HIV‐1 Protease: Role in Viral Replication, Protein–Ligand X‐Ray Crystal Structures and Inhibitor Design

Weber, Irene T.; Wang, Yuan‐Fang

doi:10.1002/9783527630943.ch5

Cited by 6 publications

(9 citation statements)

References 108 publications

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“…The two subunits of PR form a dimer interface composed of the catalytic aspartates, the two flaps, and interdomain interactions involving Arg8, Asp29, Arg87, and the four N- and C- termini. 54 The dimerization region called the terminal domain is composed of an extended antiparallel β-sheet formed by the interdigitation of N-terminal (residues 1–4) and C-terminal (residues 96–99) β-strands of each monomer. The interaction between the four termini accounts for close to 75% of the stabilizing force in the dimer.…”

Section: Resultsmentioning

confidence: 99%

Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency

et al. 2015

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HIV drug resistance continues to emerge; consequently, there is an urgent need to develop next generation antiretroviral therapeutics.1 Here we report on the structural and kinetic effects of an HIV protease drug resistant variant with the double mutations Gly48Thr and Leu89Met (PRG48T/L89M), without the stabilizing mutations Gln7Lys, Leu33Ile, and Leu63Ile. Kinetic analyses reveal that PRG48T/L89M and PRWT share nearly identical Michaelis–Menten parameters; however, PRG48T/L89M exhibits weaker binding for IDV (41-fold), SQV (18-fold), APV (15-fold), and NFV (9-fold) relative to PRWT. A 1.9 Å resolution crystal structure was solved for PRG48T/L89M bound with saquinavir (PRG48T/L89M-SQV) and compared to the crystal structure of PRWT bound with saquinavir (PRWT-SQV). PRG48T/L89M-SQV has an enlarged active site resulting in the loss of a hydrogen bond in the S3 subsite from Gly48 to P3 of SQV, as well as less favorable hydrophobic packing interactions between P1 Phe of SQV and the S1 subsite. PRG48T/L89M-SQV assumes a more open conformation relative to PRWT-SQV, as illustrated by the downward displacement of the fulcrum and elbows and weaker interatomic flap interactions. We also show that the Leu89Met mutation disrupts the hydrophobic sliding mechanism by causing a redistribution of van der Waals interactions in the hydrophobic core in PRG48T/L89M-SQV. Our mechanism for PRG48T/L89M-SQV drug resistance proposes that a defective hydrophobic sliding mechanism results in modified conformational dynamics of the protease. As a consequence, the protease is unable to achieve a fully closed conformation that results in an expanded active site and weaker inhibitor binding.

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Section: Resultsmentioning

confidence: 99%

Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency

et al. 2015

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“…The clinical inhibitors of HIV protease provide a prime example of the success of structure-guided drug design, as discussed in recent reviews [4,50]. The PIs bind in the active site of the protease dimer and compete with substrate binding to the same site, as shown in Figure 4.…”

Section: Inhibitors Designed To Bind In the Active Sitementioning

confidence: 99%

“…The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been reviewed in [4]. HIV protease performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins to release the mature proteins (Figure 1).…”

mentioning

confidence: 99%

Highly Resistant HIV-1 Proteases and Strategies for Their Inhibition

2015

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The virally encoded protease is an important drug target for AIDS therapy. Despite the potency of the current drugs, infections with resistant viral strains limit the long-term effectiveness of therapy. Highly resistant variants of HIV protease from clinical isolates have different combinations of about 20 mutations and several orders of magnitude worse binding affinity for clinical inhibitors. Strategies are being explored to inhibit these highly resistant mutants. The existing inhibitors can be modified by introducing groups with the potential to form new interactions with conserved protease residues, and the flexible flaps. Alternative strategies are discussed, including designing inhibitors to bind to the open conformation of the protease dimer, and inhibition of the protease-catalyzed processing of the Gag-Pol precursor.

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“…Structural regions critical for PR activity and stability are the dimer interface including the catalytic Asp25 from each subunit and the flexible flaps comprising residues 45 to 55 7,8 . To date, there are nine approved clinical PIs.…”

Section: Introductionmentioning

confidence: 99%

Novel P2 Tris-tetrahydrofuran Group in Antiviral Compound1(GRL-0519) Fills the S2 Binding Pocket of Selected Mutants of HIV-1 Protease

et al. 2013

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GRL-0519 (1) is a potent antiviral inhibitor of HIV-1 protease (PR) possessing tris-tetrahydrofuran (tris-THF) at P2. The high resolution X-ray crystal structures of inhibitor 1 in complexes with single substitution mutants PRR8Q, PRD30N, PRI50V, PRI54M, and PRV82A were analyzed in relation to kinetic data. The smaller valine side chain in PRI50V eliminated hydrophobic interactions with inhibitor and the other subunit consistent with 60-fold worse inhibition. Asn30 in PRD30N showed altered interactions with neighboring residues and 18-fold worse inhibition. Mutations V82A and I54M showed compensating structural changes consistent with 6-7-fold lower inhibition. Gln8 in PRR8Q replaced the ionic interactions of wild type Arg8 with hydrogen bond interactions without changing the inhibition significantly. The carbonyl oxygen of Gly48 showed two alternative conformations in all structures likely due to the snug fit of the large tris-THF group in the S2 subsite in agreement with high antiviral efficacy of 1 on resistant virus.

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HIV‐1 Protease: Role in Viral Replication, Protein–Ligand X‐Ray Crystal Structures and Inhibitor Design

Cited by 6 publications

References 108 publications

Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency

Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency

Highly Resistant HIV-1 Proteases and Strategies for Their Inhibition

Novel P2 Tris-tetrahydrofuran Group in Antiviral Compound1(GRL-0519) Fills the S2 Binding Pocket of Selected Mutants of HIV-1 Protease

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