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Flexibility of Important HIV-1 Targets and in silico Design of anti-HIV Drugs

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Background: The functions of all proteins in the biological world are attributed to their flexibility. The highly dynamical nature of proteins allows the binding of various endogenous ligands and substrates that are essential to carry out normal functions in all organisms. Since proteins play an indispensable role in the chemistry that sustains life, it is imperative to understand their functions and more importantly their dynamic behavior and harness this knowledge to design effective chemical agents as therapeutic aids.

Objective: The purpose of this review is to discuss the importance of considering flexibility in molecular modeling tools, particularly molecular docking and Quantitative Structure-Activity Relationship (QSAR), to accurately predict the binding conformation of drugs to their protein targets. More emphasis is laid on understanding the importance of modeling protein flexibility of crucial HIV-1 protein targets that has led to the design of potent anti-HIV drugs by molecular docking and QSAR.

Conclusion: We have emphasized the importance of incorporating receptor flexibility in molecular docking and QSAR studies. The benefits of allowing receptor flexibility during docking small molecules are vividly evident as the rate of picking false positives is significantly reduced. Similarly, the mechanism of binding and the type of interactions that dominate to exhibit tight binding can be explained by higher dimensional QSAR models, i.e., 4D-QSAR, which includes conformational flexibility.
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Keywords: HIV-1 reverse transcriptase; HIV-1 integrase; HIV-1 protease; Protein flexibility; QSAR; ensemble docking; molecular docking; molecular dynamics

Document Type: Review Article

Publication date: April 1, 2018

More about this publication?
  • Current Chemical Biology aims to publish full-length and mini reviews on exciting new developments at the chemistry-biology interface, covering topics relating to Chemical Synthesis, Science at Chemistry-Biology Interface and Chemical Mechanisms of Biological Systems.

    Current Chemical Biology covers the following areas: Chemical Synthesis (Syntheses of biologically important macromolecules including proteins, polypeptides, oligonucleotides, oligosaccharides etc.; Asymmetric synthesis; Combinatorial synthesis; Diversity-oriented synthesis; Template-directed synthesis; Biomimetic synthesis; Solid phase biomolecular synthesis; Synthesis of small biomolecules: amino acids, peptides, lipids, carbohydrates and nucleosides; and Natural product synthesis).

    Science at Chemistry-Biology Interface (Chemical informatics; Macromolecular catalysts and receptors; Enzymatic synthesis; Biosynthetic engineering; Combinatorial biosynthesis; Plant cell based chemistry; Bacterial and viral cell based chemistry; Chemistry of cellular processes in plants/animals; Receptor chemistry; Cell signaling chemistry; Drug design through understanding of disease processes; Synthetic biology; New high throughput screening techniques; Small molecular array fabrication; Chemical genomics; Chemical and biological approaches to carbohydrates proteins and nucleic acids design; Chemical and biological regulation of biosynthetic pathways; and Unnatural biomolecular analogs).
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