Therapeutic development by repurposing drugs targeting SARS-CoV-2 spike protein interactions by simulation studies

The human-to-human transmitted respiratory illness in COVID-19 affected by the pathogenic Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2), which appeared in the last of December 2019 in Wuhan, China, and rapidly spread in many countries. Thereon, based on the urgent need for therapeutic molecules, we conducted in silico based docking and simulation molecular interaction studies on repurposing drugs, targeting SARS-CoV-2 spike protein. Further, the best binding energy of doxorubicin interacting with virus spike protein (PDB: 6VYB) was observed to be −6.38 kcal/mol and it was followed by exemestane and gatifloxacin. The molecular simulation dynamics analysis of doxorubicin, Reference Mean Square Deviation (RMSD), Root Mean Square fluctuation (RMSF), Radius of Gyration (Rg), and formation of hydrogen bonds plot interpretation suggested, a significant deviation and fluctuation of Doxorubicin-Spike RBD complex during the whole simulation period. The Rg analysis has stated that the Doxorubicin-Spike RBD complex was stable during 15,000–35,000 ps MDS. The results have suggested that doxorubicin could inhibit the virus spike protein and prevent the access of the SARS-CoV-2 to the host cell. Thus, in-vitro/in-vivo research on these drugs could be advantageous to evaluate significant molecules that control the COVID-19 disease.     

An Immuno-informatics driven Epitope study from the molecular interaction of JEV non-structural (NS) proteins with Ribophorin (RPN)

Japanese encephalitis (JE) is an acute viral infection of the central nervous system where the JE virus infects the lumen of the endoplasmic reticulum (ER) and rapidly accumulates substantial amount of seven different nonstructural proteins (NS). These NS proteins tend to bind on a glycoprotein receptor, ribophorin (RPN) resulting in the malfunctioning of ER in host cells, subsequently triggering an unfolded protein response. Therefore, it is of interest to predict the best possible antigenic determinants in the NS protein capable of eliciting immune response as a strategy to combat JE. Hence, it is our interest to explore the most potent NS protein among all showing the best possible molecular interaction with the RPN receptor present on ER. However, the structures of these NS protein and RPN are currently unknown. Thus, we modeled their structures using the established homology modeling techniques in the MODELLER 9v10 software. The molecular docking of NS proteins with RPN was subsequently completed using the Discovery Studio 2.5 software suite. The docked conformations of RPN with NS were further analyzed and its graphical interpretations were presented for identifying the most potential NS protein for efficient epitope activity. Further, the B cell epitopes were mapped using BCPred and the predicted epitope regions are documented. The data presented in this report provides useful insights towards the design and development of potential epitopes to generate a vaccine candidate against JEV.     

Effect of testosterone on epididymal proteins in castrated rhesus monkeys

The effect of testosterone on regulation of epididymal protein synthesis has been investigated in castrated rhesus monkeys (Macaca mulatta). The proteins in the treated monkeys were characterized using polyacrylamide gel electrophoresis (under nondenaturing and denaturing conditions) and electrofocusing. At least four distinct proteins have been shown to be synthesized by the monkey epididymis under testosterone influence. Two of these proteins were detected following two days of testosterone treatment while the other two proteins were detected after a six-day treatment period. None of these proteins was detectable in monkeys treated with estradiol for six days. Electrofocusing of epididymal cytosol proteins from untreated and testosterone-treated and castrated monkeys also confirmed the presence of four androgen-dependent proteins in this species. The isoelectric points of these proteins were shown to range between 5.8 and 6.4. The molecular weights of these proteins were found to vary between 47,500 and 66,000. The in vitro incorporation of ³H-labeled amino acids was markedly greater in the androgen-primed epididymis as compared with the control tissue.