Published in Computers in biology and medicine
The vaccines used against SARS-CoV-2 by now have been able to develop some neutralising antibodies in the vaccinated population and their effectiveness has been challenged by the emergence of the new strains with numerous mutations in the spike protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus which contains Recep...
Published in Computers in biology and medicine
Since the new variant of SARS-CoV-2, Omicron (BA.1) has raised serious concerns, it is important to investigate the effects of mutations in the NTD and RBD domains of the spike protein for the development of COVID-19 vaccines. In this study, computational analysis of the Wuhan and Omicron NTDs and RBDs in their unbound and bound states to mAb 4A8 a...
Published in Saudi journal of biological sciences
Maternal embryonic leucine zipper kinase (MELK) is of vital importance due to its significant role in cancer development and its association with poor prognosis in different cancers. Here, we employed several computer aided drug design approaches to shortlist potential binding molecules of MELK. For virtual screening, asinex oncology library (conta...
Published in Biochimica et Biophysica Acta. Biomembranes
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Published in Molecular Diversity
Novel drug compound hunting was carried out for SARS-CoV-2 proteins with low mutation susceptibility. The probability of escape mutation and drug resistance is lower if conserved microbial proteins are targeted by therapeutic drugs. Mutation rate of all SARS-CoV-2 proteins were analyzed via multiple sequence alignment Non-Structural Protein 13 and ...
Published in Computational and Structural Biotechnology Journal
The effect of different branching types of glycosylation on the structure and dynamics of the horseradish peroxidase (HRP) and an engineered split horseradish peroxidase (sHRP) was studied using all-atom molecular dynamics (MD) simulations. Although tertiary structures of both proteins are stable in the presence, as well as in the absence of glycan...
Properties of polyhydroxycompounds, such as sugars and polyols, which are used to stabilize various pharmaceuticals and biological objects during freezing, desiccation, and storage, depend on water content. In this investigation, glycerol-water mixtures containing 40 to 0 wt% water are studied by FTIR spectroscopy and molecular dynamics simulation....
Published in The Journal of membrane biology
The importance of disulphide bond in mediating viral peptide entry into host cells is well known. In the present work, we elucidate the role of disulphide (SS) bond in partitioning mechanism of membrane-active Hepatitis A Virus-2B (HAV-2B) peptide, which harbours three cysteine residues promoting formation of multiple SS-bonded states. The inclusio...
Published in Journal of Molecular Structure
In the fall of 2019, a new type of coronavirus took place in Wuhan city, China, and rapidly spread across the world and urges the scientific community to develop antiviral therapeutic agents. In our effort we have synthesized a new hydrazide derivative, ( E )- N' -(1-(4-bromophenyl)ethylidene)-2-(6-methoxynaphthalen-2-yl)propanehydrazide for this p...
Published in Computational and Structural Biotechnology Journal
Cystic fibrosis (CF) is a frequent genetic disease in Caucasians that is caused by the deletion of F508 (ΔF508) in the nucleotide binding domain 1 (NBD1) of the CF transmembrane conductance regulator (CFTR). The ΔF508 compromises the folding energetics of the NBD1, as well as the folding of three other CFTR domains. Combination of FDA approved corr...
