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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] [What about the content of this article? (0)] [Affiliation(s)] [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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