1
|
Allen WJ, Fochtman BC, Balius TE, Rizzo RC. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. J Comput Chem 2017; 38:2641-2663. [PMID: 28940386 DOI: 10.1002/jcc.25052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
Abstract
De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794
| | - Brian C Fochtman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, 94158
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794.,Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, 11794.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794
| |
Collapse
|
2
|
Ding Y, Liu H, Tekwani BL, Nanayakkara NPD, Khan IA, Walker LA, Doerksen RJ. Methemoglobinemia Hemotoxicity of Some Antimalarial 8-Aminoquinoline Analogues and Their Hydroxylated Derivatives: Density Functional Theory Computation of Ionization Potentials. Chem Res Toxicol 2016; 29:1132-41. [DOI: 10.1021/acs.chemrestox.6b00063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yuanqing Ding
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Haining Liu
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Babu L. Tekwani
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - N. P. Dhammika Nanayakkara
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Ikhlas A. Khan
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Larry A. Walker
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Robert J. Doerksen
- National Center for Natural Products Research,
Research Institute
of Pharmaceutical Science, and ‡Department of BioMolecular Sciences, School
of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| |
Collapse
|