The Role of Structural Biology Task Force: Validation of the Binding Mode of Repurposed Drugs Against SARS-CoV-2 Protein Targets: Focus on SARS-CoV-2 Main Protease (Mpro): A Promising Target for COVID-19 Treatment

The main protease (Mpro) of SARS-CoV-2, a cysteine protease that plays a key role in generating the active proteins essential for coronavirus replication, is a validated drug target for treating COVID-19. The structure of Mpro has been elucidated by macromolecular crystallography, but owing to its conformational flexibility, finding effective inhibitory ligands was challenging. Screening libraries of ligands as part of EXaSCale smArt pLatform Against paThogEns (ExScalate4CoV) yielded several potential drug molecules that inhibit SARS-CoV-2 replication in vitro. We solved the crystal structures of Mpro in complex with repurposed drugs like myricetin, a natural flavonoid, and MG-132, a synthetic peptide aldehyde. We found that both inhibitors covalently bind the catalytic cysteine. Notably, myricetin has an unexpected binding mode, showing an inverted orientation with respect to that of the flavonoid baicalein. Moreover, the crystallographic model validates the docking pose suggested by molecular dynamics experiments. The mechanism of MG-132 activity against SARS-CoV-2 Mpro was elucidated by comparison of apo and inhibitor-bound crystals, showing that regardless of the redox state of the environment and the crystalline symmetry, this inhibitor binds covalently to Cys145 with a well-preserved binding pose that extends along the whole substrate binding site. MG-132 also fits well into the catalytic pocket of human cathepsin L, as shown by computational docking, suggesting that it might represent a good start to developing dual-targeting drugs against COVID-19. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Spirulina platensis from Nomayos: a potential health food for the management of COVID-19 infection

The proteins (37%), carbohydrates (24.4%) and lipids (30.1%) contents of S. platensis from Nomayos provide the body with its structural and energy needs for about 518.8 Kcal per 100g of spirulina. Polyphenols (56.4 mEq. QE / g ES.), flavanols (13.2 mEq. QE / g ES.) flavonoids (21.2 mEq. QE / g ES.), carotenoids (3, 8%) and phycocyanin (16.15%) is responsible of its antioxidant capacities (7.5 + 0.33 mg eq. Vit C/g ES) and for a significant decrease in malondialdehyde MDA (< 0.001) concentration. Zinc (25 mG/Kg), Iron (256 mG/Kg), Selenium (1.24 mG/Kg), Manganese (23mG/Kg) and Copper (28.95 mG/Kg) reinforce this antioxidant power because they are cofactors of enzymes (Superoxide dismutase, Peroxidase, Catalase) which ensure the fight against free radicals. The presence of phycocyanin is an asset for the anti-inflammatory action. The significant decrease in IL-8 (p < 0.001) and TNF alpha (p < 0.04) levels confirms this property. On the other hand, the nonsignificant increase in Il-6 (1.56 to 2.18 pg/m;p > 0.05) would be partly responsible for the rise in CD4 levels (p < 0.001) and the reduction in viral load in immune deficiency patients (p = 0.000) supplemented with spirulina. In conclusion, S. platensis from Nomayos by its antioxidant, anti-inflammatory and immuno-stimulatory properties would be a good supplement food for subjects at risk of developing severe forms of COVID-19.

Flavonoid as possible therapeutic targets against COVID-19: a scoping review of in silico studies.

OBJECTIVES: This scoping review aims to present flavonoid compounds' promising effects and possible mechanisms of action on potential therapeutic targets in the SARS-CoV-2 infection process. METHODS: A search of electronic databases such as PubMed and Scopus was carried out to evaluate the performance of substances from the flavonoid class at different stages of SARS-CoV-2 infection. RESULTS: The search strategy yielded 382 articles after the exclusion of duplicates. During the screening process, 265 records were deemed as irrelevant. At the end of the full-text appraisal, 37 studies were considered eligible for data extraction and qualitative synthesis. All the studies used virtual molecular docking models to verify the affinity of compounds from the flavonoid class with crucial proteins in the replication cycle of the SARS-CoV-2 virus (Spike protein, PLpro, 3CLpro/ MPro, RdRP, and inhibition of the host's ACE II receptor). The flavonoids with more targets and lowest binding energies were: orientin, quercetin, epigallocatechin, narcissoside, silymarin, neohesperidin, delphinidin-3,5-diglucoside, and delphinidin-3-sambubioside-5-glucoside. CONCLUSION: These studies allow us to provide a basis for in vitro and in vivo assays to assist in developing drugs for the treatment and prevention of COVID-19.

Computer Analysis of the Inhibition of ACE2 by Flavonoids and Identification of Their Potential Antiviral Pharmacophore Site.

In the present study, we investigated the antiviral activities of 17 flavonoids as natural products. These derivatives were evaluated for their in vitro antiviral activities against HIV and SARS-CoV-2. Their antiviral activity was evaluated for the first time based on POM (Petra/Osiris/Molispiration) theory and docking analysis. POM calculation was used to analyze the atomic charge and geometric characteristics. The side effects, drug similarities, and drug scores were also assumed for the stable structure of each compound. These results correlated with the experimental values. The bioinformatics POM analyses of the relative antiviral activities of these derivatives are reported for the first time.

Antiviral Flavonoids: A natural scaffold with prospects as phytomedicines against SARS-CoV2.

Flavonoids are vital candidates to fight against a wide range of pathogenic microbial infections. Due to their therapeutic potential, many flavonoids from the herbs of traditional medicine systems are now being evaluated as lead compounds to develop potential antimicrobial hits. The emergence of SARS-CoV-2 caused one of the deadliest pandemics that has ever been known to mankind. To date, more than 600 million confirmed cases of SARS-CoV2 infection have been reported worldwide. Situations are worse due to the unavailability of therapeutics to combat the viral disease. Thus, there is an urgent need to develop drugs against SARS-CoV2 and its emerging variants. Here, we have carried out a detailed mechanistic analysis of the antiviral efficacy of flavonoids in terms of their potential targets and structural feature required for exerting their antiviral activity. A catalog of various promising flavonoid compounds has been shown to elicit inhibitory effects against SARS-CoV and MERS-CoV proteases. However, they act in the high-micromolar regime. Thus a proper lead-optimization against the various proteases of SARS-CoV2 can lead to high-affinity SARS-CoV2 protease inhibitors. To enable lead optimization, a quantitative structure-activity relationship (QSAR) analysis has been developed for the flavonoids that have shown antiviral activity against viral proteases of SARS-CoV and MERS-CoV. High sequence similarities between coronavirus proteases enable the applicability of the developed QSAR to SARS-CoV2 proteases inhibitor screening. The detailed mechanistic analysis of the antiviral flavonoids and the developed QSAR models is a step forward toward the development of flavonoid-based therapeutics or supplements to fight against COVID-19.

An in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad.

Coronavirus disease 19 (COVID19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, several countries are at risk of the pandemic caused by this virus. In the absence of any vaccine or virus-specific antiviral treatments, the need is to fast track search for potential drug candidates to combat the virus. Though there are known drugs that are being repurposed to fight against the SARS-CoV-2, there is a requirement for the virus-specific drugs at the earliest. One of the main drug targets of SARS-CoV-2 is an essential non-structural protein, 3CL protease, critical for the life cycle of the virus. We have used molecular docking studies to screen a chemically diverse set of small molecules to identify potential drug candidates to target this protein. Of the 22,630 molecules from varied small molecule libraries, based on the binding affinities and physicochemical properties, we finalized 30 molecules to be potential drug candidates. Eight of these molecules bind in a manner allowing for the scope of a nearly orthogonal backside nucleophilic attack on their suitably placed electrophilic carbonyl groups by the thiol group of cysteine residue 145, while remaining inside a 4 Ǻ distance range. It is interesting since carbonyl groups are known to be attacked in a similar fashion by external nucleophiles and can be relevant when considering these molecules as potential mechanism-based irreversible inhibitors of the 3CLPro. Further, ADMET analysis and Molecular dynamics simulations and available bioactive assays led to the identification of three molecules with high potential to be explored as drug candidates/lead molecules to target 3CLPro of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Deciphering Houttuynia cordata extract as electron shuttles with anti-COVID-19 activity and its performance in microbial fuel cells.

Background: Traditional herbal medicines usually contain electron shuttle (ES)-like structures compounds which are potential candidates for antiviral compounds selection. Houttuynia cordata is applied as a biomaterial to decipher its potential applications in bioenergy extraction in microbial fuel cells (MFCs) and anti-COVID-19 via molecular docking evaluation. Methods: H. cordata leaves extracts by water and 60% ethanol solvent were analyzed for total polyphenols, antioxidant activity, cyclic voltammetry (CV), and MFCs. The bioactive compounds of H. cordata leaves extracts were assayed via LC/MS analysis. Identification of the marker substances for potential antiviral activity using a molecular docking model was provided. Significant findings: 60% ethanol extract exhibits the highest total polyphenols and antioxidant activity compared with water extracts. Bioenergy extraction in MFCs showed that 60% ethanol extracts could give 1.76-fold more power generation compared to the blank. Flavonoids and their sugar-to-glycan ratios increased after CV scanning and they are expected to be effective ES substances. Quercitrin, from the H. cordata extract that shares an ES-like structure, was found to exhibit strong binding affinities towards ACE2 and RdRp. This indicated the potential of H. cordata leaves as a promising antiviral herb.

Current Update on Role of Hesperidin in Inflammatory Lung Diseases: Chemistry, Pharmacology, and Drug Delivery Approaches.

Inflammation is a common feature of many respiratory diseases, such as pneumonia, asthma, pulmonary fibrosis, chronic obstructive pulmonary disease (COPD), lung cancer, acute lung injury, and COVID-19. Flavonoids have demonstrated their anti-inflammatory and antioxidant effects by influencing inflammation at different stages and majorly impacting several respiratory diseases' onset and development. According to current studies, hesperidin, one of the most abundant polyphenols, can inhibit transcription factors or regulatory enzymes essential for controlling inflammation-linked mediators, including nuclear factor-kappa B (NF-κB), Inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2). It also improved cellular antioxidant defences by activating the ERK/Nrf2 signalling pathway. Therefore, this review provides the latest studies on the effect of hesperidin in different respiratory diseases, its pharmacokinetic profile, and innovative drug delivery methods.

Anti-SARS-CoV-2 Activity of Ampelozizyphus amazonicus (Saracura-Mirá): Focus on the Modulation of the Spike-ACE2 Interaction by Chemically Characterized Bark Extracts by LC-DAD-APCI-MS/MS.

Traditional medicine shows several treatment protocols for COVID-19 based on natural products, revealing its potential as a possible source of anti-SARS-CoV-2 agents. Ampelozizyphus amazonicus is popularly used in the Brazilian Amazon as a fortifier and tonic, and recently, it has been reported to relieve COVID-19 symptoms. This work aimed to investigate the antiviral potential of A. amazonicus, focusing on the inhibition of spike and ACE2 receptor interaction, a key step in successful infection. Although saponins are the major compounds of this plant and often reported as its active principles, a polyphenol-rich extract was the best inhibitor of the spike and ACE2 interaction. Chemical characterization of A. amazonicus bark extracts by LC-DAD-APCI-MS/MS before and after clean-up steps for polyphenol removal showed that the latter play an essential role in maintaining this activity. The effects of the extracts on viral replication were also assessed, and all samples (aqueous and ethanol extracts) demonstrated in vitro activity, inhibiting viral titers in the supernatant of Calu-3 cells after 24 hpi. By acting both in the SARS-CoV-2 cell entry process and its replication, A. amazonicus bark extracts stand out as a multitarget agent, highlighting the species as a promising candidate in the development of anti-SARS-CoV-2 drugs.

First study on in vitro antiviral and virucidal effects of flavonoids against feline infectious peritonitis virus at the early stage of infection.

Background and Aim: Feline infectious peritonitis (FIP), one of the most important infectious diseases in cats is caused by FIP virus (FIPV), a mutated variant of feline coronavirus. Feline infectious peritonitis has a negative impact on feline health, with extremely high mortality in clinical FIP-infected cats, particularly young cats. There are no approved drugs for FIP treatment, and therapeutic possibilities for FIP treatment are limited. This study aimed to utilize nature-derived bioactive flavonoids with antiviral properties to inhibit FIPV infection in Crandell-Rees feline kidney (CRFK) cells. Materials and Methods: The cytotoxicity of 16 flavonoids was evaluated on CRFK cells using a colorimetric method (MTS) assay. Viral kinetics of FIPV at 50 tissue culture infectious dose (TCID50)/well was determined during the first 24-h post-infection (HPI). Antiviral activity was evaluated based on the replication steps of the virus life cycle, including pre-compound, attachment, penetration, post-viral entry, and virucidal assays. The antiviral efficacy of flavonoids against FIPV was determined based on positive FIPV-infected cells with the immunoperoxidase monolayer assay and viral load quantification using reverse transcription-quantitative polymerase chain reaction. Results: Two flavonoids, namely, isoginkgetin and luteolin, inhibited FIPV replication during post-viral entry in a dose-dependent manner, with 50% maximal effective concentrations = 4.77 ± 0.09 and 36.28 ± 0.03 µM, respectively. Based on viral kinetics, both flavonoids could inhibit FIPV replication at the early stage of infection at 0-6-HPI for isoginkgetin and 2-6-HPI for luteolin using a time-of-addition assay. Isoginkgetin exerted a direct virucidal effect that reduced the viral titers by 2 and 1.89 log10 TCID50/mL at 60 and 120 min, respectively. Conclusion: Isoginkgetin interfered with FIPV replication during both post-viral infection and virucidal experiments on CRFK cells, whereas luteolin inhibited the virus after infection. These results demonstrate the potential of herbal medicine for treating FIP.