In Silico Structure-based Design of a Potent, Mutation Resilient, Small Peptide Inhibitor of HIV-1 Reverse Transcriptase http://www.jbsdonline.com Abstract A crucial step in the replication of HIV-1 is the conversion of its single-stranded RNA to dou- ble-stranded DNA, which is catalyzed by the virally encoded reverse transcriptase (RT). The latter is therefore a key target for the development of anti-HIV drugs. Currently approved anti- RT drugs fall into two main classes: (i) nucleoside analog inhibitors which are incorporated into the primer strand in their metabolically activated triphosphate forms, causing termination of DNA synthesis due to their 3´-deoxy configuration and (ii) the non-nucleoside inhibitors (NNIs), which are generally specific for HIV-1 RT and bind at an allosteric site approximate- ly 10 Å from the active site causing a displacement of the catalytic aspartate residues. The so- called “first generation” NNI drugs are generally susceptible to the effects of single-point mutations within RT, while more recent “second generation” NNIs, such as efavirenz, the car- boxanilide UC-781 and certain quinoxalines demonstrate much greater resilience to mutations in RT. The crystal structures of the complexes of wild type and mutant RTs with first and sec- ond generation NNIs have shown that, for an inhibitor to be potent as well as mutation resilient, it should (i) make hydrogen bonds with the main chain of RT, (ii) have a large number of inter- actions with RT and (iii) have the ability to rearrange and adapt to a mutated NNI pocket. Based on the crystal structures of the complexes of wild type RT and Tyr188Cys mutant of RT with UC-781, we have designed a small peptide inhibitor. Docking results on this pep- tide using AutoDock3.0 and SYBYL 6.8.1 indicate that the peptide has a potency compara- ble to that of UC-781 with a retention of activity against the Tyr188Cys mutant RT. The pro- posed, small peptide is seen to possess all the desirable features of a potent and mutation resilient inhibitor and is hence a potential lead compound. Introduction HIV-1 Reverse Transcriptase (RT) is one of the primary targets for the anti-HIV drugs widely used in the highly active antiretroviral therapy for AIDS. Currently approved anti-RT drugs are of two types: the nucleoside analog inhibitors which cause termi- nation of DNA synthesis, and non-nucleoside inhibitors (NNI’s), a chemically diverse set of compounds which bind at an allosteric site approximately 10 Å from the active site causing a distortion of the active site residues (1-3). However, because of the high replication rate of HIV, which leads to a rapid selection of escape mutants (4), the current drug regimens are likely to become ineffective with time. Therefore, newer drugs with activity against the emerging drug-resistant viruses are required. The so called “first generation” NNI drugs, such as nevirapine and delavirdine have been found to be very susceptible to the effects of single point resistance mutations within RT (5, 6), while more recent “second generation” NNI’s, such as efavirenz, the carboxanalide UC-781 and certain quinoxalines demonstrate much greater resilience to the presence of such mutations in RT (7-9). Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 21, Issue Number 2, (2003) ©Adenine Press (2003) Gita Subba Rao 1,* Sonika Bhatnagar 2 1 Department of Biophysics All India Institute of Medical Sciences New Delhi-110029, India 2 Division of Biotechnology Netaji Subhas Institute of Technology New Delhi-110045, India 171 * Phone: 91-11-2659 4816; Fax: 91-11-2658 8663; Email: gitarao@aiims.ac.in