Stilbene-based natural compounds as promising drug candidates against COVID-19

Repurposing of antimycobacterium drugs for COVID-19 treatment by targeting SARS CoV-2 main protease: An in-silico perspective

The global mortality rate has been significantly impacted by the COVID-19 pandemic, caused by the SARS CoV-2 virus. Although the pursuit for a potent antiviral is still in progress, experimental therapies based on repurposing of existing drugs is being attempted. One important therapeutic target for COVID-19 is the main protease (Mpro) that cleaves the viral polyprotein in its replication process. Recently minocycline, an antimycobacterium drug, has been successfully implemented for the treatment of COVID-19 patients. But it's mode of action is still far from clear. Furthermore, it remains unresolved whether alternative antimycobacterium drugs can effectively regulate SARS CoV-2 by inhibiting the enzymatic activity of Mpro. To comprehend these facets, eight well-established antimycobacterium drugs were put through molecular docking experiments. Four of the antimycobacterium drugs (minocycline, rifampicin, clofazimine and ofloxacin) were selected by comparing their binding affinities towards Mpro. All of the four drugs interacted with both the catalytic residues of Mpro (His41 and Cys145). Additionally, molecular dynamics experiments demonstrated that the Mpro-minocyline complex has enhanced stability, experiences reduced conformational fluctuations and greater compactness than other three Mpro-antimycobacterium and Mpro-N3/lopinavir complexes. This research furnishes evidences for implementation of minocycline against SARS CoV-2. In addition, our findings also indicate other three antimycobacterium/antituberculosis drugs (rifampicin, clofazimine and ofloxacin) could potentially be evaluated for COVID-19 therapy.

Exploring Novel 1-Hydroxynaphthalene-2-Carboxanilides Based Inhibitors Against C-Jun N-Terminal Kinases Through Molecular Dynamic Simulation and WaterSwap Analysis

Cancer is a disease of mutation and lifestyle modifications. A large number of normal genes can transform normal cells to cancer cells due to their deregulations including overexpression and loss of expression. Signal transduction is a complex signaling process that involves multiple interactions and different functions. C-Jun N-terminal kinases (JNKs) is an important protein involved in signaling process. JNK mediated pathways can detect, integrate, and amplify various external signals that may cause alterations in gene expression, enzyme activities, and different cellular functions that affect cellular behavior like metabolism, proliferation, differentiation, and cell survival. In this study, we performed molecular docking protocol (MOE) to predict the binding interactions of some known anticancer 1-hydroxynaphthalene-2-carboxanilides candidates. A set of 10 active compounds was retrieved after initial screening on the basis of docking scores, binding energies, and number of interactions and was re-docked in the active site of JNK protein. The results were further validated through molecular dynamics simulation and MMPB/GBSA calculations. The active compounds 4p and 5 k were ranked on top. After computationally exploring interactions of 1-hydroxynaphthalene-2-carboxanilides with JNK protein, we believe compounds 4p and 5 k can serve as potential inhibitors of JNK protein. It is believed that the results of current research would help to develop novel and structurally diverse anticancer compounds that will be useful not only treat cancer but also for the medication for the other diseases caused by protein deregulation.

Exploring the hub genes and potential drugs involved in Fanconi anemia using microarray datasets and bioinformatics analysis

Fanconi anemia (FA) is a genetic disorder that occurs when certain genes responsible for repairing DNA replication and promoting homologous recombination fail to function properly. This leads to severe clinical symptoms and a wide range of cancer-related characteristics. Recent treatment approaches for FA involve hematopoietic stem cell transplantation (HSCT), which helps restore the population of stem cells. A survival study using p-values indicated that specific hub genes play a significant role in diagnosing and predicting the disease. To find potential medications that interact with the identified hub genes, researchers inferred drugs. Among hub genes, TP53 was found to be particularly promising through computational analysis. Further investigation focused on two drugs, Topiramate and Tocofersolan predicted based on drug bank database analysis. Molecular docking strategies were employed to assess the best binding pose of these drugs with TP53. Topiramate showed a binding affinity of -6.5 kcal/mol, while Tocofersolan showed -8.5 kcal/mol against the active residues within the binding pocket. Molecular dynamics (MD) simulations were conducted to observe the stability of each drug's interaction with the TP53 protein over time. Both drugs exhibited stable confirmation with only slight changes in the loop region of the TP53 protein during the simulation intervals. Results also shows that there was a high fluctuation observed during apo-sate simulation time intervals as compared to complex system. Hence, it is suggested that the exploration of structure-based drug design holds promising results to specific target. This could potentially lead to a breakthrough in future experimental approaches for FA treatment.Communicated by Ramaswamy H. Sarma.

In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites

To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson-Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to -20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections.Communicated by Ramaswamy H. Sarma.

Cheminformatics and biomolecular dynamics studies towards the discovery of anti-staphylococcal nuclease domain-containing 1 (SND1) inhibitors to treat metastatic breast cancer

Metastatic breast cancer is a prime health concern and leading health burden across the globe. Previous efforts have shown that protein-protein interaction between Metadherin and Staphylococcal nuclease domaincontaining 1 (SND1) promotes initiation of breast cancer, progression, therapy resistance and metastasis. Therefore, small drug molecules that can interrupt the Metadherin and SND1 interaction may be ideal to suppress tumor growth, metastasis and increases chemotherapy sensitivity of triple negative breast cancer. Here, in this study, structure based virtual screening was conducted against the reported active site of SND1 enzyme, which revealed three promising lead molecules from Asinex library. These compounds were; BAS_00381028, BAS_00327287, and BAS_01293454 with binding energy score -10.25 kcal/mol, -9.65 kcal/mol and -9.32 kcal/mol, respectively. Compared to control (5-chloro-2-methoxy-N-([1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide) the lead molecules showed robust hydrophilic and hydrophobic interactions with the enzyme and revealed stable docked conformation in molecular dynamics simulation. During the simulation time, the compounds reported stable dynamics with no obvious fluctuation in binding mode and interactions noticed. The mean root mean square deviation (RMSD) of BAS_00381028, BAS_00327287, and BAS_01293454 complexes were 1.87 Å, 1.75 Å, 1.34 Å, respectively. Furthermore, the MM/GBSA analysis was conduction on the simulation trajectories of complexes that unveiled binding energy score of -19.25 kcal/mol, -27.03 kcal/mol, -34.6 kcal/mol and -29.61 kcal/mol for control, BAS_00381028, BAS_00327287, and BAS_01293454, respectively. In MM/PBSA, the binding energy value of for control, BAS_00381028, BAS_00327287, and BAS_01293454 was -20.45 kcal/mol, -27.89 kcal/mol, -36.41 kcal/mol and -32.01 kcal/mol, respectively. Additionally, the compounds were classified as druglike and have favorable pharmacokinetic properties. The compounds were predicted as promising leads and might be used in experimental investigation to study their anti-SND1 activity.

Four new stilbenes and one new flavonoid with potential antibacterial and anti-SARS-CoV-2 activity from Cajanus cajan

Four new stilbenes (1-4) and one new flavonoid (5), named cajanines D-H, together with three known stilbenes (6-8) were isolated from the leaves of Cajanus cajan (L.) Millsp. (pigeon pea). The structures of these compounds were elucidated unambiguously on the basis of IR, 1D, and 2D NMR, as well as HRESIMS data. Structurally, stilbenes 1-4 bore an isopentyl side chain, and further hydroxylation of compounds 1-3 generated a greater variety of structural forms. Compound 5 was a flavonoid owning an isopentyl side chain. Besides, antibacterial activity of the isolated compounds against Staphylococcus aureus, Bacillus cereus, and Escherichia coli was studied in vitro. Compounds 1-8 were endowed with profound antibacterial activity. Among them, the MIC values of compounds 4, 6, and 7 against S. aureus were 1.56, 0.78, and 0.78 µg/mL, respectively, among which 6 and 7 had better antibacterial activity than the positive control Vancomycin with the MIC values of 1.56 µg/mL. Additionally, the anti-SARS-CoV-2 main protease activity of all the isolated compounds was evaluated, and it was worth mentioning that the IC50 values of compounds 5-7 were 8.27, 4.65, and 8.30 µM, respectively, being comparable to the positive control Ebselen. Our findings may provide valuable guidance for the application of stilbenes as lead compounds in the future for the development of drugs with antibacterial or anti-COVID-19 activity.

Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease

To fight against the devastating coronavirus disease 2019 (COVID-19), identifying robust anti-SARS-CoV-2 therapeutics from all possible directions is necessary. To contribute to this effort, we selected a human metabolites database containing waters and lipid-soluble metabolites to screen against the 3-chymotrypsin-like proteases (3CLpro) protein of SARS-CoV-2. The top 8 hits from virtual screening displayed a docking score varying between ~ - 11 and ~ - 14 kcal/mol. Molecular dynamics simulations complement the virtual screening study in conjunction with the molecular mechanics generalized Born surface area (MM/GBSA) scheme. Our analyses revealed that (HMDB0132640) has the best glide docking score, - 14.06 kcal/mol, and MM-GBSA binding free energy, - 18.08 kcal/mol. The other three lead molecules are also selected along with the top molecule through a critical inspection of their pharmacokinetic properties. HMDB0132640 displayed a better binding affinity than the other three compounds (HMDB0127868, HMDB0134119, and HMDB0125821) due to increased favorable contributions from the intermolecular electrostatic and van der Waals interactions. Further, we have investigated the ligand-induced structural dynamics of the main protease. Overall, we have identified new compounds that can serve as potential leads for developing novel antiviral drugs against SARS-CoV-2 and elucidated molecular mechanisms of their binding to the main protease. Identification of probable hits from human metabolites against SARS-CoV-2 using integrated computational approaches-Missed against MS.

Pharmaceutical approaches for COVID-19: An update on current therapeutic opportunities

SARS-CoV-2, a newly discovered coronavirus, has been linked to the COVID-19 pandemic and is currently an important public health issue. Despite all the work done to date around the world, there is still no viable treatment for COVID-19. This study examined the most recent evidence on the efficacy and safety of several therapeutic options available including natural substances, synthetic drugs and vaccines in the treatment of COVID-19. Various natural compounds such as sarsapogenin, lycorine, biscoclaurine, vitamin B₁₂, glycyrrhizic acid, riboflavin, resveratrol and kaempferol, various vaccines and drugs such as AZD1222, mRNA-1273, BNT162b2, Sputnik V, and remdesivir, lopinavir, favipiravir, darunavir, oseltamivir, and umifenovir, resp., have been discussed comprehensively. We attempted to provide exhaustive information regarding the various prospective therapeutic approaches available in order to assist researchers and physicians in treating COVID-19 patients.

An integrated computational approach towards novel drugs discovery against polyketide synthase 13 thioesterase domain of Mycobacterium tuberculosis

The acquired drug resistance by Mycobacterium tuberculosis (M. tuberculosis) to antibiotics urges the need for developing novel anti-M. tuberculosis drugs that possess novel mechanism of action. Since traditional drug discovery is a labor-intensive and costly process, computer aided drug design is highly appreciated tool as it speeds up and lower the cost of drug development process. Herein, Asinex antibacterial compounds were virtually screened against thioesterase domain of Polyketide synthase 13, a unique enzyme that forms α-alkyl β-ketoesters as a direct precursor of mycolic acids which are essential components of the lipid-rich cell wall of M. tuberculosis. The study identified three drug-like compounds as the most promising leads; BBB_26582140, BBD_30878599 and BBC_29956160 with binding energy value of - 11.25 kcal/mol, - 9.87 kcal/mol and - 9.33 kcal/mol, respectively. The control molecule binding energy score is -9.25 kcal/mol. Also, the docked complexes were dynamically stable with maximum root mean square deviation (RMSD) value of 3 Å. Similarly, the MM-GB\PBSA method revealed highly stable complexes with mean energy values < - 75 kcal/mol for all three systems. The net binding energy scores are validated by WaterSwap and entropy energy analysis. Furthermore, The in silico druglike and pharmacokinetic investigation revealed that the compounds could be suitable candidates for additional experimentations. In summary, the study findings are significant, and the compounds may be used in experimental validation pipeline to develop potential drugs against drug-resistant tuberculosis.

Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment: An Overview

Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed.

Identification of novel inhibitors against hantaviruses through 2D fingerprinting and molecular modeling approaches

With the immensely growing outbreaks of hantavirus with still no effective treatment available, there is an urgent need of exploring new computational approaches which will target potential virulent proteins that will eventually reduce its growth. In this study, an envelope glycoprotein, Gn, was targeted. The glycoproteins, which are the sole targets of neutralizing antibodies, drive virus entry via receptor-mediated endocytosis and endosomal membrane fusion. Inhibitors are herein proposed to negate its action mechanism. On the basis of the scaffolds of favipiravir, a FDA compound already used against hantavirus, a library was designed using a 2D fingerprinting approach. Upon molecular docking analysis, the top four docked compounds-(1) favipiravir (-4.5 kcal/mol), (2) N-hydroxy-3-oxo-3, 4-dihydropyrazine-2-carboxamide (-4.7 kcal/mol), (3) N, 5, 6-trimethyl-2-oxo-1H-pyrazine-3-carboxamide (-4.5 kcal/mol), and (4) 3-propyl-1H-pyrazin-2-one (-3.8)-were prioritized on the basis of the lowest binding energies score. Through molecular docking, the best-categorized compound was subjected to molecular dynamics simulation for a 100-ns time span. Molecular dynamics sheds light on each ligand behavior within the active site. Among the four complexes, only favipiravir and 6320122 compound were found to be stable inside the pocket. This is due to the presence of common rings, pyrazine and carboxamide ring, which make a significant interaction with active key residues Furthermore, the MMPB/GBSA binding free energy analysis calculated for all complexes supported the dynamics results by calculating the most stable values for favipiravir complex (-9.9933 and -8.6951 kcal/mol) and for 6320122 compound complex (-13.8675 and -9.3439 kcal/mol), which demonstrated that the selected compounds have a proper binding affinity with the targeted proteins. The hydrogen bond analysis similarly revealed a strong bonding interaction. The results yielded a strong interaction between the enzyme and the inhibitor throughout the simulation; thus, the inhibitor has the potential to become a lead compound and could be subjected to experimental evaluation to unveil their blockage ability.

Biotechnological Approach to Increase Oxyresveratrol Production in Mulberry In Vitro Plants under Elicitation

Morus alba L. is used for a range of therapeutic purposes in Asian traditional medicine, and its extracts are reported to be effective against lipidemia, diabetes, and obesity, as well as being hepatoprotective and tyrosinase-inhibitory. They are also included in cosmetic products as anti-aging and skin-whitening agents. Stilbenes, the major bioactive compounds found in M. alba, have received renewed attention recently because of their putative activity against COVID-19. In this study M. alba plants were established in vitro, and the effect of elicitation on plant growth and stilbene accumulation, specifically oxyresveratrol and trans-resveratrol, was investigated. Different concentrations of the elicitors including methyl jasmonate and cyclodextrins were applied, and stilbene levels were determined in leaves, roots, and the culture medium. Elicitation of the M. alba plants with 5 mM cyclodextrins, alone or in combination with 10 µM methyl jasmonate, significantly increased the total phenolic content in the culture medium and leaves after 7 days of treatment. The higher total phenolic content in the roots of control plants and those treated only with methyl jasmonate indicated that cyclodextrins promoted metabolite release to the culture medium. Notably, the cyclodextrin-treated plants with the highest levels of oxy- and trans-resveratrol also had the highest total phenolic content and antioxidant capacity. These results indicate that elicited M. alba in vitro plants constitute a promising alternative source of bioactive stilbenes to supply pharmaceutical and cosmeceutical industries.

Recalibrating the calcium trap in amino acid carboxyl groups via classical molecular dynamics simulations

In order to use classical molecular dynamics to complement experiments accurately, it is important to use robust descriptions of the system. The interactions between biomolecules, like aspartic and glutamic acid, and dissolved ions are often studied using standard biomolecular force-fields, where the interactions between biomolecules and cations are often not parameterized explicitly. In this study, we have employed metadynamics simulations to investigate different interactions of Ca with aspartic and glutamic acid and constructed the free energy profiles of Ca²⁺-carboxylate association. Starting from a generally accepted, AMBER-based force field, the association was substantially over and under-estimated, depending on the choice of water model (TIP3P and SPC/fw, respectively). To rectify this discrepancy, we have replaced the default calcium parameters. Additionally, we modified the σ_ij value in the hetero-atomic Lennard-Jones interaction by 0.5% to further improve the interaction between Ca and carboxylate, based on comparison with the experimentally determined association constant for Ca with the carboxylate group of L-aspartic acid. The corrected description retrieved the structural properties of the ion pair in agreement with the original biomolecule - Ca²⁺ interaction in AMBER, whilst also producing an association constant comparable to experimental observations. This refined force field was then used to investigate the interactions between amino acids, calcium and carbonate ions during biogenic and biomimetic calcium carbonate mineralisation.

Bioactive compounds as potential angiotensin-converting enzyme II inhibitors against COVID-19: a scoping review

OBJECTIVE AND DESIGN

The current study aimed to summarize the evidence of compounds contained in plant species with the ability to block the angiotensin-converting enzyme 2 (ACE-II), through a scoping review.

METHODS

PubMed and Scopus electronic databases were used for the systematic search and a manual search was performed RESULTS: Studies included were characterized as in silico. Among the 200 studies retrieved, 139 studies listed after the exclusion of duplicates and 74 were included for the full read. Among them, 32 studies were considered eligible for the qualitative synthesis. The most evaluated class of secondary metabolites was flavonoids with quercetin and curcumin as most actives substances and terpenes (isothymol, limonin, curcumenol, anabsinthin, and artemisinin). Other classes that were also evaluated were alkaloid, saponin, quinone, substances found in essential oils, and primary metabolites as the aminoacid L-tyrosine and the lipidic compound 2-monolinolenin.

CONCLUSION

This review suggests the most active substance from each class of metabolites, which presented the strongest affinity to the ACE-II receptor, what contributes as a basis for choosing compounds and directing the further experimental and clinical investigation on the applications these compounds in biotechnological and health processes as in COVID-19 pandemic.

Phytomedicines explored under in vitro and in silico studies against coronavirus: An opportunity to develop traditional medicines

The widespread COVID-19 pandemic, caused by novel coronavirus SARS-CoV-2, has emanated as one of the most life-threatening transmissible diseases. Currently, the repurposed drugs such as remdesivir, azithromycine, chloroquine, and hydroxychloroquine are being employed in the management of COVID-19 but their adverse effects are a matter of concern. In this regard, alternative treatment options i.e., traditional medicine, medicinal plants, and their phytochemicals, which exhibit significant therapeutic efficacy and show a low toxicity profile, are being explored. The current review aims at unraveling the promising medicinal plants, phytochemicals, and traditional medicines against SARS-CoV-2 to discover phytomedicines for the management of COVID-19 on the basis of their potent antiviral activities against coronaviruses, as demonstrated in various biochemical and computational chemical biology studies. The review consists of integrative and updated information on the potential traditional medicines against COVID-19 and will facilitate researchers to develop traditional medicines for the management of COVID-19.

Plant Molecular Pharming and Plant-Derived Compounds towards Generation of Vaccines and Therapeutics against Coronaviruses

The current century has witnessed infections of pandemic proportions caused by Coronaviruses (CoV) including severe acute respiratory syndrome-related CoV (SARS-CoV), Middle East respiratory syndrome-related CoV (MERS-CoV) and the recently identified SARS-CoV2. Significantly, the SARS-CoV2 outbreak, declared a pandemic in early 2020, has wreaked devastation and imposed intense pressure on medical establishments world-wide in a short time period by spreading at a rapid pace, resulting in high morbidity and mortality. Therefore, there is a compelling need to combat and contain the CoV infections. The current review addresses the unique features of the molecular virology of major Coronaviruses that may be tractable towards antiviral targeting and design of novel preventative and therapeutic intervention strategies. Plant-derived vaccines, in particular oral vaccines, afford safer, effectual and low-cost avenues to develop antivirals and fast response vaccines, requiring minimal infrastructure and trained personnel for vaccine administration in developing countries. This review article discusses recent developments in the generation of plant-based vaccines, therapeutic/drug molecules, monoclonal antibodies and phytochemicals to preclude and combat infections caused by SARS-CoV, MERS-CoV and SARS-CoV-2 viruses. Efficacious plant-derived antivirals could contribute significantly to combating emerging and re-emerging pathogenic CoV infections and help stem the tide of any future pandemics.

Antiviral and Anti-Inflammatory Plant-Derived Bioactive Compounds and Their Potential Use in the Treatment of COVID-19-Related Pathologies

The highly contagious coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic and public health emergency as it has taken the lives of over 5.7 million in more than 180 different countries. This disease is characterized by respiratory tract symptoms, such as dry cough and shortness of breath, as well as other symptoms, including fever, chills, and fatigue. COVID-19 is also characterized by the excessive release of cytokines causing inflammatory injury to the lungs and other organs. It is advised to undergo precautionary measures, such as vaccination, social distancing, use of masks, hygiene, and a healthy diet. This review is aimed at summarizing the pathophysiology of COVID-19 and potential biologically active compounds (bioactive) found in plants and plant food. We conclude that many plant food bioactive compounds exhibit antiviral and anti-inflammatory properties and support in attenuating organ damage due to reduced cytokine release and improving the recovery process from COVID-19 infection.

Antihypertensive potential of Brassica rapa leaves: An in vitro and in silico approach

Aim: Plants contain many essential constituents and their optimization can result in the discovery of new medicines. One such plant is Brassica rapa that is commonly used as a vegetable to fulfill daily food requirements worldwide. This study intends to screen the phytochemicals, antihypertensive potential, GC-MS, and in silico analysis of the leaves of Brassica rapa.

Methods: Powdered leaves were subjected to proximate analysis followed by estimation of primary metabolites. Extracts were obtained by hot and cold extraction and investigated for secondary metabolites. All crude extracts were screened for their antihypertensive potential using an angiotensin-converting enzyme (ACE) inhibition assay. GC-MS analysis was carried out to standardize the extract, and an antihypertensive metabolite was confirmed using an in silico approach.

Results: Physicochemical evaluation resulted in moisture content (9.10% ± 0.1), total ash value (18.10% ± 0.6), and extractive values (water 9.46% ± 0.5 and alcohol soluble 4.99% ± 0.1), while phytochemical investigation revealed primary metabolites (total proteins 11.90 mg/g ± 0.9; total fats 3.48 mg/g ± 0.5; and total carbohydrates 57.45 mg/g ± 1.2). Methanol extract showed the highest number of secondary metabolites including polyphenols 93.63 mg/g ± 0.6; flavonoids 259.13 mg/g ± 0.6; and polysaccharides 56.63 mg/g ± 1.4, while water extract (70 mg/g ± 2) was rich in glycosaponins. Methanol extract showed the highest antihypertensive potential by inhibiting ACE (79.39%) amongst all extracts, compared to the standard drug captopril, which inhibited 85.81%. Standardization of methanol extract via GC-MS analysis revealed potent phytoconstituents, and a molecular docking study confirmed that oleic acid is the main antihypertensive metabolite.

Conclusion: We conclude that leaves of Brassica rapa can successfully lower hypertension by inhibiting ACE, however; in vivo investigations are required to confirm this antihypertensive activity.

Semistabilized Diazatrienyl Anions from Pyridine Imines and Acetylenes: An Access to (Z)-Stilbene/Imidazopyridine Ensembles, Benzyl Imidazopyridines, and Beyond

Semistabilized diazatrienyl anions are generated by the reaction of 2-pyridylarylimines with arylacetylenes in superbase systems MO^tBu (M = Li, Na, K)/DMSO at ambient temperature for 15 min. The initial intermediate N-centered propargyl-1,3-diaza-1,3,5-trienyl anions undergo intermolecular cyclization to benzyl imidazopyridine anions (formally [3 + 2] cycloaddition), further intercepting a second molecule of the starting pyridylimines or a proton of medium to afford (Z)-stilbene/imidazopyridine ensembles and benzyl imidazopyridines. The charge distribution in all intermediate anions and their synthetic evolution are consistent with quantum-chemical analysis (B2PLYPD/6-311+G**//B3LYP/6-31+G*).

Nitrostilbenes: Synthesis and Biological Evaluation as Potential Anti-Influenza Virus Agents

Resveratrol (RSV) is a natural stilbene polyphenolic compound found in several plant species. It is characterized by antioxidant properties, and its role in controlling viral replication has been demonstrated for different viral infections. Despite its promising antiviral properties, RSV biological activity is limited by its low bioavailability and high metabolic rate. In this study, we optimized its structure by synthesizing new RSV derivatives that maintained the phenolic scaffold and contained different substitution patterns and evaluated their potential anti-influenza virus activity. The results showed that viral protein synthesis decreased 24 h post infection; particularly, the nitro-containing compounds strongly reduced viral replication. The molecules did not exert their antioxidant properties during infection; in fact, they were not able to rescue the virus-induced drop in GSH content or improve the antioxidant response mediated by the Nrf2 transcription factor and G6PD enzyme. Similar to what has already been reported for RSV, they interfered with the nuclear-cytoplasmic traffic of viral nucleoprotein, probably inhibiting cellular kinases involved in the regulation of specific steps of the virus life cycle. Overall, the data indicate that more lipophilic RSV derivatives have improved antiviral efficacy compared with RSV and open the way for new cell-targeted antiviral strategies.

In-silico study for the screening and preparation of ionic liquid-AVDs conjugate to combat COVID-19 surge

The pandemic due to COVID-19 caused by SARS-CoV-2 has led to the recorded deaths worldwide and is still a matter of concern for scientists to find an effective counteragent. The combination therapy is always been a successful attempt in treating various threatful diseases. Recently, Ionic liquids (ILs) are known for their antiviral activity. Fascinating tunable properties of ILs make them a potential candidate for designing the therapeutic agent. The concern while using ILs in biomedical field remains is toxicity therefore, choline-based ILs were used in the study as they are considered to be greener as compared to other ILs. In the present study strategically, we performed the blind molecular docking of antiviral drug (Abacavir, Acyclovir, and Galidesivir)-choline based ILs conjugates with the target protein (Mpro protease). The molecules were screened on the basis of binding energy. The data suggested that the combination of AVDs-ILs have greater antiviral potential as compared to the drugs and ILs alone. Further, the ADME properties and toxicity analysis of the screened conjugates was done which revealed the non-toxicity of the conjugates. Additionally, the energetic profiling of the ILs drugs and their conjugates was done using DFT calculations which revealed the stability of the conjugates and have a better option to be developed as a therapeutic agent. Also, from molecular dynamic simulation was done and results showed the stability of the complex formed between target protein and the designed conjugates of AVDs and ILs.

Developing New Treatments for COVID-19 through Dual-Action Antiviral/Anti-Inflammatory Small Molecules and Physiologically Based Pharmacokinetic Modeling

Broad-spectrum antiviral agents that are effective against many viruses are difficult to develop, as the key molecules, as well as the biochemical pathways by which they cause infection, differ largely from one virus to another. This was more strongly highlighted by the COVID-19 pandemic, which found health systems all over the world largely unprepared and proved that the existing armamentarium of antiviral agents is not sufficient to address viral threats with pandemic potential. The clinical protocols for the treatment of COVID-19 are currently based on the use of inhibitors of the inflammatory cascade (dexamethasone, baricitinib), or inhibitors of the cytopathic effect of the virus (monoclonal antibodies, molnupiravir or nirmatrelvir/ritonavir), using different agents. There is a critical need for an expanded armamentarium of orally bioavailable small-molecular medicinal agents, including those that possess dual antiviral and anti-inflammatory (AAI) activity that would be readily available for the early treatment of mild to moderate COVID-19 in high-risk patients. A multidisciplinary approach that involves the use of in silico screening tools to identify potential drug targets of an emerging pathogen, as well as in vitro and in vivo models for the determination of a candidate drug’s efficacy and safety, are necessary for the rapid and successful development of antiviral agents with potentially dual AAI activity. Characterization of candidate AAI molecules with physiologically based pharmacokinetics (PBPK) modeling would provide critical data for the accurate dosing of new therapeutic agents against COVID-19. This review analyzes the dual mechanisms of AAI agents with potential anti-SARS-CoV-2 activity and discusses the principles of PBPK modeling as a conceptual guide to develop new pharmacological modalities for the treatment of COVID-19.

Randomized double-blind placebo-controlled proof-of-concept trial of resveratrol for outpatient treatment of mild coronavirus disease (COVID-19)

Resveratrol is a polyphenol that has been well studied and has demonstrated anti-viral and anti-inflammatory properties that might mitigate the effects of COVID-19. Outpatients (N = 105) were recruited from central Ohio in late 2020. Participants were randomly assigned to receive placebo or resveratrol. Both groups received a single dose of Vitamin D3 which was used as an adjunct. The primary outcome measure was hospitalization within 21 days of symptom onset; secondary measures were ER visits, incidence of pneumonia, and incidence of pulmonary embolism. Five patients chose not to participate after randomization. Twenty-one-day outcome was determined of all one hundred participants (mean [SD] age 55.6 [8.8] years; 61% female). There were no clinically significant adverse events attributed to resveratrol. Outpatients in this phase 2 study treated with resveratrol had a lower incidence compared to placebo of: hospitalization (2% vs. 6%, RR 0.33, 95% CI 0.04-3.10), COVID-19 related ER visits (8% vs. 14%, RR 0.57, 95% CI 0.18-1.83), and pneumonia (8% vs. 16%, RR 0.5, 95% CI 0.16-1.55). One patient (2%) in each group developed pulmonary embolism (RR 1.00, 95% CI: 0.06-15.55). This underpowered study was limited by small sample size and low incidence of primary adverse events consequently the results are statistically similar between treatment arms. A larger trial could determine efficacy.Trial Registrations: ClinicalTrials.gov NCT04400890 26/05/2020; FDA IND #150033 05/05/2020.

Natural therapeutics and nutraceuticals for lung diseases: Traditional significance, phytochemistry, and pharmacology

BACKGROUND

Lung diseases including chronic obstructive pulmonary disease (COPD), infections like influenza, acute respiratory distress syndrome (ARDS), asthma and pneumonia lung cancer (LC) are common causes of sickness and death worldwide due to their remoteness, cold and harsh climatic conditions, and inaccessible health care facilities.

PURPOSE

Many drugs have already been proposed for the treatment of lung diseases. Few of them are in clinical trials and have the potential to cure infectious diseases. Plant extracts or herbal products have been extensively used as Traditional Chinese Medicine (TCM) and Indian Ayurveda. Moreover, it has been involved in the inhibition of certain genes/protiens effects to promote regulation of signaling pathways. Natural remedies have been scientifically proven with remarkable bioactivities and are considered a cheap and safe source for lung disease.

METHODS

This comprehensive review highlighted the literature about traditional plants and their metabolites with their applications for the treatment of lung diseases through experimental models in humans. Natural drugs information and mode of mechanism have been studied through the literature retrieved by Google Scholar, ScienceDirect, SciFinder, Scopus and Medline PubMed resources against lung diseases.

RESULTS

In vitro, in vivo and computational studies have been explained for natural metabolites derived from plants (like flavonoids, alkaloids, and terpenoids) against different types of lung diseases. Probiotics have also been biologically active therapeutics against cancer, anti-inflammation, antiplatelet, antiviral, and antioxidants associated with lung diseases.

CONCLUSION

The results of the mentioned natural metabolites repurposed for different lung diseases especially for SARS-CoV-2 should be evaluated more by advance computational applications, experimental models in the biological system, also need to be validated by clinical trials so that we may be able to retrieve potential drugs for most challenging lung diseases especially SARS-CoV-2.

In vitro antimicrobial, physicochemical, pharmacokinetics and molecular docking studies of benzoyl uridine esters against SARS-CoV-2 main protease

Different esters were found potential against microorganisms, and could be a better choice to solve the multidrug resistant (MDR) pathogenic global issue due to their improved biological and pharmacokinetic properties. In this view, several 4-t-butylbenzoyl uridine esters 4-15 with different aliphatic and aromatic groups were synthesized for antimicrobial, physicochemical and biological studies. In vitro antimicrobial tests against nine bacteria and three fungi along with prediction of activity spectra for substances (PASS) indicated promising antifungal functionality of these uridine esters compared to the antibacterial activities. In support of this observation their cytotoxicity and molecular docking studies have been performed against lanosterol 14α-demethylase (CYP51A1) and Aspergillus flavus (1R51). Significant binding affinities were observed against SARS-CoV-2 main protease (7BQY) considering hydroxychloroquine (HCQ) as standard. ADMET predictions were investigated to evaluate their absorption, metabolism and toxic properties. Most of the uridine esters showed better results than that of the HCQ. Overall, the present study might be useful for the development of uridine-based novel MDR antimicrobial and COVID-19 drugs.

Over 1000-Fold Synergistic Boost in Viniferin Levels by Elicitation of Vitis vinifera cv. Gamay Red Cell Cultures over Accumulating Phenylalanine

Elicitation treatments of grape cell cultures with methyl jasmonate (MeJA), ultraviolet-C (UV-C) irradiation, and sucrose induce mild production of stilbenes and flavonoids due to limited substrate availability. However, these treatments cause a synergistic boost of stilbenes production when applied to two phenylalanine (Phe)-enriched transgenic grape cell lines, AroG* + STS and AroG* + FLS. The combined treatment of UV-C elicitation on the Phe-fed AroG* + STS line resulted in the highest content of stilbenes (37.8-fold increase, 17.39 mg/g dry weight (DW)) mainly due to resveratrol (64-fold, 3.23 mg/g DW) and viniferin (1343-fold, 13.43 mg/g DW). The synergistic increase following either UV-C or MeJA elicitation was due to the induction of stilbene-related genes, while sucrose treatment had no effect on gene expression levels and served as an additional carbon source for phenylpropanoids. The combined strategy presented may enable future usage of grape cell cultures for the production of stilbenes and in particular viniferin.

Predicting global diet-disease relationships at the atomic level: a COVID-19 case study

Over the past few months, numerous studies harnessed in silico methods such as molecular docking to evaluate food compounds for inhibitory activity against coronavirus infection and replication. These studies capitalize on the efficiency of computational methods to quickly guide subsequent research and examine diet-disease relationships, and their sudden widespread utility may signal new opportunities for future antiviral and bioactive food research. Using Coronavirus Disease 2019 (COVID-19) research as a case study, we herein provide an overview of findings from studies using molecular docking to study food compounds as potential inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), explore considerations for the critical interpretation of study findings, and discuss how these studies help shape larger conversations of diet and disease.

Vine Shoots as a Source of Trans-Resveratrol and ε-Viniferin: A Study of 23 Italian Varieties

Stilbenes are a family of phenolic secondary metabolites that are known for their important roles in plant protection and human health. Numerous studies show that vine shoots, one of the most abundant winery wastes, could be used as a source of bioactive compounds such as stilbenes. The predominant stilbenoids in vine shoots are trans-resveratrol (Rsv) and ε-viniferin (Vf), whose content varies depending on numerous intrinsic and extrinsic factors. The present work investigates the influence of pre-treatment and variety on stilbene concentration in vine shoots. Vine shoots of the Primitivo and Negroamaro varieties were submitted to four different trials before stilbene extraction (untreated, dried at 50 °C for 24 h, dried at 70 °C for 15 min, and dried at 80 °C for 10 min). The results showed that the heat pre-treatments had a slight impact on the total phenol and stilbene content. In contrast, the variety variable had a stronger impact on stilbene concentration, ranging from 2700 to 6400 mg kg⁻¹ DW for untreated vine shoots of 23 Italian varieties. In all vine shoots, the most abundant stilbene compound was Rsv and the highest content was found in vine shoots of the Nero di Troia (5298.1 mg kg⁻¹ DW) and Negroamaro (5249.4 mg kg⁻¹ DW) varieties.

Design, Synthesis and Cytotoxicity of Thiazole-Based Stilbene Analogs as Novel DNA Topoisomerase IB Inhibitors

A series of new thiazole-based stilbene analogs were designed, synthesized and evaluated for DNA topoisomerase IB (Top1) inhibitory activity. Top1-mediated relaxation assays showed that the synthesized compounds possessed variable Top1 inhibitory activity. Among them, (E)-2-(3-methylstyryl)-4-(4-fluorophenyl)thiazole (8) acted as a potent Top1 inhibitor with high Top1 inhibition of ++++ which is comparable to that of CPT. A possible binding mode of compound 8 with Top1–DNA complex was further provided by molecular docking. An MTT assay against human breast cancer (MCF-7) and human colon cancer (HCT116) cell lines revealed that the majority of these compounds showed high cytotoxicity, with IC₅₀ values at micromolar concentrations. Compounds 8 and (E)-2-(4-tert-butylstyryl)-4-(4-fluorophenyl)thiazole (11) exhibited the most potent cytotoxicity with IC₅₀ values of 0.78 and 0.62 μM against MCF-7 and HCT116, respectively. Moreover, the preliminary structure–activity relationships of thiazole-based stilbene analogs was also discussed.

Assessment of Antioxidant, Immunomodulatory Activity of Oxidised Epigallocatechin-3-Gallate (Green Tea Polyphenol) and Its Action on the Main Protease of SARS-CoV-2—An In Vitro and In Silico Approach

Owing to the instability of Epigallocatechin Gallate (EGCG), it may undergo auto-oxidation and form oxidised products or dimers. In the present study, we aimed to evaluate the therapeutic effects, including antioxidation and immunomodulatory action, of the Oxidised Epigallocatechin Gallate (O-EGCG) as compared to native EGCG and the action of these compounds on main protease (Mpro) docking against SARS-CoV-2. HCT-116 (Human Colon Cancer) cell lines were used to estimate the total antioxidant capacity and lipid peroxidation levels and pro-inflammatory markers (human IL-6, IL-1β, TNF-α). Further, molecular docking analysis was performed by AutoDock and visualised in Discovery studio. Improved antioxidant capacity of O-EGCG was observed, and there was a significant decrease in the inflammatory markers (IL-1β, IL-6, and TNF-α) when O-EGCG was applied as compared to EGCG. The O-EGCG was shown to be strongly associated with the highest docking score and active site residues of IL-1, IL-6, and TNF- α, as well as the Mpro of SARS-CoV-2, according to in silico approach. The in vitro and in silico analyses indicate an improved therapeutic action of the oxidised form of EGCG. The effective inhibitory action of O-EGCG against SARS-CoV-2 suggests further exploration of the compound against COVID-19 and its efficacy. However, in vivo studies and understanding of the mechanism of action of O-EGCG may yield a better opinion on the use of O-EGCG and future human clinical trials.

Nutraceuticals in HIV and COVID-19-Related Neurological Complications: Opportunity to Use Extracellular Vesicles as Drug Delivery Modality

Simple Summary

In this review, we discuss the potential use of extracellular vesicles (EVs) to deliver dietary supplements to the brain to reduce brain complications associated with HIV, COVID-19, and other brain disorders. Brain-related complications affect people with HIV and COVID-19 alike. Moreover, since HIV patients are at a higher risk of contracting COVID-19, their neurological problems can be exacerbated by COVID-19. The use of dietary supplements together with available treatment options has been shown to reduce the severity of infections. However, these treatments are not chemically compatible with the body’s blood–brain barrier defense mechanism. Therefore, a viable delivery method is needed to deliver drugs and nutraceuticals to the brain in HIV and COVID-19 comorbid patients.

Abstract

People living with HIV/AIDS (PLWHA) are at an increased risk of severe and critical COVID-19 infection. There is a steady increase in neurological complications associated with COVID-19 infection, exacerbating HIV-associated neurocognitive disorders (HAND) in PLWHA. Nutraceuticals, such as phytochemicals from medicinal plants and dietary supplements, have been used as adjunct therapies for many disease conditions, including viral infections. Appropriate use of these adjunct therapies with antiviral proprieties may be beneficial in treating and/or prophylaxis of neurological complications associated with these co-infections. However, most of these nutraceuticals have poor bioavailability and cannot cross the blood–brain barrier (BBB). To overcome this challenge, extracellular vesicles (EVs), biological nanovesicles, can be used. Due to their intrinsic features of biocompatibility, stability, and their ability to cross BBB, as well as inherent homing capabilities, EVs hold immense promise for therapeutic drug delivery to the brain. Therefore, in this review, we summarize the potential role of different nutraceuticals in reducing HIV- and COVID-19-associated neurological complications and the use of EVs as nutraceutical/drug delivery vehicles to treat HIV, COVID-19, and other brain disorders.

A review of natural foods consumed during the COVID-19 pandemic life

Coronavirus 2019 (COVID-19) is an infectious disease that has brought life to a standstill around the world. Until a vaccine was found to combat COVID-19, the world conducted research and made recommendations for nutritional natural foods. Considering the risks incurred by contracting the disease, even though the production of various vaccines and vaccination of healthy people has started in some countries, individuals need useful foods to be ready for the COVID-19 pandemic. Recently, nutrient contents such as antioxidant compounds, vitamins, minerals, and probiotics that contribute to the immune system have been investigated. This paper attempts to determine the role of these dietary supplements in reducing the risk of COVID-19 and/or changing the course of the disease in COVID-19 patients and their effects on mortality. Supplements used and recommended for the COVID-19 pandemic life were investigated. In conclusion, more research is needed to determine the effectiveness of nutrients, vitamins, minerals, probiotics, prebiotics, and antioxidants used during the COVID-19 pandemic to inhibit the effect of SARS-CoV-2. In order to overcome the new global crisis, nutritional cures and treatments should be upgraded. However, additional research on the subject is needed.

Withanone and Withaferin-A are predicted to interact with transmembrane protease serine 2 (TMPRSS2) and block entry of SARS-CoV-2 into cells

Coronavirus disease 2019 (COVID-19) initiated in December 2019 in Wuhan, China and became pandemic causing high fatality and disrupted normal life calling world almost to a halt. Causative agent is a novel coronavirus called Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2/2019-nCoV). While new line of drug/vaccine development has been initiated world-wide, in the current scenario of high infected numbers, severity of the disease and high morbidity, repurposing of the existing drugs is heavily explored. Here, we used a homology-based structural model of transmembrane protease serine 2 (TMPRSS2), a cell surface receptor, required for entry of virus to the target host cell. Using the strengths of molecular docking and molecular dynamics simulations, we examined the binding potential of Withaferin-A (Wi-A), Withanone (Wi-N) and caffeic acid phenethyl ester to TPMRSS2 in comparison to its known inhibitor, Camostat mesylate. We found that both Wi-A and Wi-N could bind and stably interact at the catalytic site of TMPRSS2. Wi-N showed stronger interactions with TMPRSS2 catalytic residues than Wi-A and was also able to induce changes in its allosteric site. Furthermore, we investigated the effect of Wi-N on TMPRSS2 expression in MCF7 cells and found remarkable downregulation of TMPRSS2 mRNA in treated cells predicting dual action of Wi-N to block SARS-CoV-2 entry into the host cells. Since the natural compounds are easily available/affordable, they may even offer a timely therapeutic/preventive value for the management of SARS-CoV-2 pandemic. We also report that Wi-A/Wi-N content varies in different parts of Ashwagandha and warrants careful attention for their use.Communicated by Ramaswamy H. Sarma.

The Natural Stilbenoid (-)-Hopeaphenol Inhibits Cellular Entry of SARS-CoV-2 USA-WA1/2020, B.1.1.7, and B.1.351 Variants

Antivirals are urgently needed to combat the global SARS-CoV-2/COVID-19 pandemic, supplement existing vaccine efforts, and target emerging SARS-CoV-2 variants of concern. Small molecules that interfere with binding of the viral spike receptor binding domain (RBD) to the host angiotensin-converting enzyme II (ACE2) receptor may be effective inhibitors of SARS-CoV-2 cell entry. Here, we screened 512 pure compounds derived from natural products using a high-throughput RBD/ACE2 binding assay and identified (-)-hopeaphenol, a resveratrol tetramer, in addition to vatalbinoside A and vaticanol B, as potent and selective inhibitors of RBD/ACE2 binding and viral entry. For example, (-)-hopeaphenol disrupted RBD/ACE2 binding with a 50% inhibitory concentration (IC50) of 0.11 μM, in contrast to an IC50 of 28.3 μM against the unrelated host ligand/receptor binding pair PD-1/PD-L1 (selectivity index, 257.3). When assessed against the USA-WA1/2020 variant, (-)-hopeaphenol also inhibited entry of a VSVΔG-GFP reporter pseudovirus expressing SARS-CoV-2 spike into ACE2-expressing Vero-E6 cells and in vitro replication of infectious virus in cytopathic effect and yield reduction assays (50% effective concentrations [EC50s], 10.2 to 23.4 μM) without cytotoxicity and approaching the activities of the control antiviral remdesivir (EC50s, 1.0 to 7.3 μM). Notably, (-)-hopeaphenol also inhibited two emerging variants of concern, B.1.1.7/Alpha and B.1.351/Beta in both viral and spike-containing pseudovirus assays with similar or improved activities over the USA-WA1/2020 variant. These results identify (-)-hopeaphenol and related stilbenoid analogues as potent and selective inhibitors of viral entry across multiple SARS-CoV-2 variants of concern.

Molecular Mechanisms of Possible Action of Phenolic Compounds in COVID-19 Protection and Prevention

The worldwide outbreak of COVID-19 was caused by a pathogenic virus called Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Therapies against SARS-CoV-2 target the virus or human cells or the immune system. However, therapies based on specific antibodies, such as vaccines and monoclonal antibodies, may become inefficient enough when the virus changes its antigenicity due to mutations. Polyphenols are the major class of bioactive compounds in nature, exerting diverse health effects based on their direct antioxidant activity and their effects in the modulation of intracellular signaling. There are currently numerous clinical trials investigating the effects of polyphenols in prophylaxis and the treatment of COVID-19, from symptomatic, via moderate and severe COVID-19 treatment, to anti-fibrotic treatment in discharged COVID-19 patients. Antiviral activities of polyphenols and their impact on immune system modulation could serve as a solid basis for developing polyphenol-based natural approaches for preventing and treating COVID-19.

In silico identification of potential inhibitors against main protease of SARS-CoV-2 6LU7 from Andrographis panniculata via molecular docking, binding energy calculations and molecular dynamics simulation studies

Background

The ongoing global outbreak of new corona virus (SARS-CoV-2) has been recognized as global public health concern since it causes high morbidity and mortality every day. Due to the rapid spreading and re-emerging, we need to find a potent drug against SARS-CoV-2. Synthetic drugs, such as hydroxychloroquine, remdisivir have paid more attention and the effects of these drugs are still under investigation, due to their severe side effects. Therefore, the aim of the present study was performed to identify the potential inhibitor against main protease SARS-CoV-2 6LU7.

Objective

In this study, RO5, ADME properties, molecular dynamic simulations and free binding energy prediction were mainly investigated.

Results

The molecular docking study findings revealed that andrographolide had higher binding affinity among the selected natural diterpenoids compared to co-crystal native ligand inhibitor N3. The persistent inhibition of Ki for diterpenoids was analogous. Furthermore, the simulations of molecular dynamics and free binding energy findings have shown that andrographolide possesses a large amount of dynamic properties such as stability, flexibility and binding energy.

Conclusion

In conclusion, findings of the current study suggest that selected diterpenoids were predicted to be the significant phytonutrient-based inhibitor against SARS-CoV-2 6LU7 (M^pro). However, preclinical and clinical trials are needed for the further scientific validation before use.

Role of ACE2-Ang (1-7)-Mas axis in post-COVID-19 complications and its dietary modulation

Severe acute respiratory syndrome-coronavirus-2 (COVID-19) virus uses Angiotensin-Converting Enzyme 2 (ACE2) as a gateway for their entry into the human body. The ACE2 with cleaved products have emerged as major contributing factors to multiple physiological functions and pathogenic complications leading to the clinical consequences of the COVID-19 infection Decreased ACE2 expression restricts the viral entry into the human cells and reduces the viral load. COVID-19 infection reduces the ACE2 expression and induces post-COVID-19 complications like pneumonia and lung injury. The modulation of the ACE2-Ang (1–7)-Mas (AAM) axis is also being explored as a modality to treat post-COVID-19 complications. Evidence indicates that specific food components may modulate the AAM axis. The variations in the susceptibility to COVID-19 infection and the post-COVID its complications are being correlated with varied dietary habits. Some of the food substances have emerged to have supportive roles in treating post-COVID-19 complications and are being considered as adjuvants to the COVID-19 therapy. It is possible that some of their active ingredients may emerge as the direct treatment for the COVID-19.

Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models

The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.

Targeting autophagy with natural products to prevent SARS-CoV-2 infection

Autophagy is a catabolic process that maintains internal homeostasis and energy balance through the lysosomal degradation of redundant or damaged cellular components. During virus infection, autophagy is triggered both in parenchymal and in immune cells with different finalistic objectives: in parenchymal cells, the goal is to destroy the virion particle while in macrophages and dendritic cells the goal is to expose virion-derived fragments for priming the lymphocytes and initiate the immune response. However, some viruses have developed a strategy to subvert the autophagy machinery to escape the destructive destiny and instead exploit it for virion assembly and exocytosis. Coronaviruses (like SARS-CoV-2) possess such ability. The autophagy process requires a set of proteins that constitute the core machinery and is controlled by several signaling pathways. Here, we report on natural products capable of interfering with SARS-CoV-2 cellular infection and replication through their action on autophagy. The present study provides support to the use of such natural products as adjuvant therapeutics for the management of COVID-19 pandemic to prevent the virus infection and replication, and so mitigating the progression of the disease.

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

The ongoing COVID-19 pandemic, caused by SARS-CoV-2, has now spread across the nations with high mortality rates and multifaceted impact on human life. The proper treatment methods to overcome this contagious disease are still limited. The main protease enzyme (Mpro, also called 3CLpro) is essential for viral replication and has been considered as one of the potent drug targets for treating COVID-19. In this study, virtual screening was performed to find out the molecular interactions between 36 natural compounds derived from sesame and the Mpro of COVID-19. Four natural metabolites, namely, sesamin, sesaminol, sesamolin, and sesamolinol have been ranked as the top interacting molecules to Mpro based on the affinity of molecular docking. Moreover, stability of these four sesame-specific natural compounds has also been evaluated using molecular dynamics (MD) simulations for 200 nanoseconds. The molecular dynamics simulations and free energy calculations revealed that these compounds have stable and favorable energies, causing strong binding with Mpro. These screened natural metabolites also meet the essential conditions for drug likeness such as absorption, distribution, metabolism, and excretion (ADME) properties as well as Lipinski's rule of five. Our finding suggests that these screened natural compounds may be evolved as promising therapeutics against COVID-19.

The Repurposed ACE2 Inhibitors: SARS-CoV-2 Entry Blockers of Covid-19

The highly infectious disease COVID-19 is induced by SARS-coronavirus 2 (SARS-CoV-2), which has spread rapidly around the globe and was announced as a pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 binds to the host cell's angiotensin converting enzyme 2 (ACE2) receptor through the viral surface spike glycoprotein (S-protein). ACE2 is expressed in the oral mucosa and can therefore constitute an essential route for entry of SARS-CoV-2 into hosts through the tongue and lung epithelial cells. At present, no effective treatments for SARS-CoV-2 are yet in place. Blocking entry of the virus by inhibiting ACE2 is more advantageous than inhibiting the subsequent stages of the SARS-CoV-2 life cycle. Based on current published evidence, we have summarized the different in silico based studies and repurposing of anti-viral drugs to target ACE2, SARS-CoV-2 S-Protein: ACE2 and SARS-CoV-2 S-RBD: ACE2. This review will be useful to researchers looking to effectively recognize and deal with SARS-CoV-2, and in the development of repurposed ACE2 inhibitors against COVID-19.

Identification of potential drug candidates to combat COVID-19: a structural study using the main protease (mpro) of SARS-CoV-2

The recent outbreak of the SARS-CoV-2 virus leading to the disease COVID 19 has become a global pandemic that is spreading rapidly and has caused a global health emergency. Hence, there is an urgent need of the hour to discover effective drugs to control the pandemic caused by this virus. Under such conditions, it would be imperative to repurpose already known drugs which could be a quick and effective alternative to discovering new drugs. The main protease (Mpro) of SARS-COV-2 is an attractive drug target because of its essential role in the processing of the majority of the non-structural proteins which are translated from viral RNA. Herein, we report the high-throughput virtual screening and molecular docking studies to search for the best potential inhibitors against Mpro from FDA approved drugs available in the ZINC database as well as the natural compounds from the Specs database. Our studies have identified six potential inhibitors of Mpro enzyme, out of which four are commercially available FDA approved drugs (Cobicistat, Iopromide, Cangrelor, and Fortovase) and two are from Specs database of natural compounds (Hopeaphenol and Cyclosieversiodide-A). While Cobicistat and Fortovase are known as HIV drugs, Iopromide is a contrast agent and Cangrelor is an anti-platelet drug. Furthermore, molecular dynamic (MD) simulations using GROMACS were performed to calculate the stability of the top-ranked compounds in the active site of Mpro. After extensive computational studies, we propose that Cobicistat and Hopeaphenol show potential to be excellent drugs that can form the basis of treating COVID-19 disease.Communicated by Ramaswamy H. Sarma.

Nutraceuticals and Herbs in Reducing the Risk and Improving the Treatment of COVID-19 by Targeting SARS-CoV-2

The worldwide transmission of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a deadly or devastating disease is known to affect thousands of people every day, many of them dying all over the planet. The main reason for the massive effect of COVID-19 on society is its unpredictable spread, which does not allow for proper planning or management of this disease. Antibiotics, antivirals, and other prescription drugs, necessary and used in therapy, obviously have side effects (minor or significant) on the affected person, there are still not clear enough studies to elucidate their combined effect in this specific treatment, and existing protocols are sometimes unclear and uncertain. In contrast, it has been found that nutraceuticals, supplements, and various herbs can be effective in reducing the chances of SARS-CoV-2 infection, but also in alleviating COVID-19 symptoms. However, not enough specific details are yet available, and precise scientific studies to validate the approved benefits of natural food additives, probiotics, herbs, and nutraceuticals will need to be standardized according to current regulations. These alternative treatments may not have a direct effect on the virus or reduce the risk of infection with it, but these products certainly stimulate the human immune system so that the body is better prepared to fight the disease. This paper aims at a specialized literary foray precisely in the field of these “cures” that can provide real revelations in the therapy of coronavirus infection

Recent progress in the development of potential drugs against SARS-CoV-2

SARS-CoV-2, a newly emerged and highly pathogenic coronavirus, is identified as the causal agent of Coronavirus Disease (2019) (COVID-19) in the late December 2019, in China. The virus has rapidly spread nationwide and spilled over to the other countries around the globe, resulting in more than 120 million infections and 2.6 million deaths until the time of this review. Unfortunately, there are still no specific drugs available against this disease, and it is very necessary to call upon more scientists to work together to stop a further spread. Hence, the recent progress in the development of drugs may help scientific community quickly understand current research status and further develop new effective drugs. Herein, we summarize the cellular entry and replication process of this virus and discuss the recent development of potential viral based drugs that target bio-macromolecules in different stages of the viral life cycle, especially S protein, 3CLPro, PLPro, RdRp and helicase.

Randomized Double-blind Placebo-controlled Proof-of-concept Trial of Resveratrol for Outpatient Treatment of Mild Coronavirus Disease (COVID-19)

Resveratrol is a polyphenol that has been well studied and has demonstrated anti-viral and anti-inflammatory properties that might mitigate the effects of COVID-19. Outpatients (N=105) were recruited from central Ohio in late 2020. Participants were randomly assigned to receive placebo or resveratrol. Both groups received a single dose of Vitamin D3 which was used as an adjunct. The primary outcome measure was hospitalization within 21 days of symptom onset; secondary measures were ER visits, incidence of pneumonia and pulmonary embolism. Five patients chose not to participate after randomization. Twenty-one day outcome was determined of all one hundred participants (mean [SD] age 55.6 [8.8] years; 61% female) (or their surrogates). There were no clinically significant adverse events attributed to resveratrol. Outpatients in this phase 2 study treated with resveratrol had a lower incidence compared to placebo of: hospitalization (2% vs. 6%, RR 0.33, 95% CI 0.04-3.10), COVID-related ER visits (8% vs. 14%, RR 0.57, 95% CI 0.18-1.83), and pneumonia (8% vs. 16%, RR 0.5, 95% CI 0.16-1.55). One patient (2%) in each group developed pulmonary embolism (RR 1.00, 95% CI: 0.06-15.55). This underpowered study was limited by small sample size and low incidence of primary adverse events. A larger trial could determine efficacy. TRIAL REGISTRATIONS: ClinicalTrials.gov NCT04400890 26/05/2020; FDA IND #150033 05/05/2020.

Possibility of HIV-1 protease inhibitors-clinical trial drugs as repurposed drugs for SARS-CoV-2 main protease: a molecular docking, molecular dynamics and binding free energy simulation study

Initially, the SARS-CoV-2 virus was emerged from Wuhan, China and rapidly spreading across the world and urges the scientific community to develop antiviral therapeutic agents. Among several strategies, drug repurposing will help to react immediately to overcome the COVID-19 pandemic. In the present study, we have chosen two clinical trial drugs against HIV-1 protease namely, TMB607 and TMC310911 to use as the inhibitors of SARS-CoV-2 main protease (Mpro) enzyme. To make use of these two inhibitors as the repurposed drugs for COVID-19, it is essential to know the molecular basis of the binding mechanism of these two molecules with the SARS-CoV-2 Mpro. To understand the binding mechanism, we have performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations against the SARS-CoV-2 Mpro. The docking results indicate that both molecules form intermolecular interactions with the active site amino acids of Mpro enzyme. However, during the MD simulations, TMB607 forms strong interaction with the key amino acids of Mpro, and remains intact. The RMSD and RMSF values of both complexes were stable throughout the MD simulations. The MM-GBSA binding free energy values of both complexes are -43.7 and -34.9 kcal/mol, respectively. This in silico study proves that the TMB607 molecule binds strongly with the SARS-CoV-2 Mpro enzyme and it may be suitable for the drug repurposing of COVID-19 and further drug designing.Communicated by Ramaswamy H. Sarma.

In-silico investigation of phytochemicals from Asparagus racemosus as plausible antiviral agent in COVID-19

COVID-19 has ravaged the world and is the greatest of pandemics in human history, in the absence of treatment or vaccine the mortality and morbidity rates are very high. The present investigation was undertaken to screen and identify the potent leads from the Indian Ayurvedic herb, Asparagus racemosus (Willd.) against SARS-CoV-2 using molecular docking and dynamics studies. The docking analysis was performed on the Glide module of Schrödinger suite on two different proteins from SARS-CoV-2 viz. NSP15 Endoribonuclease and spike receptor-binding domain. Asparoside-C, Asparoside-D and Asparoside -F were found to be most effective against both the proteins as confirmed through their docking score and affinity. Further, the 100 ns molecular dynamics study also confirmed the potential of these compounds from reasonably lower root mean square deviations and better stabilization of Asparoside-C and Asparoside-F in spike receptor-binding domain and NSP15 Endoribonuclease respectively. MM-GBSA based binding free energy calculations also suggest the most favourable binding affinities of Asparoside-C and Asparoside-F with binding energies of -62.61 and -55.19 Kcal/mol respectively with spike receptor-binding domain and NSP15 Endoribonuclease. HighlightsAsparagus racemosus have antiviral potentialPhytochemicals of Shatavari showed promising in-silico docking and MD resultsAsparaoside-C and Asparoside-F has good binding with target proteinsAsparagus racemosus holds promise as SARS-COV-2 (S) and (N) proteins inhibitor Communicated by Ramaswamy H. Sarma.