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Bandyopadhyay D, Kreatsoulas C, Brady PG, Boyer J, He Z, Scavello G, Peryea T, Jadhav A, Nguyen DT, Guha R. Scaffold-Based Analytics: Enabling Hit-to-Lead Decisions by Visualizing Chemical Series Linked across Large Datasets. J Chem Inf Model 2019; 59:4880-4892. [DOI: 10.1021/acs.jcim.9b00243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Deepak Bandyopadhyay
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | | | - Pat G. Brady
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Joseph Boyer
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Zangdong He
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Genaro Scavello
- GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Tyler Peryea
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rajarshi Guha
- National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Torres IO, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2016; 59:1580-98. [PMID: 26699912 PMCID: PMC5080985 DOI: 10.1021/acs.jmedchem.5b01527] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600,000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ∼ 3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.
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Affiliation(s)
- Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Daniel D. Le
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Noah Younger
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Elisabet Gregori-Puigjané
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Oxford OX3 7BN, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Radosław P. Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Eriko Iwasa
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Samuel B. Pollock
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Botnar Research Center, University of Oxford, Oxford OX3 7LD, U.K
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
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Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol 2014; 9:1528-35. [PMID: 24807704 PMCID: PMC4215856 DOI: 10.1021/cb5001636] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.
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Affiliation(s)
- Sarah Barelier
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
| | - Oliv Eidam
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
| | - Inbar Fish
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Department
of Biochemistry and Molecular Biology, George S. Wise Faculty of Life
SciencesTel-Aviv University, Ramat Aviv, Israel
| | | | | | - Ruta Nachane
- ZoBio, Eisteinweg 55, 2300-RA Leiden, The Netherlands
| | - John J. Irwin
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada M5S 3E1
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada M5S 3E1
| | - Gregg Siegal
- ZoBio, Eisteinweg 55, 2300-RA Leiden, The Netherlands
- Leiden University, Eisteinweg 55, 2300-RA Leiden, The Netherlands
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Sheridan RP, Zorn N, Sherer EC, Campeau LC, Chang C(Z, Cumming J, Maddess ML, Nantermet PG, Sinz CJ, O’Shea PD. Modeling a Crowdsourced Definition of Molecular Complexity. J Chem Inf Model 2014; 54:1604-16. [DOI: 10.1021/ci5001778] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Robert P. Sheridan
- Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Nicolas Zorn
- Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Edward C. Sherer
- Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Louis-Charles Campeau
- Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Charlie (Zhenyu) Chang
- Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jared Cumming
- Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Matthew L. Maddess
- Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Philippe G. Nantermet
- Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Christopher J. Sinz
- Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Paul D. O’Shea
- Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
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