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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Toward The Design Of Mutation-Resistant Enzyme Inhibitors: Further Evaluation Of The Substrate Envelope Hypothesis, Visvaldas Kairys, Michael Gilson, Viney Lather, Celia Schiffer, Miguel Fernandes
Toward The Design Of Mutation-Resistant Enzyme Inhibitors: Further Evaluation Of The Substrate Envelope Hypothesis, Visvaldas Kairys, Michael Gilson, Viney Lather, Celia Schiffer, Miguel Fernandes
Celia A. Schiffer
Previous studies have shown the usefulness of the substrate envelope concept in the analysis and prediction of drug resistance profiles for human immunodeficiency virus protease mutants. This study tests its applicability to several other therapeutic targets: Abl kinase, chitinase, thymidylate synthase, dihydrofolate reductase, and neuraminidase. For the targets where many (> or =6) mutation data are available to compute the average mutation sensitivity of inhibitors, the total volume of an inhibitor molecule that projects outside the substrate envelope V(out), is found to correlate with average mutation sensitivity. Analysis of a locally computed volume suggests that the same correlation would hold …
Cooperative Fluctuations Of Unliganded And Substrate-Bound Hiv-1 Protease: A Structure-Based Analysis On A Variety Of Conformations From Crystallography And Molecular Dynamics Simulations, Nese Kurt, Walter Scott, Celia Schiffer, Turkan Haliloglu
Cooperative Fluctuations Of Unliganded And Substrate-Bound Hiv-1 Protease: A Structure-Based Analysis On A Variety Of Conformations From Crystallography And Molecular Dynamics Simulations, Nese Kurt, Walter Scott, Celia Schiffer, Turkan Haliloglu
Celia A. Schiffer
The dynamics of HIV-1 protease, both in unliganded and substrate-bound forms have been analyzed by using an analytical method, Gaussian network model (GNM). The method is applied to different conformations accessible to the protein backbone in the native state, observed in crystal structures and snapshots from fully atomistic molecular dynamics (MD) simulation trajectories. The modes of motion obtained from GNM on different conformations of HIV-1 protease are conserved throughout the MD simulations. The flaps and 40's loop of the unliganded HIV-1 protease structure are identified as the most mobile regions. However, in the liganded structure these flaps lose mobility, and …
Drug Resistance Against Hcv Ns3/4a Inhibitors Is Defined By The Balance Of Substrate Recognition Versus Inhibitor Binding, Keith P. Romano, Akbar Ali, William E. Royer, Celia A. Schiffer
Drug Resistance Against Hcv Ns3/4a Inhibitors Is Defined By The Balance Of Substrate Recognition Versus Inhibitor Binding, Keith P. Romano, Akbar Ali, William E. Royer, Celia A. Schiffer
Celia A. Schiffer
Hepatitis C virus infects an estimated 180 million people worldwide, prompting enormous efforts to develop inhibitors targeting the essential NS3/4A protease. Resistance against the most promising protease inhibitors, telaprevir, boceprevir, and ITMN-191, has emerged in clinical trials. In this study, crystal structures of the NS3/4A protease domain reveal that viral substrates bind to the protease active site in a conserved manner defining a consensus volume, or substrate envelope. Mutations that confer the most severe resistance in the clinic occur where the inhibitors protrude from the substrate envelope, as these changes selectively weaken inhibitor binding without compromising the binding of substrates. …
Evaluating The Substrate-Envelope Hypothesis: Structural Analysis Of Novel Hiv-1 Protease Inhibitors Designed To Be Robust Against Drug Resistance, Madhavi Nalam, Akbar Ali, Michael Altman, G. S. Kiran Kumar Reddy, Sripriya Chellappan, Visvaldas Kairys, Aysegul Ozen, Hong Cao, Michael Gilson, Bruce Tidor, Tariq Rana, Celia Schiffer
Evaluating The Substrate-Envelope Hypothesis: Structural Analysis Of Novel Hiv-1 Protease Inhibitors Designed To Be Robust Against Drug Resistance, Madhavi Nalam, Akbar Ali, Michael Altman, G. S. Kiran Kumar Reddy, Sripriya Chellappan, Visvaldas Kairys, Aysegul Ozen, Hong Cao, Michael Gilson, Bruce Tidor, Tariq Rana, Celia Schiffer
Celia A. Schiffer
Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrate-envelope hypothesis which predicts that HIV-1 protease inhibitors that fit within the overlapping consensus volume of the substrates are less likely to be susceptible to drug-resistant mutations, as a mutation impacting such inhibitors would simultaneously impact the processing of substrates. To evaluate this hypothesis, over 130 HIV-1 protease inhibitors were designed and synthesized using three different approaches with and without substrate-envelope constraints. A subset of 16 representative inhibitors with binding affinities to wild-type …
Structure-Based Prediction Of Potential Binding And Nonbinding Peptides To Hiv-1 Protease, Nese Kurt, Turkan Haliloglu, Celia Schiffer
Structure-Based Prediction Of Potential Binding And Nonbinding Peptides To Hiv-1 Protease, Nese Kurt, Turkan Haliloglu, Celia Schiffer
Celia A. Schiffer
HIV-1 protease is a major drug target against AIDS as it permits viral maturation by processing the gag and pol polyproteins of the virus. The cleavage sites in these polyproteins do not have obvious sequence homology or a binding motif and the specificity of the protease is not easily determined. We used various threading approaches, together with the crystal structures of substrate complexes which served as template structures, to study the substrate specificity of HIV-1 protease with the aim of obtaining a better differentiation between binding and nonbinding sequences. The predictions from threading improved when distance-dependent interaction energy functions were …