MD simulations indicate Omicron P132H of SARS-CoV-2 M is a potential allosteric mutant involved in modulating the dynamics of catalytic site entry loop.

The SARS-CoV-2 main protease M, essential for viral replication is an important drug target. It plays a critical role in processing viral polyproteins necessary for viral replication assembly. One of the predominant SARS-CoV-2 M mutations of Omicron variant is Pro132His.

Over-representation analysis of angiogenic factors in immunosuppressive mechanisms in neoplasms and neurological conditions during COVID-19.

Background: Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus Disease (COVID-19) caused up to 33-55 % death rates in COVID-19 patients with malignant neoplasms and Alzheimer's disease. Given this scenario, we identified biological processes and pathways involved in various diseases which are most likely affected by COVID-19.

Community detection in Epstein-Barr virus associated carcinomas and role of tyrosine kinase in etiological mechanisms for oncogenesis.

Background: Epstein-Barr virus (EBV) affects more than 90% of global population. The role of the virus in causing infectious mononucleosis (IM) affecting B-cells and epithelial cells and in the development of EBV associated cancers is well documented. Investigating the associated interactions can pave way for the discovery of novel therapeutic targets for EBV associated lymphoproliferative (Burkitt's Lymphoma and Hodgkin's Lymphoma) and non-lymphoproliferative diseases (Gastric cancer and Nasopharyngeal cancer).

Physiological models to study the effect of molecular crowding on multi-drug bound proteins: insights from SARS-CoV-2 main protease.

Molecular Dynamics simulations are often used in drug design. However, such simulations do not account for the physiological environment of the receptor; hence overlook its impact on biomolecular interactions. To address this lacuna, we identified three objectives to pursue - develop models of physiological environment, study a drug-receptor complex in such environments, and identify methods to analyze these complicated simulations.

Aspergillus caespitosus ASEF14, an oleaginous fungus as a potential candidate for biodiesel production using sago processing wastewater (SWW).

Background: Oleaginous microorganisms are sustainable alternatives for the production of biodiesel. Among them, oleaginous fungi are known for their rapid growth, short life cycles, no light requirement, easy scalability, and the ability to grow in cheap organic resources. Among all the sources used for biodiesel production, industrial wastewater streams have been least explored.

How does clinical profile and outcome differ in patients with Chronic Kidney Disease undergoing percutaneous coronary revascularization according to the severity of CKD? - CHANNEL Study.

Background: Chronic kidney disease (CKD) is an independent risk factor for the development of coronary artery disease. We evaluated outcomes amongst patients of CKD undergoing percutaneous coronary intervention (PCI) as assessed on severity of CKD based on estimated glomerular filtration rate (eGFR) at the time of PCI.

Method And Materials: We analyzed 100 consecutive CKD patients who underwent PCI and were followed up for 1 year; an observational, prospective, open-label study.

Targeting allosteric pockets of SARS-CoV-2 main protease M.

Repurposing of antivirals is an attractive therapeutic option for the treatment of COVID-19. Main protease (M, also called 3 C-like protease (3CL) is a key protease of SARS-CoV-2 involved in viral replication, and is a promising drug target for antivirals. A major challenge to test the efficacy of antivirals is the conformational plasticity of M and its future mutation prone flexibility.

Bacterial Cellulose Nano Fiber (BCNF) as carrier support for the immobilization of probiotic, Lactobacillus acidophilus 016.

The present study was conducted to develop bacterial cellulose nanofibers (BCNF) and to evaluate its ability as a carrier material for the incorporation of the probiotic bacteria Lactobacillus acidophilus 016. Bacterial cellulose (5%) dissolved in trifluoroacetic acid (TFA) solution was amended with an equal volume of polyvinyl alcohol (PVA) solution to produce nanofibers via electrospinning. Fourier-transform infrared spectra of BCNF confirmed the absence of TFA used in the dissolution process.

Molecular crowding and conserved interface interactions of human argonaute protein-miRNA-target mRNA complex.

RNA interference (RNAi) has been of interest given its role in genetic interference. More significantly, recent studies provided evidence of it being one of the antiviral response mechanisms in humans. Argonaute (Ago) protein plays a central role in the RNA-induced silencing complex (RISC) that cleaves mRNA.

Insights into the effect of molecular crowding on the structure, interactions and functions of siRNA-PAZ complex through molecular dynamics studies.

siRNA molecules are well known to be involved in the post-transcriptional regulation of gene expression and play a key role in understanding the intricacies of eukaryotic gene regulation. While it is widely known that 3' end of siRNA binds to the PAZ domain of Argonaute proteins, it remains unclear whether the molecular crowding facilitates or hinders the overall siRNA-protein interactions during RNA interference. The biological interaction networks controlling the cellular functions of any biological cell may behave very differently in crowded environment as compared to the dilute conditions.

Advantages of novel BioMimeTM Sirolimus Eluting Coronary Stent system. Moving towards biomimicry.

Since the first reported use of percutaneous transluminal coronary angioplasty (PTCA), advancements in interventional cardiology arena have been fast paced. Within the last ten years, these developments have been exponential. Developers & clinicians are fast adapting from the learning curve awarded by the time course of DES evolution.

Stability and dynamics of domain-swapped bovine-seminal ribonuclease.

The proteins of the ribonuclease-A (RNase-A) family are monomeric, with the exception of bovine-seminal ribonuclease (BS-RNase). BS-RNase is formed by swapping the N-terminal helices across the two monomeric units. A molecular-dynamics (MD) study has been performed on the protein for a simulation time of 5.

Dynamics of the native and the ligand-bound structures of eosinophil cationic protein: network of hydrogen bonds at the catalytic site.

Eosinophil Cationic Protein (ECP) is sequentially and structurally similar to ribonuclease A (RNase A). It belongs to the RNase A family of proteins and the RNA catalysis is essential to its biological function. In the present study, we have generated the dinucleotide-bound structures of ECP by docking the dinucleotides to a number of molecular dynamics (MD) generated ECP structures.

Conformational transitions in eosinophil cationic protein: a molecular dynamics study in aqueous environment.

Extensive molecular dynamics simulations have been performed on eosinophil cationic protein (ECP). The two structures found in the crystallographic dimer (ECPA and ECPB) have been independently simulated. A small difference in the pattern of the sidechain hydrogen bonds in the starting structure has resulted in interesting differences in the conformations accessed during the simulations.

Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study.

It is known that water molecules play an important role in the biological functioning of proteins. The members of the ribonuclease A (RNase A) family of proteins, which are sequentially and structurally similar, are known to carry out the obligatory function of cleaving RNA and individually perform other diverse biological functions. Our focus is on elucidating whether the sequence and structural similarity lead to common hydration patterns, what the common hydration sites are and what the differences are.

Computer modeling and molecular dynamics simulations of ligand bound complexes of bovine angiogenin: dinucleotide topology at the active site of RNase a family proteins.

We have undertaken the modeling of substrate-bound structures of angiogenin. In our recent study, we modeled the dinucleotide ligand binding to human angiogenin. In the present study, the substrates CpG, UpG, and CpA were docked onto bovine angiogenin.