QSAR and molecular docking studies on designing potent inhibitors of SARS-CoVs main protease.

Background: Severe acute respiratory syndrome coronavirus (SARS-CoVs) have emerged as a global health threat, which had caused a high rate of mortality. There is an urgent need to find effective drugs against these viruses. Objective: This study aims to predict the activity of unsymmetrical aromatic disulfides by constructing a QSAR model, and to design new compounds according to the structural and physicochemical attributes responsible for higher activity towards SARS-CoVs main protease. Methods: All molecules were constructed in ChemOffice software and molecular descriptors were calculated by CODESSA software. A regression-based linear heuristic method was established by changing descriptors datasets and calculating predicted IC50 values of compounds. Then, some new compounds were designed according to molecular descriptors from the heuristic method model. The compounds with predicted values smaller than a set point were constantly screened out. Finally, the properties analysis and molecular docking were conducted to further understand the structure-activity relationships of these finalized compounds. Results: The heuristic method explored the various descriptors responsible for bioactivity and gained the best linear model with R2 0.87. The success of the model fully passed the testing set validation, proving that the model has both high statistical significance and excellent predictive ability. A total of 5 compounds with ideal predicted IC50 were found from the 96 newly designed derivatives and their properties analyze was carried out. Molecular docking experiments were conducted for the optimal compound 31a, which has the best compound activity with good target protein binding capability. Conclusion: The heuristic method was quite reliable for predicting IC50 values of unsymmetrical aromatic disulfides. The present research provides meaningful guidance for further exploration of the highly active inhibitors for SARS-CoVs.

Potential of vibrational spectroscopy coupled with machine learning as a non-invasive diagnostic method for COVID-19.

BACKGROUND AND OBJECTIVE: Efforts to alleviate the ongoing coronavirus disease 2019 (COVID-19) crisis showed that rapid, sensitive, and large-scale screening is critical for controlling the current infection and that of ongoing pandemics. METHODS: Here, we explored the potential of vibrational spectroscopy coupled with machine learning to screen COVID-19 patients in its initial stage. Herein presented is a hybrid classification model called grey wolf optimized support vector machine (GWO-SVM). The proposed model was tested and comprehensively compared with other machine learning models via vibrational spectroscopic fingerprinting including saliva FTIR spectra dataset and serum Raman scattering spectra dataset. RESULTS: For the unknown vibrational spectra, the presented GWO-SVM model provided an accuracy, specificity and F1_score value of 0.9825, 0.9714 and 0.9778 for saliva FTIR spectra dataset, respectively, while an overall accuracy, specificity and F1_score value of 0.9085, 0.9552 and 0.9036 for serum Raman scattering spectra dataset, respectively, which showed superiority than those of state-of-the-art models, thereby suggesting the suitability of the GWO-SVM model to be adopted in a clinical setting for initial screening of COVID-19 patients. CONCLUSIONS: Prospectively, the presented vibrational spectroscopy based GWO-SVM model can facilitate in screening of COVID-19 patients and alleviate the medical service burden. Therefore, herein proof-of-concept results showed the chance of vibrational spectroscopy coupled with GWO-SVM model to help COVID-19 diagnosis and have the potential be further used for early screening of other infectious diseases.

Novel quantitative structure-activity relationship model to predict activities of natural products against COVID-19.

Currently, COVID-19 is spreading in a large scale while no efficient vaccine has been produced. A high-effective drug for COVID-19 is very necessary now. We established a satisfied quantitative structure-activity relationship model by gene expression programming to predict the IC50 value of natural compounds. A total of 27 natural products were optimized by heuristic method in CODESSA program to build a liner model. Based on it, only two descriptors were selected and utilized to build a nonlinear model in gene expression programming. The square of correlation coefficient and s2 of heuristic method were 0.80 and 0.10, respectively. In gene expression programming, the square of correlation coefficient and mean square error for training set were 0.91 and 0.04. The square of correlation coefficient and mean square error for test set are 0.86 and 0.1. This nonlinear model has stronger predictive ability to develop the targeted drugs of COVID-19.