Deciphering molecular properties and docking studies of hepatitis C and non-hepatitis C antiviral inhibitors - A computational approach

High-affinity, broad-spectrum, "centipede-like" multi-branched drug conjugates, anchored to the S protein, for blocking coronavirus infection

Over the past two decades, various coronaviruses have posed a severe threat to human life and health, with the spike protein (S protein) being a critical protein for infecting host cells. Glycyrrhizic acid (GA), as a natural drug, can inhibit the infection of coronaviruses by binding to the receptor-binding domain (RBD) of the S protein. However, issues like poor water solubility and weak binding affinity with the S protein have hindered its further application. Therefore, drawing inspiration from the biological structure of centipedes, a ROS-responsive multi-branched drug conjugate (ODPAG) was constructed through a "polymer-drug linkage" strategy using dextran as the backbone and GA as the active "claw". ODPAG exhibited drug loading of 22.0 ± 0.2% (OD40kPAG) and 19.7 ± 0.1% (OD450kPAG), showing ROS responsiveness with a half-life 6.4 times that of GA (OD40kPAG) and 5.4 times longer (OD450kPAG). In in vitro antiviral experiments, ODPAG exhibited an enhanced binding affinity to the S protein, with IC50 values of 1.33 μM (OD40kPAG) and 0.89 μM (OD450kPAG) against SARS-CoV-2 pseudovirus, demonstrating exceptional antiviral efficacy. These results collectively indicate that ODPAG can block coronavirus infection by binding to the S protein, exhibiting significant potential in addressing the current challenges posed by the novel coronavirus. Additionally, the "polymer-drug conjugate" strategy employed in this process is efficient, cost-effective, and offers new insights for combating future emergent coronaviruses.

Computational Drug Design against Ebola Virus Targeting Viral Matrix Protein VP30

Ebola viral disease (EVD) is a deadly infectious hemorrhagic viral fever caused by the Ebola virus with a high mortality rate. Until date, there is no effective drug or vaccination available to combat this condition. This study focuses on designing an effective antiviral drug for Ebola viral disease targeting viral protein 30 (VP30) of Ebola virus, highly required for transcription initiation. The lead molecules were screened for Lipinski rule of five, ADMET study following which molecular docking and bioactivity prediction was carried out. The compounds with the least binding energy were analyzed using interaction software. The results revealed that 6-Hydroxyluteolin and (-)-Arctigenin represent active lead compounds that inhibit the activity of VP30 protein and exhibits efficient pharmacokinetics. Both these compounds are plant-derived flavonoids and possess no known adverse effects on human health. In addition, they bind strongly to the predicted binding site centered on Lys180, suggesting that these two lead molecules can be imperative in designing a potential drug for EVD.

The activity prediction of indole inhibitors against HCV NS5B polymerase

Non-structural viral protein 5B (NS5B) is a viral protein in hepatitis C virus. Although various inhibitors against NS5B have been found, the activity prediction of similar untested inhibitors is still highly desirable. In this respect, the Tchebichef moments (TMs) calculated from the images of molecular structures were regarded as the independent variables while the inhibitory activity (pIC₅₀ ) was the dependent variable, and the predictive model was established by means of stepwise regression. The R-squared of leave-one-out cross-validation (Q² ) for the training set and the R-squared of prediction ( R p 2 ) for external independent test set were 0.919 and 0.927, respectively. The obtained model was also evaluated strictly. Compared with the multivariate curve resolution with alternating least squares (MCR-ALS) and the QSAR approaches derived from the literature, the proposed method is more accurate and reliable. This study not only provides an effective approach to predict the biological activity of RNA replication's inhibitors, but also extends the QSAR modeling technique.

Structure-based drug design of novel peptidomimetic cellulose derivatives as HCV-NS3 protease inhibitors

Hepatitis C Virus (HCV) represents a global health threat not only due to the large number of reported worldwide HCV infections, but also due to the absence of a reliable vaccine for its prevention. HCV NS3 protease is one of the most important targets for drug design aiming at the deactivation of HCV. In the present work, molecular docking simulations are carried out for suggested novel NS3 protease inhibitors applied to the Egyptian genotype 4. These inhibitors are modifications of dimer cellulose by adding a hexa-peptide to the cellulose at one of the positions 2, 3, 6, 2', 3' or 6'. Results show that the inhibitor compound with the hexa-peptide at position 6 shows significantly higher simulation docking score with HCV NS3 protease active site. This is supported by low total energy value of docking system, formation of two H-bonds with HCV NS3 protease active site residues, high binding affinity and increased stability in the interaction system.