ABSTRACT
The COVID-19 pandemic that erupted in November 2019 is continuing, with no effective antiviral agent to date. Synthetic antiviral agents have limitations such as a narrow range of therapeutic effectiveness of the activity, toxicity, and resistant viral strains and traditional antiviral medicines at large seem not to have these limitations. Here, some of the existing phytochemicals are cherry-picked for repurposing against the enzyme or protein targets of SARS CoV2, by the principles of structure-based drug design based on molecular docking studies. The most important drug targets of SARS CoV2 namely, Mpro protease (6LU7), RdRp polymerase (7BTF), and Spike glycoprotein of SARS CoV2(6VSB) were employed for docking analysis with chosen phytochemicals and binding affinity was calculated using PRODIGY software and docking sites determined using Chimera software. For docking studies, 160 phytochemicals were selected from a large pool of phytochemicals. Based on the binding affinity values, 61 phytoconstituents were selected for further in-silico screening which resulted in 15 phytochemicals, with higher binding affinity to spike glycoprotein of SARS CoV2. Moreover, Guaijaverin, Quercetin, Quercitrin, Quinic acid, and spiraeoside binds both to the spike glycoprotein of SARS Cov2 and the host receptor of human ACE2. Hence these compounds may serve as two-pronged drug candidates for SARS CoV2. In nutshell, we present a few phytochemical candidates with higher binding affinity to the Spike protein of SARS CoV2, which needs to be further optimized by in vitro studies to minimize the cytotoxicity and increase or retain the binding affinity, towards an effective antiviral drug against COVID 19. © 2022, Editorial board of Journal of Experimental Biology and Agricultural Sciences. All rights reserved.
ABSTRACT
BACKGROUND: The derivatives of quercetin is known for their immune-modulating antiviral, anti-blood clotting, antioxidant, and also for its anti-inflammatory efficacy. The current study was therefore conducted to examine the noted novel derivatives of quercetin present in plant sources as an immune modulator and as an antiviral molecule in the COVID-19 disease and also to study their affinity of binding with potential three targets reported for coronavirus, i.e., papain-like protease, spike protein receptor-binding domain, and 3C-like protease. Based on the high-positive drug-likeness score, the reported derivatives of quercetin obtained from an open-source database were further filtered. Compounds with positive and high drug-likeness scores were further predicted for their potential targets using DIGEP-Pred software, and STRING was used to evaluate the interaction between modulated proteins. The associated pathways were recorded based on the Kyoto Encyclopedia of Genes and Genomes pathway database. Docking was performed finally using PyRx having AutoDock Vina to identify the efficacy of binding between quercetin derivatives with papain-like protease, spike protein receptor-binding domain, and 3C-like protease. The ligand that scored minimum binding energy was chosen to visualize the interaction between protein and ligand. Normal mode analysis in internal coordinates was done with normal mode analysis to evaluate the physical movement and stability of the best protein-ligand complexes using the iMODS server. RESULTS: Forty bioactive compounds with the highest positive drug-likeness scores were identified. These 40 bioactives were responsible for regulating different pathways associated with antiviral activity and modulation of immunity. Finally, three lead molecules were identified based on the molecular docking and dynamics simulation studies with the highest anti-COVID-19 and immunomodulatory potentials. Standard antiviral drug remdesivir on docking showed a binding affinity of - 5.8 kcal/mol with PLpro, - 6.4 kcal/mol with 3CLpro, and - 8.6 kcal/mol with spike protein receptor-binding domain of SARS-CoV-2, the discovered hit molecules quercetin 3-O-arabinoside 7-O-rhamnoside showed binding affinity of - 8.2 kcal/mol with PLpro, whereas quercetin 3-[rhamnosyl-(1- > 2)-alpha-L-arabinopyranoside] and quercetin-3-neohesperidoside-7-rhamnoside was predicted to have a binding affinity of - 8.5 kcal/mol and - 8.8 kcal/mol with spike protein receptor-binding domain and 3CLpro respectively CONCLUSION: Docking study revealed quercetin 3-O-arabinoside 7-O-rhamnoside to possess the highest binding affinity with papain-like protease, quercetin 3-[rhamnosyl-(1- > 2)-alpha-L-arabinopyranoside] with spike protein receptor-binding domain, and quercetin-3-neohesperidoside-7-rhamnoside with 3C-like protease and all the protein-ligand complexes were found to be stable after performing the normal mode analysis of the complexes in internal coordinates.
ABSTRACT
The medical burden caused by respiratory manifestations of influenza virus (IV) outbreak as an infectious respiratory disease is so great that governments in both developed and developing countries have allocated significant national budget toward the development of strategies for prevention, control, and treatment of this infection, which is seemingly common and treatable, but can be deadly. Frequent mutations in its genome structure often result in resistance to standard medications. Thus, new generations of treatments are critical to combat this ever-evolving infection. Plant materials and active compounds have been tested for many years, including, more recently, active compounds like flavonoids. Quercetin is a compound belonging to the flavonols class and has shown therapeutic effects against influenza virus. The focus of this review includes viral pathogenesis as well as the application of quercetin and its derivatives as a complementary therapy in controlling influenza and its related symptoms based on the targets. We also touch on the potential of this class of compounds for treatment of SARS-COV-2, the cause of new pandemic.