Inhibitory effect of compounds extracted from Monochoria hastata (L.) Solms on SARS-CoV-2 main protease: An insight from molecular docking and MD-simulation studies

Computational Insights into Acrylamide Fragment Inhibition of SARS-CoV-2 Main Protease

The pathogen of COVID-19, SARS-CoV-2, has caused a severe global health crisis. So far, while COVID-19 has been suppressed, the continuous evolution of SARS-CoV-2 variants has reduced the effectiveness of vaccines such as mRNA-1273 and drugs such as Remdesivir. To uphold the effectiveness of vaccines and drugs prior to potential coronavirus outbreaks, it is necessary to explore the underlying mechanisms between biomolecules and nanodrugs. The experimental study reported that acrylamide fragments covalently attached to Cys145, the main protease enzyme (Mpro) of SARS-CoV-2, and occupied the substrate binding pocket, thereby disrupting protease dimerization. However, the potential mechanism linking them is unclear. The purpose of this work is to complement and validate experimental results, as well as to facilitate the study of novel antiviral drugs. Based on our experimental studies, we identified two acrylamide fragments and constructed corresponding protein-ligand complex models. Subsequently, we performed molecular dynamics (MD) simulations to unveil the crucial interaction mechanisms between these nanodrugs and SARS-CoV-2 Mpro. This approach allowed the capture of various binding conformations of the fragments on both monomeric and dimeric Mpro, revealing significant conformational dissociation between the catalytic and helix domains, which indicates the presence of allosteric targets. Notably, Compound 5 destabilizes Mpro dimerization and acts as an effective inhibitor by specifically targeting the active site, resulting in enhanced inhibitory effects. Consequently, these fragments can modulate Mpro's conformational equilibrium among extended monomeric, compact, and dimeric forms, shedding light on the potential of these small molecules as novel inhibitors against coronaviruses. Overall, this research contributes to a broader understanding of drug development and fragment-based approaches in antiviral covalent therapeutics.

Management strategies of translocated pondweed Monochoria hastata and its ecological and economic impacts

Understanding the impacts of, and options for, controlling invasive species is crucial to their management. Wetlands are a widely invaded ecosystem, since dispersal of aquatic species is facilitated by seasonal flooding. This study evaluated the effects of the translocated pondweed Monochoria hastata on fish and rice production in two wetlands of Bangladesh over six years (2017-2022). Fish and rice production were compared between control (negligible M. hastata) and three treatments under different M. hastata management methods comprising manual-, herbicide- and mechanical-treatment. Density of M. hastata increased significantly in all treatment groups over time in both wet and dry seasons. However, M. hastata density was lower by 270% in the dry season than the wet season. For fishes, a negative relationship between M. hastata density and fish production was recorded for snakeheads and catfishes, the most saleable fishes, whereas a mixed pattern was recorded for barbs and minnows across treatments. A positive relationship occurred between the density of M. hastata and production of the most common fish, mud eel, and therefore, the overall fish production increased in all treatment groups. Compared to control plots, rice production was lower in M. hastata infested plot groups. Among the M. hastata infested plot groups, rice production in herbicide-and mechanical-treatment groups was similar but lower than the manual-treatment group. Although manual-treatment plots yielded greater rice production, the weed management cost was also higher. This study provides evidence that translocated M. hastata can be of an invasive nature and impact rice production, not only by reducing yield but also by increasing the production costs through additional management for M. hastata control. Its presence in wetlands in Bangladesh can increase overall fish production due to the overriding influence of increased mud eel yield which has little demand locally but can decrease the species of high demand (e.g. snakehead and catfish). None of the existing control measures are effective in controlling M. hastata. Further research is needed on better management approaches for both agricultural and fish production in areas invaded by M. hastata.

SARS-CoV-2 main protease mutation analysis via a kinematic method

The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic. COVID-19 continues to cause millions of deaths globally in part due to immune-evading mutations. SARS-CoV-2 main protease (Mpro) is an important enzyme for viral replication and potentially an effective drug target. Mutations affect the dynamics of enzymes and thereby their activity and ability to bind ligands. Here, we use kinematic flexibility analysis (KFA) to identify how mutations and ligand binding changes the conformational flexibility of Mpro. KFA decomposes macromolecules into regions of different flexibility near-instantly from a static structure, allowing conformational dynamics analysis at scale. Altogether, we analyzed 47 mutation sites across 69 Mpro-ligand complexes resulting in more than 3300 different structures which includes 69 mutated structures with all 47 sites mutated simultaneously and 3243 single residue mutated structures. We found that mutations generally increased the conformational flexibility of the protein. Understanding the impact of mutations on the flexibility of Mpro is essential for identifying potential drug targets in the treatment of SARS-CoV-2. Further studies in this area can offer valuable insights into the mechanisms of molecular recognition.

A review on application of molecular simulation technology in food molecules interaction

Molecular simulation is a new technology to analyze the interaction between molecules. This review mainly summarizes the application of molecular simulation technology in the food industry. This technology has been employed to assess structural changes of biomolecules, the interaction between components, and the mechanism of physical and chemical property alterations. These conclusions provide a deeper understanding of the molecular interaction mechanism in foods, break through the limitations of scientific experiments and avoid blind and time-consuming scientific research. In this paper, the advantages and development trends of molecular simulation technology in the food research field are described. This methodology can be used to contribute to further studies of the mechanism of molecular interactions in food, confirm experimental results and provide new ideas for research in the field of food sciences.