Interactions of Conformationally Biased North and South 2‘-Fluoro-2‘,3‘-dideoxynucleoside 5‘-Triphosphates with the Active Site of HIV-1 Reverse Transcriptase

• Published in: Biochemistry (Easton) 2000-09, Vol.39 (37), p.11205-11215
• Main Authors: Mu, Lan, Sarafianos, Stefan G, Nicklaus, Marc C, Russ, Pamela, Siddiqui, Maqbool A, Ford, Harry, Mitsuya, Hiroaki, Le, Richard, Kodama, Eiichi, Meier, Chris, Knispel, Tina, Anderson, Lynne, Barchi, Joseph J, Marquez, Victor E
• Format: Article
• Language: English
• Subjects: AIDS/HIV; Anti-HIV Agents - chemistry; Binding Sites - drug effects; Deoxyadenine Nucleotides - chemistry; Deoxyadenine Nucleotides - metabolism; Dideoxyadenosine - analogs & derivatives; Dideoxyadenosine - chemistry; Dideoxyadenosine - metabolism; dideoxynucleoside-5'-triphosphate; Dideoxynucleotides; Dinucleoside Phosphates - chemistry; HIV Reverse Transcriptase - antagonists & inhibitors; HIV Reverse Transcriptase - chemistry; HIV Reverse Transcriptase - metabolism; Human immunodeficiency virus 1; Humans; Models, Chemical; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Reverse Transcriptase Inhibitors - chemistry; Thermodynamics; Tyrosine - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi001090n

Molecular dynamics simulations of a ternary complex of HIV-1 reverse transcriptase (RT), double-stranded DNA, and bound dideoxynucleoside-5‘-triphosphate (RT−DNA−ddNTP), utilizing the ddNTPs ddATP, βFddATP, and αFddATP, explain the experimentally observed order of potency of these 5‘-triphosphates as inhibitors of RT:  ddATP > βFddATP > αFddATP. On the basis of RT's known preference to bind the incoming dNTP (or ddNTP) with a north conformation at the polymerase site, αFddATP, which in solution prefers almost exclusively a north conformation, was predicted to be the most potent inhibitor. However, Tyr115, which appears to function as a steric gate to preclude the binding of ribonucleoside 5‘-triphosphates, prevents the effective binding of αFddATP in its preferred north conformation. The south-biased βFddATP, while able to bind to RT without hindrance by Tyr115, has to pay a high energy penalty to be flipped to the active north conformation at the polymerase site. Finally, the more flexible and less conformationally biased ddATP is able to switch to a north conformation at the RT site with a smaller energy penalty than βFddATP. These results highlight the opposite conformational preferences of HIV-1 RT for αFddATP and βFddATP and help establish conformational guidelines for optimal binding at the polymerase site of this enzyme.