Marine Alga Ulva fasciata-Derived Molecules for the Potential Treatment of SARS-CoV-2: An In Silico Approach

SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This in silico study aimed to elucidate therapeutic efficacies against SARS-CoV-2 of phyco-compounds from the seaweed, Ulva fasciata. Twelve phyco-compounds were isolated and toxicity was analyzed by VEGA QSAR. Five compounds were found to be nonmutagenic, noncarcinogenic and nontoxic. Moreover, antiviral activity was evaluated by PASS. Binding affinities of five of these therapeutic compounds were predicted to possess probable biological activity. Fifteen SARS-CoV-2 target proteins were analyzed by the AutoDock Vina program for molecular docking binding energy analysis and the 6Y84 protein was determined to possess optimal binding affinities. The Desmond program from Schrödinger’s suite was used to study high performance molecular dynamic simulation properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol—6Y84 for better drug evaluation. The ligand with 6Y84 had stronger binding affinities (−5.9 kcal/mol) over two standard drugs, Chloroquine (−5.6 kcal/mol) and Interferon α-2b (−3.8 kcal/mol). Swiss ADME calculated physicochemical/lipophilicity/water solubility/pharmacokinetic properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, showing that this therapeutic agent may be effective against SARS-CoV-2.

Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer's Disease

Calcium homeostasis modulator 1 (CALHM1) is a protein responsible for causing Alzheimer’s disease. In the absence of an experimentally designed protein molecule, homology modelling was performed. Through homology modelling, different CALHM1 models were generated and validated through Rampage. To carry out further in silico studies, through molecular docking and molecular dynamics simulation experiments, various flavonoids and alkaloids from Bauhinia variegata were utilised as inhibitors to target the protein (CALHM1). The sequence of CALHM1 was retrieved from UniProt and the secondary structure prediction of CALHM1 was done through CFSSP, GOR4, and SOPMA methods. The structure was identified through LOMETS, MUSTER, and MODELLER and finally, the structures were validated through Rampage. Bauhinia variegata plant was used to check the interaction of alkaloids and flavonoids against CALHM1. The protein and protein–ligand complex were also validated through molecular dynamics simulations studies. The model generated through MODELLER software with 6VAM A was used because this model predicted the best results in the Ramachandran plot. Further molecular docking was performed, quercetin was found to be the most appropriate candidate for the protein molecule with the minimum binding energy of −12.45 kcal/mol and their ADME properties were analysed through Molsoft and Molinspiration. Molecular dynamics simulations showed that CALHM1 and CALHM1–quercetin complex became stable at 2500 ps. It may be seen through the study that quercetin may act as a good inhibitor for treatment. With the help of an in silico study, it was easier to analyse the 3D structure of the protein, which may be scrutinized for the best-predicted model. Quercetin may work as a good inhibitor for treating Alzheimer’s disease, according to in silico research using molecular docking and molecular dynamics simulations, and future in vitro and in vivo analysis may confirm its effectiveness.

In Silico Molecular Docking and Simulation Studies of Protein HBx Involved in the Pathogenesis of Hepatitis B Virus-HBV

Current drug discovery involves finding leading drug candidates for further development. New scientific approaches include molecular docking, ADMET studies, and molecular dynamic simulation to determine targets and lead compounds. Hepatitis B is a disease of concern that is a life-threatening liver infection. The protein considered for the study was HBx. The hepatitis B X-interacting protein crystal structure was obtained from the PDB database (PDB ID-3MSH). Twenty ligands were chosen from the PubChem database for further in silico studies. The present study focused on in silico molecular docking studies using iGEMDOCK. The triethylene glycol monoethyl ether derivative showed an optimum binding affinity with the molecular target HBx, with a high negative affinity binding energy of −59.02 kcal/mol. Lipinski’s rule of five, Veber, and Ghose were followed in subsequent ADMET studies. Molecular dynamic simulation was performed to confirm the docking studies and to analyze the stability of the structure. In these respects, the triethylene glycol monoethyl ether derivative may be a promising molecule to prepare future hepatitis B drug candidates. Substantial research effort to find a promising drug for hepatitis B is warranted in the future.

Antiviral activity of astragaloside II, astragaloside III and astragaloside IV compounds against dengue virus: Computational docking and in vitro studies

This study was aimed to identify the phytocompounds possessing anti-dengue virus activity using in silico and in vitro approaches. A total of 7000 phytocompounds were virtually screened against protein targets (envelope, NS2b/NS3, and NS5) of dengue virus using iGEMDOCK and individually docked using Maestro 10.7 module of Schrödinger software. In vitro cytotoxicity and antiviral studies were performed using vero cell line. Finally, three phytocompounds namely astragaloside II, astragaloside III, and astragaloside IV were screened based on their highest binding energy values against protein targets. Astragaloside III exhibited the highest interaction energy value of -8.718 kcal/mol and -8.447 kcal/mol against envelope, and NS2b/NS3 targets, respectively. Astragaloside IV exhibited -7.244 kcal/mol against SAM site, and -9.179 kcal/mol against RNA cap site of NS5 targets. In silico ADMET analysis revealed that astragaloside II, III, and IV were non-mutagenic and non-carcinogenic in nature and these compounds were also non-toxic to vero cells upto 1000 μg/mL. Against dengue virus serotype 3, astragaloside II exhibited substantial antiviral activity at the concentration of 1.56 μg/mL followed by astragaloside III at 6.25 μg/mL and astragaloside IV at 12.5 μg/mL. Also, against dengue serotype 1, astragaloside II showed the maximum antiviral activity at 1.56 μg/mL followed by astragaloside III and IV at 3.125 μg/mL. This study concludes that astragaloside II, III, and IV compounds had potential in vitro anti-dengue virus activity.