Sample projects:
Project 01
Characterization of kisspeptin receptor structural features and its plausible mechanism of activation by kisspeptin :
Project Description: We report the characterization of kisspeptin receptor (kiss1r) – an essential gatekeeper for reproduction and onset of puberty in vertebrates via cloning it from the brain of catla catla. The full-length cDNA sequence of kiss1r is 1786 bp consist of 5'-UTR (untranslated region) of 261 bp, 3'-UTR of 424 bp and open reading frame of 1101 bp respectively. Open reading frame (ORF) of 1101 bp encoding a putative protein of 366 amino acids. Basal tissue expression pattern of kiss1r mRNA confirmed that it is mainly expressed in brain, and testes. We also report the structure of the kiss1r, along with plausible activation mechanism of this receptor by kisspeptin - a neuropeptide; using computational modelling and molecular dynamic simulations approach of multiple 100 ns of timescale. Our modelling and simulations studies have shed light on the molecular level of interactions suggesting that SER10; ARG347; GLU191; ARG192; GLN206; SER16; GLY317; GLU191 and TYR188 residues could be crucial role players in initial binding of receptor and the kisspeptin towards leading to allosteric modulatory effects of kisspeptin on the receptor. To best our knowledge, this is the first report on computational modelling and molecular dynamic simulations of kiss1r in animals.
Project 02
Noninvasive Cellular Internalization Of Silver Molecules By Chitosan Nanoneedles: A Novel Nanocarrier :
Project Description: We explore with Molecular modeling, Dynamics simulations and a statistical model, for theability of Chitosan nanoneedles to be internalized into a model lipid bilayer as a function of theirlength; keeping in view of their applications in the field of biomedicine for advanced targeteddrug delivery. In the present study, we have computationally modeled and studied the structuralgeometry and the stability of Chitosan Nanoneedles (CNN) formed by 4, 6, and 8 subunits. Wereported the molecular surface analysis of the modeled CNN’s along with Molecular Dynamic(MD) simulations studies towards revealing the non-invasive cellular internalization potential ofthese chitosan nanoneedles and a case study has been carried to study the ability of CNN’s totranslocate silver nanoparticles across membrane. The present results are strongly in support offurther exploration of 8 subunits based CNN’s for their application as target drug deliveryvehicles. The hydrophilicity of the CNN’s has been attributed as one of the key factorsresponsible for the internalization process. Moreover, our MD simulation studies marched theability of Chitosan Nanoneedles to translocate silver nanoparticles through biological membranein a similar manner that resembles cell-penetrating peptides.
Project 03
Molecular docking and dynamic simulation studies evidenced plausible immunotherapeutic anticancer property by Withaferin A targeting indoleamine 2,3-dioxygenase :
Project Description: Indoleamine 2,3-dioxygenase (IDO) is emerging as an important new therapeutic drug target for the treatment of cancercharacterized by pathological immune suppression. IDO catalyzes the rate-limiting step of tryptophan degradation alongthe kynurenine pathway. Reduction in local tryptophan concentration and the production of immunomodulatory tryptophanmetabolites contribute to the immunosuppressive effects of IDO. Presence of IDO on dentritic cells in tumor-draininglymph nodes leading to the activation of T cells toward forming immunosuppressive microenvironment for thesurvival of tumor cells has confirmed the importance of IDO as a promising novel anticancer immunotherapy drug target.On the other hand, Withaferin A (WA) – active constituent of Withania Somnifera ayurvedic herb has shown to behaving a wide range of targeted anticancer properties. In the present study conducted here is an attempt to explore thepotential of WA in attenuating IDO for immunotherapeutic tumor arresting activity and to elucidate the underlying modeof action in a computational approach. Our docking and molecular dynamic simulation results predict high binding affinityof the ligand to the receptor with up to −11.51 kcal/mol of energy and 3.63 nM of IC50 value. Further, de novomolecular dynamic simulations predicted stable ligand interactions with critically important residues SER167; ARG231;LYS377, and heme moiety involved in IDO’s activity. Conclusively, our results strongly suggest WA as a valuable smallligand molecule with strong binding affinity toward IDO.
Project 04
A comprehensive Insilico analysis on the structural and functional impact of SNPs in the Congenital Heart Defects associated with NKX2-5 Gene - A Molecular Dynamic Simulation Approach::
Project Description: Congenital Heart Defects (CHD) is an important cause of childhood morbidity and mortality worldwide, presented as structural defects in the heart and blood vessels during birth. Many SNPs in different genes have been associated with various types of congenital heart defects. NKX 2-5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including atrial septal defect (ASD), atrial ventricular block (AVB), tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional misbehaviour of its encoded protein. In this study, we retrieved SNPs from the dbSNP database, followed by identificationof potentially deleterious non-synonymous Single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein, and therefore, altering its biological function. The most important SNP that was found using our approach was rs137852685 (R161P), which was predicted to cause the most damage to the protein’s structural features. Mapping nsSNPs in genes such as the NKX 2-5 gene provides valuable information about individuals carrying those polymorphisms, where such variations can be used as diagnostic markers.
Project 05
Ligand and Structure Based Virtual Screening Studies to Identify Potent Inhibitors against Herpes Virus Targeting gB-gH-gL Complex Interface as a Novel Drug Target:
Project Description: Glycoproteins gB and gHgL are highly conserved cell entry machinery, which are involved in attachment and fusion of herpes virus to the host cell. gB is a homotrimer with structural characteristics to undergo conformational rearrangement when triggered, thus inferred to be the effector of viral fusion, whereas, gHgL glycoprotein is a heterodimer complex proposed to be the activator of gB glycoprotein, probably through direct binding. Critical dependence of herpes virus on the formation of this gB-gH-gL complex for its entry into the host cell, making this interface a promising anti herpes drug target. Arresting this complex formation by blocking the interactions between the key residues of these glycoproteins seems to be the most promising mechanism to inhibit the viral infection. From our previous research, we identified (3-Chloro Phenyl) Methyl3,4,5 Trihydroxybenzoate (CPMTHB) as a potent inhibitor for gHgL heterodimer complex. In this present study, a ligand based virtual screening with a threshold of >50% similarity was performed, based on the structure of CPMTHB using ZINC database, and resulted 505 compounds were utilized to perform a structure based virtual screening on glycoproteins gB and gHgL complex separately, targeting key residues involved in their binding activity. 31 compounds were identified as better inhibitors based on free binding energy and ADMET constraints, compared to CPMTHB. The capability of CPMTHB and 31 better compounds to disrupt gB-gH-gL complex formation was evident from our flexible and semiflexible docking studies, suggesting the possible mode of action of these tested compounds to inhibit herpes virus, is by attenuating this complex formation, thus leaving significant evidence in support of this complex as a promising anti herpes drug target.