1
|
Hong RS, Mattei A, Sheikh AY, Bhardwaj RM, Bellucci MA, McDaniel KF, Pierce MO, Sun G, Li S, Wang L, Mondal S, Ji J, Borchardt TB. Novel Physics-Based Ensemble Modeling Approach That Utilizes 3D Molecular Conformation and Packing to Access Aqueous Thermodynamic Solubility: A Case Study of Orally Available Bromodomain and Extraterminal Domain Inhibitor Lead Optimization Series. J Chem Inf Model 2021; 61:1412-1426. [PMID: 33661005 DOI: 10.1021/acs.jcim.0c01410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug design with patient centricity for ease of administration and pill burden requires robust understanding of the impact of chemical modifications on relevant physicochemical properties early in lead optimization. To this end, we have developed a physics-based ensemble approach to predict aqueous thermodynamic crystalline solubility, with a 2D chemical structure as the input. Predictions for the bromodomain and extraterminal domain (BET) inhibitor series show very close match (0.5 log unit) with measured thermodynamic solubility for cases with low crystal anisotropy and good match (1 log unit) for high anisotropy structures. The importance of thermodynamic solubility is clearly demonstrated by up to a 4 log unit drop in solubility compared to kinetic (amorphous) solubility in some cases and implications thereof, for instance on human dose. We have also demonstrated that incorporating predicted crystal structures in thermodynamic solubility prediction is necessary to differentiate (up to 4 log unit) between solubility of molecules within the series. Finally, our physics-based ensemble approach provides valuable structural insights into the origins of 3-D conformational landscapes, crystal polymorphism, and anisotropy that can be leveraged for both drug design and development.
Collapse
Affiliation(s)
- Richard S Hong
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alessandra Mattei
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Ahmad Y Sheikh
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Michael A Bellucci
- XtalPi, Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Keith F McDaniel
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - M Olivia Pierce
- Schrödinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Guangxu Sun
- XtalPi, Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Sizhu Li
- XtalPi, Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Lingle Wang
- Schrödinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Sayan Mondal
- Schrödinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Jianguo Ji
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thomas B Borchardt
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| |
Collapse
|
2
|
Marchese Robinson RL, Geatches D, Morris C, Mackenzie R, Maloney AGP, Roberts KJ, Moldovan A, Chow E, Pencheva K, Vatvani DRM. Evaluation of Force-Field Calculations of Lattice Energies on a Large Public Dataset, Assessment of Pharmaceutical Relevance, and Comparison to Density Functional Theory. J Chem Inf Model 2019; 59:4778-4792. [DOI: 10.1021/acs.jcim.9b00601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Richard L. Marchese Robinson
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dawn Geatches
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Chris Morris
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rebecca Mackenzie
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Andrew G. P. Maloney
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Kevin J. Roberts
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Alexandru Moldovan
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ernest Chow
- Pfizer Worldwide R&D, Ramsgate Road, Sandwich CT13 9NJ, United Kingdom
| | | | | |
Collapse
|