Molecular Modeling of the HIV-1 Protease and Its Substrate Binding Site

Weber, Irene T.; Miller, Maria; Jaskólski, M.; Leis, Jonathan; Skalka, Anna Marie; Wlodawer, Alexander

doi:10.1126/science.2537531

Cited by 166 publications

(79 citation statements)

References 28 publications

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“…Subtle changes in specificity may also result from spatial reorientation of the conserved contact residues by changes in adjacent residues in either linear or spatial terms. However, the finding that the enzymes from HIV-1 and HIV-2 are both (relatively) susceptible to inhibition by the acetyl-derivative of pepstatin which contains the acetyl moiety in the P4 position is exactly in keeping with the structural findings that a smaller residue would bind preferentially in the $4 position [3]. It would seem feasible that a single inhibitor would be effective towards both viral enzymes and that such a potentially therapeutic inhibitor should contain an acetyl moiety in P4 (if indeed such a large inhibitor should be necessary).…”

Section: Resultssupporting

confidence: 58%

“…From the 3-dimensional structure of the HIV-1 enzyme [2] it was predicted which residues in the enzyme might make contact with residues in individual positions in a substrate or inhibitor [2,3]. Comparison of the HIV-1 and HIV-2 (predicted) amino acid sequences [5] indicates that, with the exception of 3 conservative replacements (two Val --, lie; one Leu ~ Met), all of these (presumed) contact residues are identical in the two enzymes.…”

Section: Resultsmentioning

confidence: 99%

“…The proteolytic enzyme encoded by the virus which facilitates this processing thus becomes a potential target for therapeutic intervention to block HIV infection [1]. The crystal structure of this enzyme from HIV-1 has been solved at m~dium resolution [2] and molecular modelling of its substrate-binding site [3] together with biochemical studies with various inhibitors [4] have shown that the HIV-1 proteinase has the molecular topography characteristics of an aspartic proteinase.…”

Section: Introductionmentioning

confidence: 99%

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Inhibition of the aspartic proteinase from HIV‐2

et al. 1989

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Section: Resultssupporting

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Inhibition of the aspartic proteinase from HIV‐2

et al. 1989

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“…In the two cocrystal structures of HIV-l PR [4,5], the inhibitor, as proposed from a model complex [7], binds in an extended P-conformation with similar interactions to those observed in the structures of complexes of nonviral aspartic proteases with inhibitors [ 13,16-201. There are hydrogen bond interactions to the inhibitor provided by residues near the two catalytic triplets, and by residues from the flap (residues 74 to 76 in pepsin).…”

Section: Resultsmentioning

confidence: 99%

Comparison of inhibitor binding in HIV‐1 protease and in non‐viral aspartic proteases: the role of the flap

Gustchina

Weber

1990

FEBS Letters

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The crystal structure of HIV-l protease with an inhibitor has been compared with the structures of non-viral aspartic proteases complexed with inhibitors. In the dimeric HIV-l protease, two 4-stranded /?-sheets are formed by half of the inhibitor, residues 27-29, and the flap from each monomer. In the monomeric non-viral enzyme the single flap does not form a/I-sheet with an inhibitor. The HIV-l protease shows more interactions with a longer peptide inhibitor than are observed in non-viral aspartic protease-inhibitor complexes. This, and the large movement of the flaps, restricts the conformation of the protease cleavage sites in the retroviral polyprotein precursor.Retroviral protease; Aspartic protease; Enzyme-substrate interaction; Retroviral polyprotein precursor

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“…1 PR is required for proteolytic cleavage of viral Gag and Gag-Pol polyproteins into individual structural and functional proteins during viral maturation. 2 In the absence of this proteolysis, immature noninfectious virions are produced, thus making PR a prime target for structureassisted drug design in antiviral therapy.…”

mentioning

confidence: 99%

Carbamylation of N-Terminal Proline

Olajuyigbe

Demitri²,

Ajele

et al. 2010

ACS Med. Chem. Lett.

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Protein carbamylation is of great concern both in vivo and in vitro. Here, we report the first structural characterization of a protein carbamylated at the N-terminal proline. The unexpected carbamylation of the R-amino group of the least reactive codified amino acid has been detected in high-resolution electron density maps of a new crystal form of the HIV-1 protease/saquinavir complex. The carbamyl group is found coplanar to the proline ring with a trans conformation. The reaction of N-terminal with cyanate ion derived from the chaotropic agent urea was confirmed by mass spectra analysis on protease single crystals. Implications of carbamylation process in vitro and in vivo are discussed.KEYWORDS Carbamylation, N-terminal proline, HIV-1 protease/saquinavir complex, single crystals T he HIV protease (PR) is an aspartic protease that shares sequence homology around the active site with other retroviral proteases, as the conserved Asp-ThrGly catalytic triad. 1 PR is required for proteolytic cleavage of viral Gag and Gag-Pol polyproteins into individual structural and functional proteins during viral maturation. 2 In the absence of this proteolysis, immature noninfectious virions are produced, thus making PR a prime target for structureassisted drug design in antiviral therapy. 3,4 The structure-assisted drug design and discovery process utilizes techniques such as protein crystallography, nuclear magnetic resonance (NMR), and computational biochemistry to guide synthesis of potential drugs. PR has been widely characterized biochemically and structurally, which has led to the discovery of HIV protease inhibitors (PIs). Their utilization in highly active antiretroviral therapy (HAART) has been a major turning point in the management of HIV/acquired immune-deficiency syndrome (AIDS). 5 Recently, we have demonstrated that high-resolution X-ray crystallography can be used as a powerful method to identify the most potent PR inhibitor present in an epimeric mixture. 6 The pseudosymmetric peptidomimetic inhibitor based on a novel Phe-Pro isostere core matched the 2-fold symmetry of the homodimeric structure of the PR. Fourier maps obtained by high-resolution diffraction data (1.3 Å) clearly showed the catalytic site fully occupied by a single ordered stereoisomer. On the contrary, several X-ray crystal structures of PR complexed with more asymmetric FDAapproved inhibitors, like darunavir, nelfinavir, and saquinavir (SQV), have the catalytic site occupied by the inhibitor oriented in two almost equivalent positions related by a pseudo-2-fold symmetry. [7][8][9][10][11][12] To investigate this order/disorder phenomenon and its possible relationship with crystal packing, we have undertaken a systematic search for new crystal forms of wild-type PR in complex with SQV. Single crystals of the PR/SQV complex were obtained by a vapor diffusion technique and analyzed by X-ray diffraction. These crystals belong to a new monoclinic crystal form, which contains two dimers of the complex in the asymmetric unit. Other crystal...

show abstract

Molecular Modeling of the HIV-1 Protease and Its Substrate Binding Site

Cited by 166 publications

References 28 publications

Inhibition of the aspartic proteinase from HIV‐2

Inhibition of the aspartic proteinase from HIV‐2

Comparison of inhibitor binding in HIV‐1 protease and in non‐viral aspartic proteases: the role of the flap

Carbamylation of N-Terminal Proline

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