Biology subjects

Vaithyanathan, P. A.

Publications and source records attributed to Vaithyanathan, P. A..

2 recordsLinked to original sources

bioRxiv2023

Active and Allosteric Site Binding MOLECULAR MECHANICS-QUANTUM MECHANICS studies of STEVIOSIDE Derivative in PCSK9 Protein Intended to provide a safe Antilipidemic agent

Interaction of low-density lipoprotein receptors with proprotein convertase subtilisin/ kexin type 9 (PCSK9) plays a vital role in causing atherosclerosis. It is the hidden precursor of clinical myocardial infarction (MI), stroke, CVD and estimates 60% of deaths worldwide. The current need is to design small molecules to prevent the interaction between PCSK9 with LDL receptors. This study aims to evaluate the PCSK9 antagonistic effect of a derivative of Stevioside (also referred as Methylidene tetracyclo derivative) and atorvastatin. Also, a comparative study was performed to analyze the binding interaction of molecules inside the active and allosteric sites of PCSK9. The RCSB downloaded protein 7S5H and above said ligands were optimized to the local minima energy level and docked inside the active and allosteric sites. The stability of non-bonded interaction of complex was analyzed using Desmond MD simulation studies. The results of docking showed that the Methylidene tetracyclo molecule possesses a two-fold higher affinity of -10.159 kcal/mol in the active site and -10.824 kcal/mol in the allosteric site. The Phe377 amino acid made the Methylidene tetracyclo molecule orient inside the active site. Nine H-bonds with 5 amino acids of allosteric site increase the binding affinity compared to Atorvastatin. The MD simulation studies exposed that the nonbonded interaction of Methylidene tetracyclo molecule was stable throughout 100ns. This confirms the Methylidene tetracyclo molecule will be the better hit as well as the lead molecule to inhibit PCSK9 protein.

bioinformatics↗

bioRxiv2021

Identification of binding interaction between Curcumin derivative and PERK13 Proline rich receptor like protein kinase protein using In silico docking techniques - to help plants tackle salt water

IntroductionArabidopsis thaliana, mouse ear cress or thale cress are small flowering plants included in the cruciferae family. They comprise of various characteristics such as diploid genetics, small genome size, rapid growth cycle, and relatively low repetitive DNA content, making it a perfect model for plant genome projects. ObjectiveThe aim of this present Insilico research study is to carry out molecular drug docking studies between PERK13-Proline rich receptor like protein kinase and De O Acetylated Curcumin Di Galactose or di-galactosylated curcumin, a derivative of curcumin. PERK13 protein is considered to play a significant role in helping plants tackle salinity levels in water. MethodsIn this study, protein modelling tools and servers are used to model the 3D structure and the same is validated using Protein structure validation tools. Automated drug docking servers were used to dock the modelled protein with the chemical compound to analyse the electrostatic (H bond) interaction between PERK13 and De O Acetylated Curcumin Di Galactose, a better water-soluble compound than curcumin. The docked structure was visualized using an advanced molecular visualization tool. Results and DiscussionThe overall results obtained from this study on De O Acetylated Curcumin Di Galactose and PERK13 protein shows that De O Acetylated Curcumin Di Galactose, directly binds with the active site and other potentially binding regions of PERK13. Hence, it is concluded that De O Acetylated Curcumin Di Galactose could potentially play a vital role in future research related to the problem of helping the plants tackle increased saline levels in water.

bioinformatics↗