High resolution structures of HIV-1 RT from four RT–inhibitor complexes

Abstract

We have determined the structures of four complexes of HIV-1 reverse transcriptase with non-nucleoside inhibitors, three fully refined at high resolution. The highest resolution structure is of the RT-nevirapine complex which has an R-factor of 0.186 and a root-mean-square bond length deviation of 0.015 A for all data to 2.2 A. The structures reveal a common mode of binding for these chemically diverse compounds. The common features of binding are largely hydrophobic interactions and arise from induced shape complementarity achieved by conformational rearrangement of the enzyme and conformational/configurational rearrangement of the compounds.

Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics

“…The ''thumb down'' and ''thumb upright'' structures are compared to cartoons of human hands. In the structures of HIV-1 RT/NNRTI complexes, [11][12][13][14][15]20 the p66 thumb is also in an upright position, similar (but not identical) to that observed in the RT/dsDNA/Fab complex, 16,17,25 indicating that the binding of either nonnucleoside inhibitor or nucleic acid template-primer influences the position of the p66 thumb subdomain.…”

“…[6][7][8][9][10] NRTIs are analogues of normal deoxynucleoside triphosphates (dNTPs), while NNRTIs inhibit RT by binding at a common site, approximately 10 Å away from the polymerase active site. 6,[11][12][13][14][15] RT is a dimeric protein of 1,000 amino acid residues, that consists of a 66 kDa (p66) and a 51 kDa (p51) subunit. The p66 subunit is composed of the polymerase domain (440 amino acids) and the ribonuclease H (RNase-H) domain (120 amino acids).…”

“…The p66 fingers, palm, and thumb subdomains form a large cleft that binds the template-primer dsDNA. 16,17 Reported crystal structures of RT include those of unliganded RT, [18][19][20][21][22] RT/NNRTIs complexes, [11][12][13][14][15]23,24 RT complexed to a double-stranded DNA template-primer and an antibody Fab fragment (referred to as RT/dsDNA/ Fab), 16,17,25 and the complex of RT with a DNA templateprimer and dNTP. 26 The overall folding of RT is similar in all the structures reported; however, comparisons among the structures have shown that certain regions can adopt different conformations.…”

Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors

“…Subsequent structures of the enzyme with a number of different NNRTIs bound have demonstrated that these inhibitors bind to the same pocket, with only minor differences in protein conformation, and substantially overlap the site occupied by nevirapine (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Comparison of these structures with those of the apoenzyme shows that the NNRTI-binding pocket is induced upon NNRTI binding (21)(22)(23)(24).…”

Caracterização de estado sólido de insumos farmacêuticos ativos: clorpropamida, nevirapina e dietilcarbamazina

“…É válido ressaltar que esta conformação em borboleta é mantida mesmo quando a NVP encontra-se ligada à TR. 103,104 A existência de polimorfismo da NVP surgiu em 2004, por meio de uma discussão científica na qual a EMEA (European Medicines Agency) reportou a existência de uma forma hemi-hidratada, obtida a partir da forma anidra que foi testada e aprovada para uso em suspensões, apesar de a forma anidra ser utilizada em comprimidos (adultos) e em suspensões (crianças). 105 …”