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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus possessing a spike (S) protein that facilitates the entry of the virus into human cells. The emergence of highly transmissible and fit SARS-CoV-2 variants has been driven by the positive selection of mutations within the S-protein. Notable among these variants are alpha, beta, gamma, delta, and omicron (BA.1), with the latter contributing to significant global health challenges and impacting populations worldwide. Recently, a novel subvariant of BA.1, named BF.7, has surfaced, purportedly exhibiting elevated transmissibility and infectivity rates. In order to comprehend and compare the transmissibility and disease progression characteristics of distinct SARS-CoV-2 variants, we performed an extensive comparative analysis utilizing all-atom molecular dynamics (MD) simulations (in triplicate) to investigate the structural, dynamic, and binding features of BA.1, BA.4/5, and BF.7. Our simulation findings, energetic analysis, and assessment of physicochemical properties collectively illuminate the dominance of the BA.1 variant over the others, a trend that is further substantiated by the sustained global prevalence of BA.1 relative to BA.4/5 and BF.7. Additionally, our simulation results align well with the reported cryoelectron microscopy (cryo-EM) structural data and epidemiological characteristics obtained from the Global Initiative on Sharing All Influenza Data (GISAID). This study presents a comprehensive comparative elucidation of the critical structural, dynamic, and binding attributes of these variants, providing insights into the predominance of BA.1 and its propensity to continuously generate numerous novel subvariants., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Protein aggregation through homotypic interactions is a hallmark of neurodegenerative diseases. Recently, heterotypic amyloid interactions through cross-seeding were found to modify protein aggregation and are reported in the brain of Alzheimer's disease patients. However, whether amyloid-β (Aβ) assembly can be modulated by heterotypic interactions between Aβ aggregation-prone regions (APRs) and short homologous segments in unrelated human proteins needs to be elucidated. A recent study revealed that the aggregation kinetics and fibril morphology of Aβ is altered by heterotypic interactions between its APRs and homologous segments of unrelated proteins. The data provide novel insights into the structure, origins, and aggregation principles of the amyloid assembly process.

The COVID-19 pandemic has emerged as a global medico-socio-economic disaster. Given the lack of effective therapeutics against SARS-CoV-2, scientists are racing to disseminate suggestions for rapidly deployable therapeutic options, including drug repurposing and repositioning strategies. Molecular dynamics (MD) simulations have provided the opportunity to make rational scientific breakthroughs in a time of crisis. Advancements in these technologies in recent years have become an indispensable tool for scientists studying protein structure, function, dynamics, interactions, and drug discovery. Integrating the structural data obtained from high-resolution methods with MD simulations has helped in comprehending the process of infection and pathogenesis, as well as the SARS-CoV-2 maturation in host cells, in a short duration of time. It has also guided us to identify and prioritize drug targets and new chemical entities, and to repurpose drugs. Here, we discuss how MD simulation has been explored by the scientific community to accelerate and guide translational research on SARS-CoV-2 in the past year. We have also considered future research directions for researchers, where MD simulations can help fill the existing gaps in COVID-19 research.

Parkinson's disease is associated with aggregation of pathological α-synuclein (αSyn) proteins. The central hydrophobic region of αSyn, called NAC, encodes the segment that is crucial and sufficient for the toxic aggregation of αSyn. However, if any other region, including the NAC flanking region, modulates αSyn, aggregation is still unknown. A master-regulator sequence motif is now identified that is critical to controlling the aggregation of the αSyn NAC region. Interestingly, this region was also found to be important for membrane vesicle fusion. This master-regulator region could be targeted to prevent αSyn aggregation. The results reveal several unanswered questions about the αSyn aggregation mechanism.

Fascioliasis, a neglected foodborne disease caused by liver flukes (genus Fasciola ), affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of these flukes. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ∼1.04 Gb with an N50 and N90 of 129 and 149 kb, respectively. A total of 20 858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. The pathway included all of the genes of glycolysis, Krebs cycle, and fatty acid metabolism but lacked the key genes of the fatty acid biosynthesis pathway. This indicates that the fatty acid required for survival of the fluke may be acquired from the host bile. It may be hypothesized that the relatively larger F. gigantica genome did not evolve through genome duplications but rather is interspersed with many repetitive elements. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

The deposition of amyloid-β (Aβ) plaques and tau-based neurofibrillary tangles is a neuropathological feature of Alzheimer's disease (AD). While studies have shown that the Aβ and tau interaction results in elevated AD pathology, the molecular linkage and mechanism of interaction of Aβ and tau are unclear. A recent study demonstrated the direct interaction between the Aβ core and specific regions of tau that facilitates pathological cross-seeding via a shared epitope. The data suggest that targeting the common epitope could be a more effective treatment strategy rather than targeting only Aβ or only tau. The findings have an important clinical significance for AD and related tauopathies.