Altered Substrate Specificity of Drug-Resistant Human Immunodeficiency Virus Type 1 Protease

Dauber, Deborah S.; Ziermann, Rainer; Parkin, Neil; Maly, Dustin J.; Mahrus, Sami; Harris, Jennifer L.; Ellman, Jon; Petropoulos, Christos J.; Craik, Charles S.

doi:10.1128/jvi.76.3.1359-1368.2002

Cited by 49 publications

(41 citation statements)

References 50 publications

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“…For example, the large regression coefficients from particular physicochemical properties of the P 1 9-P 2 , P 1 9-P 1 , P 1 9-P 3 9, and P 1 -P 3 residue pairs indicate the presence of interactions for these pairs, while no such interactions take place for the P 3 -P 2 pair according to the model, in accordance with experimental results [22]. Cooperativity between P 1 -P 2 , P 1 -P 3 , and P 1 -P 4 residue pairs, indicated by the model, has also been shown to be important for specificity features [21]. In earlier specificity studies of retroviral proteases, many series of substrates were used, each of which often differ only by one or two residues, prohibiting a complete analysis of all residues at every subsite [21].…”

Section: Interpretation Of the Chemical Effects In Substrates Determisupporting

confidence: 74%

“…Next, we consecutively chose 15 substrates predicted to be noncleavable by the CLM by HXB2 HIV-1 protease, allowing at most four amino acids to be identical at any same positions among all the substrates already selected (including the cleavable substrates already chosen above). If none of the remaining substrates met the requirements, a five-amino-acid similarity was allowed (Table 3, numbers [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. We then used the CLM to predict cleavability of the chosen 30 substrates by mutant HIV-1 proteases I84V, L90M, and I84V þ L90M.…”

Section: Methodsmentioning

confidence: 99%

“…Specificity studies for retroviral proteases have found that highly complicated and not easily interpretable interior interactions take place in the substrates [21]. Such interactions become easy to interpret in the model by the crossterms, however.…”

Section: Interpretation Of the Chemical Effects In Substrates Determimentioning

confidence: 99%

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A Look inside HIV Resistance through Retroviral Protease Interaction Maps

Kontijevskis¹,

Prūsis²,

Petrovska³

et al. 2005

PLoS Comput Biol

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Retroviruses affect a large number of species, from fish and birds to mammals and humans, with global socioeconomic negative impacts. Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral proteases. Using multivariate analysis of the sequence-based physiochemical descriptions of 61 retroviral proteases comprising wild-type proteases, natural mutants, and drug-resistant forms of proteases from nine different viral species in relation to their ability to cleave 299 substrates, the authors mapped the physicochemical properties and cross-dependencies of the amino acids of the proteases and their substrates, which revealed a complex molecular interaction network of substrate recognition and cleavage. The approach allowed a detailed analysis of the molecular-chemical mechanisms involved in substrate cleavage by retroviral proteases.Citation: Kontijevskis A, Prusis P, Petrovska R, Yahorava S, Mutulis F, et al. (2007) A look inside HIV resistance through retroviral protease interaction maps. PLoS Comput Biol 3(3): e48.

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Section: Interpretation Of the Chemical Effects In Substrates Determisupporting

confidence: 74%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

A Look inside HIV Resistance through Retroviral Protease Interaction Maps

Kontijevskis¹,

Prūsis²,

Petrovska³

et al. 2005

PLoS Comput Biol

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“…This has been noted previously (13,14,59,71). However, here we showed that the reduction in processing of the NC-p1 cleavage site correlated significantly with the reduction in specific infectivity (Fig.…”

Section: Discussionsupporting

confidence: 64%

Evolution of Human Immunodeficiency Virus Type 1 Protease Genotypes and Phenotypes In Vivo under Selective Pressure of the Protease Inhibitor Ritonavir

Resch¹,

Parkin

Watkins

et al. 2005

J Virol

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We examined the population dynamics of human immunodeficiency virus type 1 pro variants during the evolution of resistance to the protease inhibitor ritonavir (RTV) in vivo. pro variants were followed in subjects who had added RTV to their previously failed reverse transcriptase inhibitor therapy using a heteroduplex tracking assay designed to detect common resistance-associated mutations. In most cases the initial variant appeared rapidly within 2 to 3 months followed by one or more subsequent population turnovers. Some of the subsequent transitions between variants were rapid, and some were prolonged with the coexistence of multiple variants. In several cases variants without resistance mutations persisted despite the emergence of new variants with an increasing number of resistance-associated mutations. Based on the rate of turnover of pro variants in the RTV-treated subjects we estimated that the mean fitness of newly emerging variants was increased 1.2-fold (range, 1.02 to 1.8) relative to their predecessors. A subset of pro genes was introduced into infectious molecular clones. The corresponding viruses displayed impaired replication capacity and reduced susceptibility to RTV. A subset of these clones also showed increased susceptibility to two nonnucleoside reverse transcriptase inhibitors and the protease inhibitor saquinavir. Finally, a significant correlation between the reduced replication capacity and reduced processing at the gag NC-p1 processing site was noted. Our results reveal a complexity of patterns in the evolution of resistance to a protease inhibitor. In addition, these results suggest that selection for resistance to one protease inhibitor can have pleiotropic effects that can affect fitness and susceptibility to other drugs.Protease inhibitors (PIs) potently inhibit human immunodeficiency virus type 1 (HIV-1) replication, and their initial introduction into combination antiretroviral therapy was associated with a significant decrease of HIV-1-associated mortality and morbidity (41, 45). However, in clinical practice, virologic failure of protease inhibitor-containing therapy occurs in a significant fraction of the treated population (19,22,42,46,52,70). Virologic failure of protease inhibitor treatment is often due to the selection of HIV-1 strains with mutations in the pro gene, which encodes the viral protease (PR), and in specific protease cleavage sites encoded in the gag gene that collectively confer reduced drug susceptibility to the harboring strain (11,12,28,36,43,47,72).The resistance mutations are hypothesized to be largely preexisting, generated by the highly error-prone and rapid replication of HIV-1 in large virus populations (5, 10, 57). However, in PI-naïve subjects, some critical resistance mutations cannot be detected or can only be detected at very low levels, suggesting that these mutations may confer a selective disadvantage relative to wild-type HIV-1 strains (3,18,25,32,34,63). Indeed, it has been shown that the catalytic efficiency of protease is reduced by PI resis...

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“…The NC-p1 cleavage site is the rate-determining step in the processing of the Gag polyprotein (7,37,54). The amino acid sequence of this site, with an Asn at P1 and an Ala at P2, is also the least homologous compared with the other HIV-1 protease substrates sites, which have hydrophobic residues at P1 and branched residues at P2.…”

Section: Discussionmentioning

confidence: 99%

Structural Basis for Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease

Prabu-Jeyabalan

Nalivaika

King

et al. 2004

J Virol

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Maturation of human immunodeficiency virus (HIV) depends on the processing of Gag and Pol polyproteinsby the viral protease, making this enzyme a prime target for anti-HIV therapy. Among the protease substrates, the nucleocapsid-p1 (NC-p1) sequence is the least homologous, and its cleavage is the rate-determining step in viral maturation. In the other substrates of HIV-1 protease, P1 is usually either a hydrophobic or an aromatic residue, and P2 is usually a branched residue. NC-p1, however, contains Asn at P1 and Ala at P2. In response to the V82A drug-resistant protease mutation, the P2 alanine of NC-p1 mutates to valine (AP2V). To provide a structural rationale for HIV-1 protease binding to the NC-p1 cleavage site, we solved the crystal structures of inactive (D25N) WT and V82A HIV-1 proteases in complex with their respective WT and AP2V mutant NC-p1 substrates. Overall, the WT NC-p1 peptide binds HIV-1 protease less optimally than the AP2V mutant, as indicated by the presence of fewer hydrogen bonds and fewer van der Waals contacts. AlaP2 does not fill the P2 pocket completely; PheP1 makes van der Waals interactions with Val82 that are lost with the V82A protease mutation. This loss is compensated by the AP2V mutation, which reorients the peptide to a conformation more similar to that observed in other substrate-protease complexes. Thus, the mutant substrate not only binds the mutant protease more optimally but also reveals the interdependency between the P1 and P2 substrate sites. This structural interdependency results from coevolution of the substrate with the viral protease.Human immunodeficiency virus type 1 (HIV-1) matures after the viral protease processes (35) the Gag and Pol polyproteins at 10 substrate locations (3, 15). Therefore, inhibition of HIV-1 protease represents an important avenue for antiviral therapy (13, 48). The substrate sequences cleaved by the protease are nonhomologous (3), with the sequence of the nucleocapsid-p1 (NC-p1) substrate being the most different. In spite of the poor sequence homology among the substrate sites, a series of substrate-protease crystal structures led us to hypothesize that substrate specificity in HIV-1 protease results from the enzyme's recognizing an asymmetric shape (or envelope) rather than a particular amino acid sequence (40). This shape results from the conformation that a particular substrate sequence can adopt, implying that an interdependency necessarily exists among the different substrate residue sites.All of the protease inhibitors whose designs were structure based bind competitively (8,18,28,52,53) at the active site. Since these inhibitors bind at the same site as the substrates, many protease residues contact both substrates and inhibitors. Drug resistance, which often develops in the presence of therapeutic protease inhibitors, results from high viral turnover, the infidelity of the viral reverse transcriptase (16,42,43), and selective pressure on the virus. With drug resistance, the protease no longer binds as tightly to inhibitors but r...

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Altered Substrate Specificity of Drug-Resistant Human Immunodeficiency Virus Type 1 Protease

Abstract: Resistance to human immunodeficiency virus type 1 protease (HIV PR)

Cited by 49 publications

References 50 publications

A Look inside HIV Resistance through Retroviral Protease Interaction Maps

A Look inside HIV Resistance through Retroviral Protease Interaction Maps

Evolution of Human Immunodeficiency Virus Type 1 Protease Genotypes and Phenotypes In Vivo under Selective Pressure of the Protease Inhibitor Ritonavir

Structural Basis for Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease

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