FEP-Guided Selection of Bicyclic Heterocycles in Lead Optimization for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase
Author:
Affiliation:
1. Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, and Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066
Publisher
American Chemical Society (ACS)
Subject
Colloid and Surface Chemistry,Biochemistry,General Chemistry,Catalysis
Link
https://pubs.acs.org/doi/pdf/10.1021/ja066472g
Reference9 articles.
1. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase
2. Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase
3. Optimization of pyrimidinyl- and triazinyl-amines as non-nucleoside inhibitors of HIV-1 reverse transcriptase
4. Initial structures for the inhibitors and complexes were built with theBOMBprogram and included 159 residues of HIV-RT. A total of 1250 and 2000 TIP4P water molecules were added in 25 Å caps for the complexes and unbound ligands, respectively. Each FEP utilized 20 free energy increments and typically covered 20 × 106(20 M) configurations for equilibration and 40 M configurations for averaging. The OPLS-AA force field was used for the protein and OPLS/CM1A for the inhibitors, and the MC/FEP calculations were performed withMCPRO 2.0. Details on theBOMBand FEP calculations can be found in ref 1.
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