HIV reverse transcriptase (RT) is an essential enzyme that is the target of almost half of all approved anti-AIDS drugs. The nucleoside/nucleotide RT inhibitors (NRTIs) and non-nucleoside RT inhibitor (NNRTIs) are used in combinations to treat HIV-1 infection. A new class of RT inhibitors could work synergistically with NRTIs and NNRTIs in inhibiting RT functions. An NcRTI (nucleotide- competing reverse transcriptase inhibitor) inhibits RT by blocking dNTP-binding, which is distinct from the DNA-chain-terminator NRTIs. Structural studies of RT/nucleic acid/NcRTI complexes would define the NcRTI-binding pocket and provide a basis for improvement of inhibitor potency and specificity. Obtaining the first reliable picture of the HIV-1 NcRTI-binding pocket would represent a major innovation and will enable new strategies for designing and developing novel anti-AIDS drugs. The studies proposed here will be focused on defining the NcRTI-binding pocket using X-ray crystallography and further targeting the proposed pocket by small molecules. The structural study will be complement ongoing structural studies of different complexes of HIV-1 RT in the Arnold laboratory at the Center for Advanced Biotechnology and Medicine and Rutgers University. Our recent high- resolution (2.6 E) crystal form of RT/RNA:DNA/dNTP ternary complexes and success in fragment soaking into RT crystals provide a critical foundation for the proposed structure-based NcRTI design study. Now that we have obtained high-resolution diffracting crystals of various RT complexes, our capacity to determine structures focused on NcRTI binding is limited by the dedicated personnel effort that we can commit to this study. The project is ready to progress rapidly as soon as funds are available to hire a part-time technician for structural studies and a Ph.D. level scientist to carry out computational chemistry efforts. Also, two undergraduate researchers will be hired on a part-time basis and trained to contribute to this effort.
HIV-1 reverse transcriptase (RT) is a central target for antiviral treatment of AIDS and detailed knowledge of its structure and function has important clinical and biological consequences. Both nucleoside and non-nucleoside RT inhibitors are used as effective drugs for treating AIDS, but success can be limited by the emergence of drug-resistant viral variants. The proposed studies will on determining the structural characteristics of the NcRTI (nucleoside-competing reverse transcriptase inhibitor) binding site and exploiting this to develop novel anti-AIDS drugs targeting HIV-1 RT.
| Vijayan, R S K; Arnold, Eddy; Das, Kalyan (2014) Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations. Proteins 82:815-29 |
| Das, Kalyan; Martinez, Sergio E; Bauman, Joseph D et al. (2012) HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat Struct Mol Biol 19:253-9 |
| Das, Kalyan; Bauman, Joseph D; Rim, Angela S et al. (2011) Crystal structure of tert-butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in complex with HIV-1 reverse transcriptase (RT) redefines the elastic limits of the non-nucleoside inhibitor-binding pocket. J Med Chem 54:2727-37 |
| Chu, Chun; Das, Kalyan; Tyminski, James R et al. (2011) Structure of the guanylyltransferase domain of human mRNA capping enzyme. Proc Natl Acad Sci U S A 108:10104-8 |
