Conformational variation of an extreme drug resistant mutant of HIV protease

Shen, Chen‐Hsiang; Chang, Yu-Chung; Agniswamy, Johnson; Harrison, Robert W.; Weber, Irene T.

doi:10.1016/j.jmgm.2015.09.006

Cited by 24 publications

(18 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…37 Other molecular dynamics simulations and a number of NMR studies have demonstrated that drug resistant mutations distal to the drug binding cavity are capable of altering the PR dynamics, including the flap dynamics, and conformational sampling. 38–43 For example, the highly resistant mutant PR20 bearing 19 naturally evolved drug resistant mutations exhibits altered flap conformations and an expanded binding cavity. 12 Other factors, such as long range electrostatics, solvent effects, etc.…”

Section: Resultsmentioning

confidence: 99%

Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K

et al. 2017

Self Cite

View full text Add to dashboard Cite

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/Neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D + ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly alter the drug-enzyme interactions. This is in contrast to the observations in previous 100K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100K. Graphical abstractCorresponding Author Information: To whom correspondence should be addressed: kovalevskyay@ornl.gov, 505-310-4184 (AK). PDB ID Codes: the joint XN structure of PR TM -APV complex has been deposited to the Protein Data Bank with the code 5T8H. Authors will release the atomic coordinates and experimental data upon article publication.

show abstract

Section: Resultsmentioning

confidence: 99%

Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…PR20, which has the similar twisting of hinge loop as in PR S17 , was shown to remain in open form for longer periods of time than wild-type PR, leading to weaker inhibitor binding at the active site [41]. In addition, PR20 shows altered flap dynamics and the two flaps tend to fluctuate independently of each other unlike in wild-type PR [42]. Thus, E35D, M36I and S37D mutations in PR S17 twist the hinge loop thereby breaking the ion pair anchor to the flaps.…”

Section: Resultsmentioning

confidence: 99%

Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics

et al. 2016

Self Cite

View full text Add to dashboard Cite

We report structural analysis of HIV protease variant PRS17 which was rationally selected by machine learning to represent wide classes of highly drug-resistant variants. Crystal structures were solved of PRS17 in the inhibitor-free form and in complex with antiviral inhibitor, darunavir. Despite its 17 mutations, PRS17 has only one mutation (V82S) in the inhibitor/substrate binding cavity, yet exhibits high resistance to all clinical inhibitors. PRS17 has none of the major mutations (I47V, I50V, I54ML, L76V and I84V) associated with darunavir resistance, but has 10,000-fold weaker binding affinity relative to the wild type PR. Comparable binding affinity of 8000-fold weaker than PR is seen for drug resistant mutant PR20, which bears 3 mutations associated with major resistance to darunavir (I47V, I54L and I84V). Inhibitor-free PRS17 shows an open flap conformation with a curled tip correlating with G48V flap mutation. NMR studies on inactive PRS17 D25N unambiguously confirm that the flaps adopt mainly an open conformation in solution very similar to that in the inhibitor-free crystal structure. In PRS17, the hinge loop cluster of mutations, E35D, M36I and S37D, contributes to the altered flap dynamics by a mechanism similar to that of PR20. An additional K20R mutation anchors an altered conformation of the hinge loop. Flap mutations M46L and G48V in PRS17/DRV complex alter the Phe53 conformation by steric hindrance between the side chains. Unlike the L10F mutation in PR20, L10I in PRS17 does not break the inter-subunit ion pair or diminish the dimer stability, consistent with a very low dimer dissociation constant comparable to that of wild type PR. Distal mutations A71V, L90M and I93L propagate alterations to the catalytic site of PRS17. PRS17 exhibits a molecular mechanism whereby mutations act synergistically to alter the flap dynamics resulting in significantly weaker binding yet maintaining active site contacts with darunavir.

show abstract

“…In the same year, Shen et al . performed an MD analysis to understand flap flexibility in case of a PR20 variant of HIV‐PR with the D25N mutation (PR20 D25N ). The PR20 D25N conformation includes a dimer with one flap in a ‘tucked’ conformation directed towards the active site.…”

Section: Hiv Proteasementioning

confidence: 99%

“…The increased conformational flexibility in PR20 arises due to the loss of inter-residue hydrogen bond interactions ultimately led to loss of protease grip on inhibitor which resulted in drug resistance. In the same year, Shen et al (58) performed an MD analysis to understand flap flexibility in case of a PR20 variant of HIV-PR with the D25N mutation (PR20 D25N ). The PR20 D25N conformation includes a dimer with one flap in a 'tucked' conformation directed towards the active site.…”

Section: Hiv Proteasementioning

confidence: 99%

Flap Dynamics in Aspartic Proteases: A Computational Perspective

et al. 2016

View full text Add to dashboard Cite

Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.

show abstract

Conformational variation of an extreme drug resistant mutant of HIV protease

Cited by 24 publications

References 57 publications

Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K

Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K

Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics

Flap Dynamics in Aspartic Proteases: A Computational Perspective

Contact Info

Product

Resources

About