Homology modeling, molecular dynamics and atomic level interaction study of snake venom 5′ nucleotidase

• Published in: Journal of molecular modeling 2014-03, Vol.20 (3), p.2156-2156, Article 2156
• Main Authors: Arafat, A. Syed Yasir, Arun, A., Ilamathi, M., Asha, J., Sivashankari, P. R., D’Souza, Cletus J. M., Sivaramakrishnan, V., Dhananjaya, B. L.
• Format: Article
• Language: English
• Subjects: 5'-Nucleotidase - chemistry; 5'-Nucleotidase - genetics; 5'-Nucleotidase - metabolism; Amino Acid Sequence; Animals; Benzaldehydes - chemistry; Benzaldehydes - metabolism; Binding Sites; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Ligands; Molecular Dynamics Simulation; Molecular Medicine; Molecular Sequence Data; Molecular Structure; Original Paper; Protein Binding; Protein Interaction Mapping; Protein Structure, Secondary; Protein Structure, Tertiary; Pyrones - chemistry; Pyrones - metabolism; Sequence Homology, Amino Acid; Snake Venoms - enzymology; Static Electricity; Theoretical and Computational Chemistry; Vanillic Acid - chemistry; Vanillic Acid - metabolism
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-014-2156-1

5′ Nucleotidase (5′ NUC) is a ubiquitously distributed enzyme known to be present in snake venoms (SV) that is responsible primarily for causing dysregulation of physiological homeostasis in humans by inducing anticoagulant effects and by inhibiting platelet aggregation. It is also known to act synergistically with other toxins to exert a more pronounced anti-coagulant effect during envenomation. Its structural and functional role is not yet ascertained clearly. The 3D structure of snake venom 5′ nucleotidase (SV-5′ NUC) is not yet known and was predicted by us for the first time using a comparative homology modeling approach using Demansia vestigiata protein sequence. The accuracy and stability of the predicted SV-5′ NUC structure were validated using several computational approaches. Key interactions of SV-5′ NUC were studied using experimental studies/molecular docking analysis of the inhibitors vanillin, vanillic acid and maltol. All these inhibitors were found to dock favorably following pharmacologically relevant absorption, distribution, metabolism and excretion (ADME) profiles. Further, atomic level docking interaction studies using inhibitors of the SV-5′ NUC active site revealed amino acid residues Y65 and T72 as important for inhibitor–(SV-5′ NUC) interactions. Our in silico analysis is in good agreement with experimental inhibition results of SV-5′ NUC with vanillin, vanillic acid and maltol. The present study should therefore play a guiding role in the experimental design of new SV-5′ NUC inhibitors for snake bite management. We also identified a few pharmacophoric features essential for SV-5′ NUC inhibitory activity that can be utilized further for the discovery of putative anti-venom agents of therapeutic value for snake bite management. Figure Three-dimensional modeled structure of SV-5′NUC1