The SARS-CoV-2 is the causative agent of COVID-19 pandemic that is causing a global health emergency. The lack of targeted therapeutics and limited treatment options have triggered the scientific community to develop new vaccines or small molecule therapeutics against various targets of SARS-CoV-2. The main protease (Mpro) is a well characterized and attractive drug target because of its crucial role in processing of the polyproteins which are required for viral replication. In order to provide potential lead molecules against the Mpro for clinical use, we docked a set of 65 bioactive molecules of Tea plant followed by exploration of the vast conformational space of protein-ligand complexes by long term molecular dynamics (MD) simulations (1.50 µs). Top three bioactive molecules (Oolonghomobisflavan-A, Theasinensin-D, and Theaflavin-3-O-gallate) were selected by comparing their docking scores with repurposed drugs (Atazanavir, Darunavir, and Lopinavir) against SARS-CoV-2. Oolonghomobisflavan-A molecule showed a good number of hydrogen bonds with Mpro and higher MM-PBSA binding energy when compared to all three repurposed drugs molecules during the time of simulation. Further, MD simulations and MM-PBSA studies showed Oolonghomobisflavan-A as a potential bioactive molecule to act as an inhibitor for the Mpro of SARS-CoV-2. Graphical Abstract

Computational prediction of cancer associated SNPs from the large pool of SNP dataset is now being used as a tool for detecting the probable oncogenes, which are further examined in the wet lab experiments. The lack in prediction accuracy has been a major hurdle in relying on the computational results obtained by implementing multiple tools, platforms and algorithms for cancer associated SNP prediction. Our result obtained from the initial computational compilations suggests the strong chance of Aurora-A G325W mutation (rs11539196) to cause hepatocellular carcinoma. The implementation of molecular dynamics simulation (MDS) approaches has significantly aided in raising the prediction accuracy of these results, but measuring the difference in the convergence time of mutant protein structures has been a challenging task while setting the simulation timescale. The convergence time of most of the protein structures may vary from 10 ns to 100 ns or more, depending upon its size. Thus, in this work we have implemented 200 ns of MDS to aid the final results obtained from computational SNP prediction technique. The MDS results have significantly explained the atomic alteration related with the mutant protein and are useful in elaborating the change in structural conformations coupled with the computationally predicted cancer associated mutation. With further advancements in the computational techniques, it will become much easier to predict such mutations with higher accuracy level. The genetic mutations in human were shown by single nucleotide polymorphisms (SNPs), and several of them were supposed to cause deleterious and disease associated phenotypic effects. The ability to differentiate between pathogenic and neutral nsSNPs (non-synonymous Single Nucleotide Polymorphisms) using computational approaches could significantly help in targeting the disease associated mutations. In this work we applied computational tools to prioritize the most deleterious disease associated mutation in Aurora kinases. We used sequence and structural based approaches to refine cancer associated mutation and applied a long term simulation (MDS) to understand the changes in structural conformation and function of the aurora kinases upon mutation. From the 200 ns MD simulation, we suggested that the G325W mutation induced major phenotypic damages in aurora-A kinase protein and altered its structural behaviour in 3D space, which might play an important role in inducing hepatocellular carcinoma.

Oculocutaneous albinism (OCA) is an autosomal recessive disorder caused by either complete lack of or a reduction of melanin biosynthesis in the melanocytes. The OCA1A is the most severe type with a complete lack of melanin production throughout life, while the milder forms OCA1B, OCA2, OCA3, and OCA4 show some pigment accumulation over time. Mutations in TYR, OCA2, TYRP1, and SLC45A2 are mainly responsible for causing oculocutaneous albinism. Recently, two new genes SLC24A5 and C10orf11 are identified that are responsible to cause OCA6 and OCA7, respectively. Also a locus has been mapped to the human chromosome 4q24 region which is responsible for genetic cause of OCA5. In this paper, we summarized the clinical and molecular features of OCA genes. Further, we reviewed the screening of pathological mutations of OCA genes and its molecular mechanism of the protein upon mutation byin silicoapproach. We also reviewed TYR (T373K, N371Y, M370T, and P313R), OCA2 (R305W), TYRP1 (R326H and R356Q) mutations and their structural consequences at molecular level. It is observed that the pathological genetic mutations and their structural and functional significance of OCA genes will aid in development of personalized medicine for albinism patients.

The over-expression of cyclin-dependent kinase 2 is related to multiple cancers, which has led them to be a widely researched topic for nearly two decades. The prime focus of the present research is to design new potent and specific inhibitors against CDK2 to suppress cancer cell proliferation. In this study, we have chosen Flavopiridol, SU9516, and CVT-313 as standard inhibitors to compare with in-house synthesized pyrrolone-fused benzosuberene (PBS) compounds. We scrutinized Ligand2 as a selective inhibitor of CDK2 without off-target binding (CDK1 and CDK9) based on ligand efficiency and binding affinity. Interpretation of dynamic simulations and binding free energy studies unveiled that Ligand2 has a stable and equivalent free energy to standard inhibitors. These outcomes led towards positioning a potential natural molecule as selective inhibitor for CDK2 with low side effects. GRAPHICAL ABSTRACT Communicated by Ramaswamy H. Sarma