Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1.

Smerdon, Stephen J.; Jäger, Joachim; Wang, J; Kohlstaedt, Lori A.; Chirino, Arthur J.; Friedman, Jonathan M.; Rice, Phoebe A.; Steitz, Thomas A.

doi:10.1073/pnas.91.9.3911

Cited by 312 publications

(260 citation statements)

References 33 publications

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“…Cocrystals of HIV-1 RT with nevirapine have been described (4,5). Crystals were washed at 4°C in stabilization solution containing 50 mM bis-Tris propane (pH 6.8), 25 mM ammonium sulfate, 0.1% (wt͞vol) ␤-octyl glucoside, 20% (wt͞vol) PEG-8000, 10% (vol͞vol) glycerol, 1% (vol͞vol) DMSO, and 500 M CP-94,707 (Pfizer) and allowed to soak for 2 days with several changes of fresh solution.…”

Section: Methodsmentioning

confidence: 99%

“…Resistance to NNRTIs arises rapidly upon drug treatment and results from mutation of the amino acids lining the binding pocket (5). The clinically most important mutations of HIV-1 RT occur in amino acids Lys-103, Tyr-181, and Tyr-188 (ref.…”

mentioning

confidence: 99%

“…The first structure of HIV-1 RT was complexed with the NNRTI nevirapine, which bound in a hydrophobic pocket near the polymerase active site (4,5). 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).…”

mentioning

confidence: 99%

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

Pata

Stirtan

Goldstein

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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We have determined the crystal structure of the HIV type 1 reverse transcriptase complexed with CP-94,707, a new nonnucleoside reverse transcriptase inhibitor (NNRTI), to 2.8-Å resolution. In addition to inhibiting the wild-type enzyme, this compound inhibits mutant enzymes that are resistant to inhibition by nevirapine, efavirenz, and delaviridine. In contrast to other NNRTI complexes where tyrosines 181 and 188 are pointing toward the enzyme active site, the binding pocket in this complex has the tyrosines pointing the opposite direction, as in the unliganded protein structure, to accommodate CP-94,707. This conformation of the pocket has not been observed previously in NNRTI complexes and substantially alters the shape and surface features that are available for interactions with the inhibitor. One ring of CP-94,707 makes extensive stacking interactions with tryptophan 229, one of the few residues in the NNRTI-binding pocket that cannot readily mutate to give rise to drug resistance. In this conformation of the pocket, mutations of tyrosines 181 and 188 are less likely to disrupt inhibitor binding. Modeling the asparagine mutation of lysine 103 shows that a hydrogen bond between it and tyrosine 188 could form as readily in the CP-94,707 complex as it does in the apoenzyme structure, providing an explanation for the activity of this inhibitor against this clinically important mutant.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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

Pata

Stirtan

Goldstein

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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“…The V179 and G190 residues are located in the 139-1310 hairpin, which forms part of the NNRTI-binding pocket (20,21) (Fig. 2).…”

Section: Analysis Of the Hiv-1 Rt Gene During In Vitro Selection Formentioning

confidence: 99%

“…We The nonnucleoside inhibitor binding pocket is close to the DNA-binding cleft and contains structural elements in common with the "primer grip" (7,20,21). Mutations at position 190 could distort the conformation of the primer grip or other nearby DNA-binding elements, and the NRTI-specific mutations (L74--V/I and V75-*L/I) possibly compensate for the changes across the DNA-binding cleft.…”

Section: Introductionmentioning

confidence: 99%

Selective pressure of a quinoxaline nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) on HIV-1 replication results in the emergence of nucleoside RT-inhibitor-specific (RT Leu-74-->Val or Ile and Val-75-->Leu or Ile) HIV-1 mutants.

Kleim¹,

Rösner²,

Winkler³

et al. 1996

Proc. Natl. Acad. Sci. U.S.A.

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The quinoxaline nonnucleoside RT inhibitor (NNRTI) (S)-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3,4-dihydroquinoxaline-2(1H)-thione (HBY 097) was used to select for drug-resistant HIV-1 variants in vitro. The viruses first developed mutations affecting the NNRTIbinding pocket, and five of six strains displayed the RT G190--E substitution, which is characteristic for HIV-1 resistance against quinoxalines. In one variant, a new mutant (G190->Q) most likely evolved from preexisting G190->E mutants. The negative charge introduced by the G190->E substitution was maintained at that site of the pocket by simultaneous selection for V179--D together with G190--Q. After continued exposure to the drug, mutations at positions so far known to be specific for resistance against nucleoside RT inhibitors (NRTIs) (L74-*V/I and V75->L/I) were consistently detected in all cultures. The inhibitory activities of the cellular conversion product of 2',3'-dideoxyinosine (ddl, didanosine), 2',3'-dideoxyadenosine (ddA) and of 2',3'-didehydro-3'-deoxythymidine (d4T, stavudine) against these late-passage viruses were shown to be enhanced with the L74->V/I RT mutant virus as compared with the wild-type (wt) HIV-1MN isolate. Clonal analysis proved linkage of the codon 74 and codon 75 mutations to the NNRTI-specific mutations in all RT gene fragments. The nonnucleoside-and nucleoside-resistance mutation sites are separated by approximately 35 A. We propose that the two sites "communicate" through the template-primer which is situated in the DNAbinding cleft between these two sites. Quinoxalines cause high selective pressure on HIV-1 replication in vitro; however, the implication of these findings for the treatment of infection has yet to be determined. Viral resistance against both nucleoside reverse transcriptase (RT) inhibitors (NRTIs) and nonnucleoside RT inhibitors (NNRTIs) of human immunodeficiency virus type 1 (HIV-1) replication develops in vitro (cell culture) and in vivo (patients). NRTIs select for RT amino acid substitutions at positions that can be allocated to different structural elements of the protein in the range of residue numbers 41-219 (1-5). A molecular mechanism for some alterations can be assumed on the basis of the RT crystal structure (6-8). In contrast, NNRTI-specific substitutions map exclusively to those protein secondary structure elements that together form a lipophilic pocket within the palm domain of the p66 RT subunit. All NNRTIs are believed to bind to this region, and mutations selected for by these drugs usuallyThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. occur in the segments composed of RT amino acids 98-108, 179-190, and 230-236 (9-16). Especially the Y181-*C RT mutant appears with many chemically distinct compounds, including different NNRTI combinations (12).6-Chloro-3,3-dimethyl-4-(isopropenyloxycarbonyl)-3,4-dihydroqu...

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

et al. 1999

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Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1.

Cited by 312 publications

References 33 publications

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

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

Selective pressure of a quinoxaline nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) on HIV-1 replication results in the emergence of nucleoside RT-inhibitor-specific (RT Leu-74-->Val or Ile and Val-75-->Leu or Ile) HIV-1 mutants.

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

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