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Zhang T, Liu Y, Yang X, Martin GE, Yao H, Shang J, Bugianesi RM, Ellsworth KP, Sonatore LM, Nizner P, Sherer EC, Hill SE, Knemeyer IW, Geissler WM, Dandliker PJ, Helmy R, Wood HB. Definitive Metabolite Identification Coupled with Automated Ligand Identification System (ALIS) Technology: A Novel Approach to Uncover Structure-Activity Relationships and Guide Drug Design in a Factor IXa Inhibitor Program. J Med Chem 2016; 59:1818-29. [PMID: 26871940 DOI: 10.1021/acs.jmedchem.5b01293] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A potent and selective Factor IXa (FIXa) inhibitor was subjected to a series of liver microsomal incubations, which generated a number of metabolites. Using automated ligand identification system-affinity selection (ALIS-AS) methodology, metabolites in the incubation mixture were prioritized by their binding affinities to the FIXa protein. Microgram quantities of the metabolites of interest were then isolated through microisolation analytical capabilities, and structurally characterized using MicroCryoProbe heteronuclear 2D NMR techniques. The isolated metabolites recovered from the NMR experiments were then submitted directly to an in vitro FIXa enzymatic assay. The order of the metabolites' binding affinity to the Factor IXa protein from the ALIS assay was completely consistent with the enzymatic assay results. This work showcases an innovative and efficient approach to uncover structure-activity relationships (SARs) and guide drug design via microisolation-structural characterization and ALIS capabilities.
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Affiliation(s)
- Ting Zhang
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yong Liu
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xianshu Yang
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Gary E Martin
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Huifang Yao
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jackie Shang
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Randal M Bugianesi
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kenneth P Ellsworth
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lisa M Sonatore
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Peter Nizner
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Edward C Sherer
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Susan E Hill
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ian W Knemeyer
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Wayne M Geissler
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Peter J Dandliker
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Roy Helmy
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Harold B Wood
- Department of Medicinal Chemistry, ‡Department of Process and Analytical Chemistry, and ¶Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc. , PO Box 2000, Rahway, New Jersey 07065, United States.,Department of Pharmacology and ⊥Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck Research Laboratories, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, and §Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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11
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Meng D, Andre P, Bateman TJ, Berger R, Chen YH, Desai K, Dewnani S, Ellsworth K, Feng D, Geissler WM, Guo L, Hruza A, Jian T, Li H, Metzger J, Parker DL, Reichert P, Sherer EC, Smith CJ, Sonatore LM, Tschirret-Guth R, Wu J, Xu J, Zhang T, Campeau LC, Orr R, Poirier M, McCabe-Dunn J, Araki K, Nishimura T, Sakurada I, Hirabayashi T, Wood HB. Development of a novel tricyclic class of potent and selective FIXa inhibitors. Bioorg Med Chem Lett 2015; 25:5437-43. [PMID: 26318999 DOI: 10.1016/j.bmcl.2015.07.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/20/2015] [Accepted: 07/23/2015] [Indexed: 11/24/2022]
Abstract
Using structure based drug design, a novel class of potent coagulation factor IXa (FIXa) inhibitors was designed and synthesized. High selectivity over FXa inhibition was achieved. Selected compounds were evaluated in rat IV/PO pharmacokinetic (PK) studies and demonstrated desirable oral PK profiles. Finally, the pharmacodynamics (PD) of this class of molecules were evaluated in thrombin generation assay (TGA) in Corn Trypsin Inhibitor (CTI) citrated human plasma and demonstrated characteristics of a FIXa inhibitor.
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Affiliation(s)
- Dongfang Meng
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
| | - Patrick Andre
- Department of Cardiometabolic Disease, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Thomas J Bateman
- Department of Pharmacokinetics, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Richard Berger
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Yi-Heng Chen
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Kunal Desai
- Department of Cardiometabolic Disease, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Sunita Dewnani
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Kenneth Ellsworth
- Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Daming Feng
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Wayne M Geissler
- Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Liangqin Guo
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Alan Hruza
- Department of Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Tianying Jian
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Hong Li
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Joe Metzger
- Department of Cardiometabolic Disease, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Dann L Parker
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Paul Reichert
- Department of Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Edward C Sherer
- Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Cameron J Smith
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Lisa M Sonatore
- Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Richard Tschirret-Guth
- Department of Pharmacokinetics, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Jane Wu
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Jiayi Xu
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Ting Zhang
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Louis-Charles Campeau
- Department of Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Robert Orr
- Department of Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Marc Poirier
- Department of Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Jamie McCabe-Dunn
- Department of Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Kazuto Araki
- Discovery Research, Mochida Pharmaceutical Co., LTD, 7, Yotsuya 1-Chome, Shinjuku-ku, Tokyo 160-8515, Japan
| | - Teruyuki Nishimura
- Discovery Research, Mochida Pharmaceutical Co., LTD, 7, Yotsuya 1-Chome, Shinjuku-ku, Tokyo 160-8515, Japan
| | - Isao Sakurada
- Discovery Research, Mochida Pharmaceutical Co., LTD, 7, Yotsuya 1-Chome, Shinjuku-ku, Tokyo 160-8515, Japan
| | - Tomokazu Hirabayashi
- Discovery Research, Mochida Pharmaceutical Co., LTD, 7, Yotsuya 1-Chome, Shinjuku-ku, Tokyo 160-8515, Japan
| | - Harold B Wood
- Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
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