Insilico generation of novel ligands for the inhibition of SARS-CoV-2 main protease (3CLpro) using deep learning

The recent emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) has become a global public health crisis, and a crucial need exists for rapid identification and development of novel therapeutic interventions. In this study, a recurrent neural network (RNN) is trained and optimized to produce novel ligands that could serve as potential inhibitors to the SARS-CoV-2 viral protease: 3 chymotrypsin-like protease (3CL^pro). Structure-based virtual screening was performed through molecular docking, ADMET profiling, and predictions of various molecular properties were done to evaluate the toxicity and drug-likeness of the generated novel ligands. The properties of the generated ligands were also compared with current drugs under various phases of clinical trials to assess the efficacy of the novel ligands. Twenty novel ligands were selected that exhibited good drug-likeness properties, with most ligands conforming to Lipinski's rule of 5, high binding affinity (highest binding affinity: -9.4 kcal/mol), and promising ADMET profile. Additionally, the generated ligands complexed with 3CL^pro were found to be stable based on the results of molecular dynamics simulation studies conducted over a 100 ns period. Overall, the findings offer a promising avenue for the rapid identification and development of effective therapeutic interventions to treat COVID-19.

Bioaugmentation of Soil with Pseudomonas monteilii Strain Eliminates Inhibition of Okra (Abelmoschus esculentus) Seed Germination by m-Cresol

Cresols are ubiquitous in nature due to their bulk production and end uses in various industrial processes as well as due to their natural presence. They are highly toxic to both fauna and flora and are included in the list of priority pollutants. In the present study, the effect of m-cresol on germination of ten different crop seeds was tested and the seeds of okra and eggplant were found to be very sensitive, okra being the most vulnerable. Okra seeds lost its viability in the presence of m-cresol, which was proportionate to its concentration as indicated by the standard 2,3,5-tetrazoliumtrichloride (TTC) test. Marked decrease in protease and amylase activities was observed in germinating seeds exposed to the compound. The inhibitory effect of m-cresol on germination was eliminated effectively by bioaugmentation of the soil with the cresol-degrading Pseudomonas monteilii S-CSR-0014. Normal germination and seedling vigor were obtained when the seeds were sown four and eight days after the soil inoculation with the bacterial cells, whereas the seeds sown immediately did not show proper germination. The inoculated bacterium degraded m-cresol efficiently from the spiked soil and exhibited concomitant growth. It can be concluded that m-cresol-contaminated soils could be effectively bioremediated to render the soil suitable for normal seed germination and healthy seedling growth of sensitive crops.