an intuitively attractive feature of such measures, maximizing their signal to noise ratio has proven to be a tricky balancing act. This issue surfaces primarily due to the potential of such fingerprints to create an explosion of pharmacophores as molecular complexity and flexibility increases. In this article, we describe a modification to the fingerprint generation process that normalizes pharmacophore occurrence frequency by the conformational ensemble size used to derive the descriptor. By including pharmacophore frequency and conformational count, the importance of a given pharmacophore is weighted by the probability of its existence within a given conformational ensemble, rather than treating each pharmacophore equally. In addition, a number of filters have been added to permit the removal of unwanted pharmacophores from the descriptor set. These filters are based on pharmacophore composition (e.g. permutations made up primarily of lipophilic and/or aromatic centers), and size (pharmacophore perimeter length relative to the largest perimeter length found in the molecule). The highly uneven nature of pharmacophore distributions across the conformational ensemble used to generate them is highlighted, as are enrichment comparisons with their binary fingerprint peers. In addition, the limitations in descriptor comparison validation are high-lighted as an illustration of the need for more extensive validation experiments.
Collapse
|
29
|
Good AC, Cheney DL, Sitkoff DF, Tokarski JS, Stouch TR, Bassolino DA, Krystek SR, Li Y, Mason JS, Perkins TDJ. Analysis and optimization of structure-based virtual screening protocols. 2. Examination of docked ligand orientation sampling methodology: mapping a pharmacophore for success. J Mol Graph Model 2003; 22:31-40. [PMID: 12798389 DOI: 10.1016/s1093-3263(03)00124-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [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]
Abstract
An important element of any structure-based virtual screening (SVS) technique is the method used to orient the ligands in the target active site. This has been a somewhat overlooked issue in recent SVS validation studies, with the assumption being made that the performance of an algorithm for a given set of orientation sampling settings will be representative for the general behavior of said technique. Here, we analyze five different SVS targets using a variety of sampling paradigms within the DOCK, GOLD and PROMETHEUS programs over a data set of approximately 10,000 noise compounds, combined with data sets containing multiple active compounds. These sets have been broken down by chemotype, with chemotype hit rate used to provide a measure of enrichment with a potentially improved relevance to real world SVS experiments. The variability in enrichment results produced by different sampling paradigms is illustrated, as is the utility of using pharmacophores to constrain sampling to regions that reflect known structural biology. The difference in results when comparing chemotype with compound hit rates is also highlighted.
Collapse
Affiliation(s)
- Andrew C Good
- Bristol-Myers Squibb, P.O. Box 5100, Wallingford, CT 06492, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Good AC, Cheney DL. Analysis and optimization of structure-based virtual screening protocols (1): exploration of ligand conformational sampling techniques. J Mol Graph Model 2003; 22:23-30. [PMID: 12798388 DOI: 10.1016/s1093-3263(03)00123-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [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: 11/25/2022]
Abstract
Ligand conformational flexibility has long been recognized as an important issue in virtual screening (VS). To this end, a number of different methodologies have been adapted to tackle the problem. Many of said techniques were originally designed for ligand derived pharmacophore screens, but have subsequently been fashioned for application within structure-based virtual screening (SVS). A popular adaptation is the pre-calculation of diverse ligand conformations for subsequent docking in target active sites. In this paper, we study a number of the software programs currently being used in conformer generation, analyzing their ability to regenerate known ligand binding conformations. The implications of these studies are discussed, from the perspective of VS in general and SVS in particular.
Collapse
Affiliation(s)
- Andrew C Good
- Structural Biology and Modeling, Bristol-Myers Squibb, P.O. Box 5100, Wallingford, CT 06492, USA.
| | | |
Collapse
|
31
|
Smith R, Hubbard RE, Gschwend DA, Leach AR, Good AC. Analysis and optimization of structure-based virtual screening protocols. (3). New methods and old problems in scoring function design. J Mol Graph Model 2003; 22:41-53. [PMID: 12798390 DOI: 10.1016/s1093-3263(03)00125-6] [Citation(s) in RCA: 27] [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: 11/23/2022]
Abstract
Scoring function research remains a primary focus of current structure-based virtual screening (SVS) technology development. Here, we present an alternative method for scoring function design that attempts to combine crystallographic structural information with data derived from directly within SVS calculations. The technique utilizes a genetic algorithm (GA) to optimize functions based on binding property data derived from multiple virtual screening calculations. These calculations are undertaken on protein data bank (PDB) complex active sites using ligands of known binding mode in conjunction with "noise" compounds. The advantages of such an approach are that the function does not rely on assay data and that it can potentially use the "noise" binding data to recognize the sub-optimal docking interactions inherent in SVS calculations. Initial efforts in technique exploration using DOCK are presented, with comparisons made to existing DOCK scoring functions. An analysis of the problems inherent to scoring function development is also made, including issues in dataset creation and limitations in descriptor utility when viewed from the perspective of docking mode resolution. The future directions such studies might take are also discussed in detail.
Collapse
Affiliation(s)
- Ryan Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 4DD, UK
| | | | | | | | | |
Collapse
|
32
|
Andrews DM, Chaignot H, Coomber BA, Good AC, Hind SL, Johnson MR, Jones PS, Mills G, Robinson JE, Skarzynski T, Slater MJ, Somers DO. Pyrrolidine-5,5-trans-lactams. 2. The use of X-ray crystal structure data in the optimization of P3 and P4 substituents. Org Lett 2002; 4:4479-82. [PMID: 12465917 DOI: 10.1021/ol027014p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [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: 11/29/2022]
Abstract
[reaction: see text] In this, the second of two letters, we describe the elaboration of the pyrrolidine-5,5-trans-lactam template to delineate the requirements for optimal substitution of the pyrrolidine and lactam nitrogen atoms. Central to the strategy is the use of rapid iterative synthesis in conjunction with X-ray crystal structure determination of ligand-protein complexes.
Collapse
Affiliation(s)
- David M Andrews
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Abstract
In this chapter we review the use of 3-D pharmacophores in drug discovery. Recent advances are highlighted, including the application of pharmacophore descriptors generated both from ligands and protein binding sites. The application of 3-D pharmacophore fingerprints as molecular descriptors for similarity and diversity applications such as virtual screening, library design and QSAR is discussed. In addition, we highlight the quantification of structure-based diversity using site-derived fingerprints, and review virtual screening methods using both single refined hypotheses and the fingerprints of multiple potential hypotheses. Further, we discuss methods that take protein flexibility and molecular shape-into account. Each of the above techniques are reviewed with particular reference to the recent advances, advantages and challenges of each methodology.
Collapse
Affiliation(s)
- J S Mason
- Structural Biology and Modeling, Bristol-Myers Squibb, P.O. Box 4000, Princeton, NJ 08543, USA.
| | | | | |
Collapse
|
34
|
Leach AR, Green DV, Hann MM, Judd DB, Good AC. Where are the GaPs? A rational approach to monomer acquisition and selection. J Chem Inf Comput Sci 2000; 40:1262-9. [PMID: 11045822 DOI: 10.1021/ci0003855] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gridding and partitioning (GaP) is a computational method for the classification and selection of monomers for combinatorial libraries. The molecules are described in terms of the pharmacophoric groups they contain and where those pharmacophoric groups can be located in three-dimensional space. The approach involves a detailed conformational analysis of each molecule. This conformational analysis is done within a common coordinate frame, thus enabling the monomers to be compared. The use of a partitioned space is central to this particular application as it facilitates the identification of regions of space which are not well represented by existing compounds. Several ways to extend the use of partitioned pharmacophore spaces are described. Applications of the approach in monomer acquisition and in library design are outlined.
Collapse
Affiliation(s)
- A R Leach
- Medicines Research Centre, Glaxo Wellcome Research & Development, Stevenage, Hertfordshire, UK.
| | | | | | | | | |
Collapse
|
35
|
Abstract
Combinatorial chemistry is a tool of increasing importance in the field of ligand design, as it can yield huge increases in the number of compounds available for screening. Unfortunately, it is often the case that the number of molecules which could theoretically be constructed greatly exceeds potential synthesis and screening capacity. For this new technology to be fully exploited, it will become vital to design libraries with reference to the properties of compounds already in existence, if the added value of each new molecular collection is truly to be maximized. Similarly, if we are to take full advantage of the potential of combinatorial chemistry in lead optimization, it is important that our library design paradigms are flexible, with diversity scoring functions that can be modified to suit particular projects. Here these challenges are addressed through the introduction of a novel computer-aided library design tool known as HARPick (heuristic algorithm for reagent picking). The program is accessible to the bench chemist, and incorporates several significant advances over currently available approaches. These include product-based diversity calculations that can be constrained at the reagent level; diversity measures constructed from multiple descriptors; improved pharmacophore key information and full pharmacophore profiling of entire molecular databases. The potential of these improvements to aid in diversity profiling is illustrated through comparison with established methodology, and possible further enhancements are discussed.
Collapse
Affiliation(s)
- A C Good
- Rhône-Poulenc Rorer, Dagenham, Essex, United Kingdom
| | | |
Collapse
|
36
|
McPhee F, Good AC, Kuntz ID, Craik CS. Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation. Proc Natl Acad Sci U S A 1996; 93:11477-81. [PMID: 8876160 PMCID: PMC56635 DOI: 10.1073/pnas.93.21.11477] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Dimerization of human immunodeficiency virus type 1 protease (HIV-1 PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disruption of the dimer interface inhibits this activity as does formation of heterodimers between wild-type and defective monomers. A structure-based approach was used to identify amino acid substitutions at the dimer interface of HIV-1 PR that facilitate preferential association of heterodimers and inhibit self-association of the defective monomers. Expression of the designed PR monomers inhibits activity of wild-type HIV-1 PR and viral infectivity when assayed in an ex vivo model system. These results show that it is possible to design PR monomers as macromolecular inhibitors that may provide an alternative to small molecule inhibitors for the treatment of HIV infection.
Collapse
Affiliation(s)
- F McPhee
- Department of Pharmaceutical Chemisty, University of California, San Francisco 94143, USA
| | | | | | | |
Collapse
|
37
|
Abstract
Fueled by advances in molecular structure determination, tools for structure-based drug design are proliferating rapidly. Lead discovery through searching of ligand databases with molecular docking techniques represents an attractive alternative to high-throughout random screening. The size of commercial databases imposes severe computational constraints on molecular docking, compromising the level of calculational detail permitted for each putative ligand. We describe alternative philosophies for docking which effectively address this challenge. With respect to the dynamic aspects of molecular recognition, these strategies lie along a spectrum of models bounded by the Lock-and-Key and Induced-Fit theories for ligand binding. We explore the potential of a rigid model in exploiting species specificity and of a tolerant model in predicting absolute ligand binding affinity. Current molecular docking methods are limited primarily by their ability to rank docked complexes; we therefore place particular emphasis on this aspect of the problem throughout our validation of docking strategies.
Collapse
Affiliation(s)
- D A Gschwend
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
| | | | | |
Collapse
|
38
|
|
39
|
Abstract
Distances between key functional groups have been used for some time as molecular descriptors in 3D database screening and clustering calculations. More recently, a number of groups have explored triplets of molecular centers to describe key ligand features in terms of the properties of triangles. Three-body distances are attractive, since they retain more information than pairwise representations. In most applications, the triangular descriptors have been used to detail molecular shape, using all the constituent atoms or molecular surface points as descriptor centers. As a consequence, the database keying times were such that only single conformers could be considered during molecular descriptor calculations. In this paper we reduce the points used in the molecular description down to the key functional centers, as applied in 3D pharmacophore database searches. Molecular triplets can then be calculated which describe the relative dispositions of differing functional groups, made up from multiple molecular conformations of a given molecule. The new triplet descriptors are compared with classical pairwise distance measures using a variety of pharmacophores, and their potential in database screening, clustering and pharmacophore identification is discussed.
Collapse
Affiliation(s)
- A C Good
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California at San Francisco 94143-0446, USA
| | | |
Collapse
|
40
|
Abstract
Geometric descriptors are becoming popular tools for encoding molecular shape, for use in database screening and clustering calculations. They provide condensed representations of complex objects and, as a consequence, can usually be compared quite rapidly. Here we present a number of new descriptors and methods for the quantification of molecular shape similarity. The techniques are tested using two different biological systems, with particular emphasis on their potential utility as methods for prescreening shape-based database searches. Results are compared with data sets produced using the DOCK program. We find that such similarity evaluations are useful for finding molecules with complementary shape, and that they contain an enriched number of potential DOCK hits when compared to the original databases. Significant limitations in the utility of such DOCK prescreens are discussed, and potential solutions are considered.
Collapse
Affiliation(s)
- A C Good
- School of Pharmacy, Department of Pharmaceutical Chemistry, University of California at San Francisco 94143-0446, USA
| | | | | | | |
Collapse
|
41
|
Good AC, Peterson SJ, Richards WG. QSAR's from similarity matrices. Technique validation and application in the comparison of different similarity evaluation methods. J Med Chem 1993; 36:2929-37. [PMID: 8411009 DOI: 10.1021/jm00072a012] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.3] [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: 01/30/2023]
Abstract
It has recently been shown that good quantitative structure-activity relationships can be obtained through statistical analysis of molecular similarity matrices. Here we extend the technique to seven additional molecular series, previously studied using Comparative Molecular Field Analysis (CoMFA) methodology. The results are used to confirm technique applicability across a wider range of QSAR problems and to compare quantitatively the ability of various similarity indices to describe biological systems. The relative merits of this technique in comparison to CoMFA are discussed.
Collapse
Affiliation(s)
- A C Good
- Physical Chemistry Laboratory, Oxford, United Kingdom
| | | | | |
Collapse
|
42
|
Abstract
An alternative method for determining structure-activity correlations is presented. Ligand molecules are described using data matrices derived from the results of N by N (each molecule compared to every other) molecular similarity calculations. The matrices were analyzed using a neural network pattern recognition technique and partial least squares statistics, with the results obtained compared to those achieved using comparative molecular field analysis (CoMFA). The molecular series used in the study comprised 31 steroids. The resultant pattern recognition analysis showed clustering of compounds with high, intermediate, and low affinity into separate regions of the neuron output plots. The cross-validated correlation coefficients obtained from statistical analyses of the matrices against steroid binding data compared well with those achieved using CoMFA. These results show that data matrices derived from molecular similarity calculations can provide the basis for rapid elucidation of both qualitative and quantitative structure-activity relationships.
Collapse
Affiliation(s)
- A C Good
- Physical Chemistry Laboratory, Oxford University, United Kingdom
| | | | | |
Collapse
|
43
|
Abstract
Three-dimensional (3D)-database searches are now being widely applied to determine potential new active molecules. Many structural data sets obtained as a result of these searches are still large in size. In this paper we apply molecular similarity calculations as a rapid method to screen two such data sets. In the first investigation, synthetic candidates, produced as a result of a tendamistat beta-turn mimic search, were tested for their ability to imitate the beta-turn backbone. In the second study, structures extracted through a histamine pharmacophore query search were examined on the basis of their electronic similarity to histamine. Molecular similarity is shown to provide a rapid means of gaining insight into the composition of molecular data sets, with possible implications for future full 3D-database searches.
Collapse
Affiliation(s)
- A C Good
- Physical Chemistry Laboratory, Oxford University, U.K
| | | | | |
Collapse
|
44
|
Abstract
The use of electrostatic potential comparisons between molecules for the elucidation of structure activity relationships is now a well-established modeling technique. The Carbo and Hodgkin similarity indices are used extensively to make quantitative comparisons of this nature; yet their roots are found in the overlap of electron density distribution, with both formulas utilizing a product-based numerator. Two new similarity indices are suggested that calculate the electrostatic potential similarity using a difference-based numerator. The form of the new indices allows the creation of additional software functions that enhance the flexibility of similarity calculations and permit the creation of similarity maps. The general properties of these software functions and all indices are discussed and applied to a series of dopamine D2 receptor agonists.
Collapse
Affiliation(s)
- A C Good
- Physical Chemistry Laboratory, Oxford University, UK
| |
Collapse
|