Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Pathophysiology of SARS-CoV2 Mediated Depression, Therapeutics, and Consequences: A Comprehensive Narrative

The Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), belongs to emerging and reemerging diseases, which was first identified and reported in Wuhan, China, in December 2019. The genetic sequence of SARS-CoV-2 was similar to the SARS virus, a β-coronavirus. The epidemiological studies suggest that the transmission of SARS-CoV-2 mainly occurs from an infected person to others through close contact with the respiratory droplets or by having contact with SARS-CoV-2 adhering to objects and surfaces. The incubation period ranges from 5 to14 days. The symptoms include fever, dry cough, tiredness, aches, chest pain, conjunctivitis, diarrhea, headache, difficulty in breathing or short breath, loss of taste, smell, rashes on the skin, and sore throat. Some reports indicated that males exhibited lower scores than females, the younger populations displayed increased symptoms, Chinese/Taiwanese people registered only scarce symptoms, and Canadians experienced more symptoms. The results of several studies suggested that while COVID-19 had a significant effect on depression, job instability affected anxiety and depression. The diagnostics to detect the presence of coronavirus involve ELISA and RT-PCR. There is no specific treatment available to eradicate COVID-19. The therapeutics used to treat COVID 19 exhibited severe side effects. Recently, some Indian traditional medicinal plants have shown promise in reducing the risk of viral infection and also boosting the immunity of an individual. This paper presents an overview of the current status of depression in the SARS CoV2 infected people and the measures required to overcome COVID-19 induced depression in patients even after recovery.

Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro) Identified from the Library of FDA-Approved Drugs Using Molecular Docking Studies

The Corona Virus Infectious Disease-2019 (COVID-19) outbreak originated at Wuhan, China, in December 2019. It has already spread rapidly and caused more than 6.5 million deaths worldwide. Its causal agent is a beta-coronavirus named SARS-CoV-2. Many efforts have already been made to develop new vaccines and drugs against these viruses, but over time, it has changed its molecular nature and evolved into more lethal variants, such as Delta and Omicron. These will lead us to target its more-conserved proteins. The sequences' BLAST and crystal structure of the main protease M^pro suggest a high sequence and structural conservation. M^pro is responsible for the proteolytic maturation of the polyprotein essential for the viral replication and transcription, which makes it an important drug target. Discovery of new drug molecules may take years before getting to the clinics. So, considering urgency, we performed molecular docking studies using FDA-approved drugs to identify molecules that could potentially bind to the substrate-binding site and inhibit SARS-CoV-2's main protease (M^pro). We used the Glide module in the Schrödinger software suite to perform molecular docking studies, followed by MM-GBSA-based energy calculations to score the hit molecules. Molecular docking and manual analysis suggest that several drugs may bind and potentially inhibit M^pro. We also performed molecular simulations studies for selected compounds to evaluate protein-drug interactions. Considering bioavailability, lesser toxicity, and route of administration, some of the top-ranked drugs, including lumefantrine (antimalarial), dipyridamole (coronary vasodilator), dihydroergotamine (used for treating migraine), hexoprenaline (anti asthmatic), riboflavin (vitamin B2), and pantethine (vitamin B5) may be taken forward for further in vitro and in vivo experiments to investigate their therapeutic potential.

In vitro testing and computational analysis of specific phytochemicals with antiviral activities considering their possible applications against COVID-19

The purpose of this study was to investigate the reservoir of natural products against the SARS-CoV-2 virus and to identify suitable candidates in order to recommend appropriate phytotherapy. Adequately prepared 65 molecules from traditional Chinese medicine with proven antiviral properties were subjected to docking analysis using AutoDock Vina 4 software with the aim to investigate binding affinity and interactions of compounds with Mpro from the SARS-CoV-2 virus. Biflavonoids and tannins show best docking scores with -9,80 kcal/mol for biflavonoids and -9,00 kcal/mol for tannins. Biflavonoids: amentoflavone, agathistaflavone, robustaflavone, hinokiflavone and rhusflavanone were tested for their radical scavenging activity. Partition coefficients were examined by RP-HPLC. Evaluation of drug-likeness properties of investigated biflavonoids suggested rhusflavanone as a molecule with the best ADMET characteristics. Anti-inflammatory activity of rhusflavanone was investigated in LPS stimulated RAW264.7 macrophages. Tested biflavonoids exibit beneficial effects against inflammation by scavenging free radicals and by suppressing the production of proinflammatory mediators by macrophages. Both predictions of affinity spectra for substances (PASS) and in vitro testing showed promising biological activity of investigated biflavonoids. A Quantum chemical study was performed in order to calculate the thermodynamic, molecular orbital, and electrostatic potential of selected molecules and to compare their biological and chemical features. Our results highlighted antioxidant, anti-inflammatory and antiviral properties of investigated compounds, emphasizing the significance of biflavonoid moiety to selected characteristics, which encourage further investigational strategies against COVID-19.

Targeting COVID-19 pandemic: in silico evaluation of 2-hydroxy-1, 2-diphenylethanone N(4)-methyl-N(4)-phenylthiosemicarbazone as a potential inhibitor of SARS-CoV-2

The global spread of the COVID-19 pandemic caused by the etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), triggered researchers to identify and develop novel antiviral therapeutics. Herein, we report a new molecule 2-hydroxy-1,2-diphenylethanone N(4)-methyl-N(4)-phenyl thiosemicarbazone (BMPTSC), as a potential inhibitor of SARS-CoV-2. BMPTSC was synthesized, characterized by IR and NMR studies, and the structural parameters were analyzed computationally by B3LYP/cc-pVDZ method. Molecular docking studies were performed to get insights into the energetics and compatibility of BMPTSC against various SARS-CoV-2 drug targets. The best docking poses of target protein-BMPTSC complex structures were further subjected to molecular dynamics (MD) simulations. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations on the binding of BMPTSC with the target proteins viz. spike glycoprotein and ACE-2 protein showed energy values of -179.87 and -145.61 kJ/mol, respectively. Moreover, BMPTSC obeys Lipinski's rule, and further in silico assessment of oral bioavailability, bioactivity scores, ADME, drug-likeness, and medicinal chemistry friendliness suggests that this molecule is a promising candidate for the COVID-19 drug discovery process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11224-022-02033-8.

Metabolomic profiling of three Araucaria species, and their possible potential role against COVID-19

The COVID-19 pandemic in Egypt is a part of the worldwide global crisis of coronavirus 2 (SARS-CoV-2). The contagious life-threatening condition causes acute respiratory syndrome. The present study aimed to assess the compounds identified by LC-MS of the methanolic leaves extracts from three conifers trees cultivated in Egypt (Araucaria bidwillii, Araucaria. cunninghamii and Araucaria heterophylla) via docking technique as potential inhibitor of COVID-19 virus on multiple targets; viral main protease (Mpro, 6LU7), non-structural protein-16 which is a methyl transferase (nsp16, 6W4H) and RNA dependent RNA polymerase (nsp12, 7BV2). Among the three targets, nsp16 was the best target recognized by the tested compounds as can be deduced from docking studies. Moreover, the methanolic extract of A. cunninghamii showed the highest radical-scavenging activity using (DPPH test) with 53.7 µg/mL comparable to ascorbic acid with IC50 = 46 µg/mL The anti-inflammatory potential carried using enzyme linked immunoassay showed the highest activity for A. cunninghamii and A. bidwillii followed by A. heterophylla with IC50 = 23.20 ± 1.17 µg/mL, 82.83 ± 3.21 µg/mL and 221.13 ± 6.7 µg/mL, respectively (Celecoxib was used as a standard drug with IC50 = 141.92 ± 4.52 µg/mL). Moreover, a molecular docking study was carried for the LC-MS annotated metabolites to validate their anti-inflammatory inhibitory effect using Celecoxib as a reference compound and showed a high docking score (-7.7 kcal/mol) for Octadecyl (E) P-coumarate and (-7.3 kcal/mol) for secoisolariciresinol rhamnoside.Communicated by Ramaswamy H. Sarma.

SAR and QSAR of COVID-19 Main Protease–Inhibitor Interactions of Recently X-ray Crystalized Complexes

COVID-19 is still widespread worldwide and up to now there is no established antiviral able to control the disease. Main protease is responsible for the viral replication and transcription; thus, its inhibition is a promising route to control virus proliferation. The present study aims to examine detail interactions between main protease and recently reported ninety-seven inhibitors with available X-ray crystallography to define factors enhance inhibition activity; thirty-two of most potent inhibitors were examined to identify sites and types of interaction. The study showed formation of covalent bond, H-bond and hydrophobic interaction with key residues in the active side. Covalent bond is observed in seventeen complexes, all of them by attack of the 145Cys thiol group on Michael acceptor, aldehyde or its hydrate, α-ketoamide, double bond or acetamide methyl group; the latter type requires H-bonding between acetamide carbonyl oxygen and at least one of 143Gly, 144Ser or 145Cys. Potent inhibitors, disulfiram and ebselen docked in the same binding site. Accordingly, factors identify inhibition include forming covalent bond and existing terminal hydrophobic groups and amidic or peptidomimetic structure. Binding affinity was found correlated with topological diameter up to 24 bond, molecular size, branching, polar surface area up to 199 Ų and hydrophilicity.

AI-Aided Design of Novel Targeted Covalent Inhibitors against SARS-CoV-2

The drug repurposing of known approved drugs (e.g., lopinavir/ritonavir) has failed to treat SARS-CoV-2-infected patients. Therefore, it is important to generate new chemical entities against this virus. As a critical enzyme in the lifecycle of the coronavirus, the 3C-like main protease (3CLpro or Mpro) is the most attractive target for antiviral drug design. Based on a recently solved structure (PDB ID: 6LU7), we developed a novel advanced deep Q-learning network with a fragment-based drug design (ADQN-FBDD) for generating potential lead compounds targeting SARS-CoV-2 3CLpro. We obtained a series of derivatives from the lead compounds based on our structure-based optimization policy (SBOP). All of the 47 lead compounds obtained directly with our AI model and related derivatives based on the SBOP are accessible in our molecular library. These compounds can be used as potential candidates by researchers to develop drugs against SARS-CoV-2.

AI-Aided Design of Novel Targeted Covalent Inhibitors against SARS-CoV-2

The drug repurposing of known approved drugs (e.g., lopinavir/ritonavir) has failed to treat SARS-CoV-2-infected patients. Therefore, it is important to generate new chemical entities against this virus. As a critical enzyme in the lifecycle of the coronavirus, the 3C-like main protease (3CLpro or Mpro) is the most attractive target for antiviral drug design. Based on a recently solved structure (PDB ID: 6LU7), we developed a novel advanced deep Q-learning network with a fragment-based drug design (ADQN-FBDD) for generating potential lead compounds targeting SARS-CoV-2 3CLpro. We obtained a series of derivatives from the lead compounds based on our structure-based optimization policy (SBOP). All of the 47 lead compounds obtained directly with our AI model and related derivatives based on the SBOP are accessible in our molecular library. These compounds can be used as potential candidates by researchers to develop drugs against SARS-CoV-2.

Virtual screening and molecular dynamics simulation analysis of Forsythoside A as a plant-derived inhibitor of SARS-CoV-2 3CLpro

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a more severe strain of coronavirus (CoV) that was first emerged in China in 2019. Available antiviral drugs could be repurposed and natural compounds with antiviral activity could be safer and cheaper source of medicine for SARS-CoV-2. 78 natural antiviral compounds database was identified from literature and virtual screening technique was applied to identify potential 3-chymotrypsin-like protease (3CLpro) inhibitors. Molecular docking studies were conducted to analyze the main protease (3CLpro) and inhibitors interactions with key residues of active site of target protein (PDB ID: 6LU7), active site constitute the part of active domain I and II of 3CLpro. 10 compounds with highest dock score were subjected to calculate ADMET parameters to figure out drug-likeness. Molecular dynamic (MD) simulation of the selected lead was performed by Amber simulation package to understand the conformational changes in docked complex. MD simulations analysis (RMSD, RMSF, Rg, BF, HBs, and SASA plots) of lead bounded with 3CLpro, hence revealed the important structural turns and twists during MD simulations from 0 to 100 ns. MM-PBSA/GBSA methods has also been applied for the estimation binding free energy (BFE) of the selected lead-complex. The present study has identified lead compound “Forsythoside A” an active extract of Forsythia suspense as SARS-CoV-2 3CLpro inhibitor that can block the viral replication and translation. Structural analysis of target protein and lead compound performed in this study could contribute to the development of potential drug against SARS-CoV-2 infection.

COVID-19: inflammatory responses, structure-based drug design and potential therapeutics

The COVID-19 pandemic caused by SARS-CoV-2 is responsible for the global health emergency. Here, we explore the diverse mechanisms of SARS-CoV-induced inflammation. We presume that SARS-CoV-2 likely contributes analogous inflammatory responses. Possible therapeutic mechanisms for reducing SARS-CoV-2-mediated inflammatory responses comprise FcR inactivation. Currently, there is no specific remedy available against the SARS-CoV-2. Consequently, recognizing efficacious antiviral leads to combat the virus is crucially desired. The coronavirus (CoV) main protease (Mpro also called 3CLpro), which plays an indispensable role in viral replication and transcription, is an interesting target for drug design. This review compiles the latest advances in biological and structural research, along with development of inhibitors targeting CoV Mpros. It is anticipated that inhibitors targeting CoV Mpros could be advanced into wide-spectrum antiviral drugs in case of COVID-19 and other CoV-related diseases. The crystal structural and docking results have shown that Ebselen, N3, TDZD-8 and α-ketoamide (13b) inhibitors can bind to the substrate-binding pocket of COVID-19 Mpro. α-ketoamide-based inhibitor 13b inhibits the replication of SARS-CoV-2 in human Calu3 lung cells. Quantitative real-time RT-PCR (qRT-PCR) showed that the treatment with Ebselen, TDZD-8 and N3 reduced the amounts of SARS-CoV-2, respectively, 20.3-, 10.19- and 8.4-fold compared to the treatment in the absence of inhibitor. Moreover, repurposing of already present drugs to treat COVID-19 serves as one of the competent and economic therapeutic strategies. Several anti-malarial, anti-HIV and anti-inflammatory drugs as mentioned in Table 2 were found effective for the COVID-19 treatment. Further, hydroxychloroquine (HCQ) was found more potent than chloroquine (CQ) in inhibiting SARS-CoV-2 in vitro. Furthermore, convalescent plasma from patients who have recuperated from viral infections can be employed as a therapy without the appearance of severe adverse events. Hence, it might be valuable to examine the safety and efficacy of convalescent plasma transfusion in SARS-CoV-2-infected patients.

Computational screening of potential drugs against COVID-19 disease: the Neuropilin-1 receptor as molecular target

The transmembrane receptor Neuropilin-1 (NRP-1) was reported to serve as a host cell entry factor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19 disease. Therefore, molecular compounds interfering with SARS-CoV-2 binding to NRP-1 seem to be potential candidates as new antiviral drugs. In this study, NRP-1 receptor was targeted using a library of 1167 compounds previously analyzed in COVID-19 related studies. The results show the effectiveness of Nafamostat, Y96, Selinexor, Ebastine and UGS, in binding to NRP-1 receptor, with docking scores lower than − 8.2 kcal/mol. These molecules interact with NRP-1 receptor key residues, which makes them promising drugs to pursue further biological assays to explore their potential use in the treatment of COVID-19.

Impact of Drug Repurposing on SARS-Cov-2 Main Protease

The recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public health and the global economy. The resolved crystal structure of the main protease of SARS-CoV-2 or SCV2 (M^pro) has led to its identification as an attractive target for designing potent antiviral drugs. Herein, we provide a comparative molecular impact of hydroxychloroquine (HCQ), remdesivir, and β-D-N⁴-Hydroxycytidine (NHC) binding on SCV2 M^pro using various computational approaches like molecular docking and molecular dynamics (MD) simulation. Data analyses showed that HCQ, remdesivir, and NHC binding to SARS-CoV-2 M^pro decrease the protease loop capacity to fluctuate. These binding influences the drugs’ optimum orientation in the conformational space of SCV2 M^pro and produce noticeable steric effects on the interactive residues. An increased hydrogen bond formation was observed in SCV2 M^pro–NHC complex with a decreased receptor residence time during NHC binding. The binding mode of remdesivir to SCV2 M^pro differs from other drugs having van der Waals interaction as the force stabilizing protein–remdesivir complex. Electrostatic interaction dominates in the SCV2 M^pro−HCQ and SCV2 M^pro–NHC. Residue Glu166 was highly involved in the stability of remdesivir and NHC binding at the SCV2 M^pro active site, while Asp187 provides stability for HCQ binding.

Structure-based design and synthesis of copper(ii) complexes as antivirus drug candidates targeting SARS CoV-2 and HIV

This paper describes the structure-based design and synthesis of two novel square-planar trans-N2O2 Cu(ii) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) of 2-((Z)-(4-methoxyphenylimino)methyl)-4,6-dichlorophenol (L1H) and 2-((Z)-(2,4-dibromophenylimino)methyl)-4-bromophenol (L2H) as potential inhibitors against the main protease of the SARS-CoV-2 and HIV viruses.

Molecular binding studies of anthocyanins with multiple antiviral activities against SARS-CoV-2

BACKGROUND

The search for ideal drugs with absolute antiviral activity against SARS-CoV-2 is still in place, and attention has been recently drawn to natural products. Several molecular targets have been identified as points of therapeutic intervention. The targets used in this study include SARS-CoV-2 helicase, spike protein, RNA-dependent RNA polymerase, main protease, and human ACE-2. An integrative computer-aided approach, which includes molecular docking, pharmacophore modeling, and pharmacokinetic profiling, was employed to identify anthocyanins with robust multiple antiviral activities against these SARS-CoV-2 targets.

RESULT

Four anthocyanins (Delphinidin 3-O-glucosyl-glucoside, Cyanidin 3-O-glucosyl-rutinoside, Cyanidin 3-(p-coumaroyl)-diglucoside-5-glucoside), and Nasunin) with robust multiple inhibitory interactions were identified from a library of 118 anthocyanins using computer-aided techniques. These compounds exhibited very good binding affinity to the protein targets and moderate pharmacokinetic profiles. However, Cyanidin 3-O-glucosyl-rutinoside is reported to be the most suitable drug candidate with multiple antiviral effects against SARS-CoV-2 due to its good binding affinity to all five protein targets engaged in the study.

CONCLUSIONS

The anthocyanins reported in this study exhibit robust binding affinities and strong inhibitory molecular interactions with the target proteins and could be well exploited as potential drug candidates with potent multiple antiviral effects against COVID-19.

Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (Mpro) inhibitor using docking and molecular dynamics simulations

Novel SARS-CoV-2, an etiological factor of Coronavirus disease 2019 (COVID-19), poses a great challenge to the public health care system. Among other druggable targets of SARS-Cov-2, the main protease (Mpro) is regarded as a prominent enzyme target for drug developments owing to its crucial role in virus replication and transcription. We pursued a computational investigation to identify Mpro inhibitors from a compiled library of natural compounds with proven antiviral activities using a hierarchical workflow of molecular docking, ADMET assessment, dynamic simulations and binding free-energy calculations. Five natural compounds, Withanosides V and VI, Racemosides A and B, and Shatavarin IX, obtained better binding affinity and attained stable interactions with Mpro key pocket residues. These intermolecular key interactions were also retained profoundly in the simulation trajectory of 100 ns time scale indicating tight receptor binding. Free energy calculations prioritized Withanosides V and VI as the top candidates that can act as effective SARS-CoV-2 Mpro inhibitors.

Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease

COVID-19 was declared a pandemic by the World Health Organization (WHO) in March 2020. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). The aim of this study is to target the SARS-CoV-2 virus main protease (M^pro) via structure-based virtual screening. Consequently, > 580,000 ligands were processed via several filtration and docking steps, then the top 21 compounds were analysed extensively via MM-GBSA scoring and molecular dynamic simulations. Interestingly, the top compounds showed favorable binding energies and binding patterns to the protease enzyme, forming interactions with several key residues. Trihydroxychroman and pyrazolone derivatives, SN02 and SN18 ligands, exhibited very promising binding modes along with the best MM-GBSA scoring of -40.9 and -41.2 kcal mol^-1, resp. MD simulations of 300 ns for the ligand-protein complexes of SN02 and SN18 affirmed the previously attained results of the potential inhibition activity of these two ligands. These potential inhibitors can be the starting point for further studies to pave way for the discovery of new antiviral drugs for SARS-CoV-2.

Interaction of SARS-CoV-2 spike protein with angiotensin converting enzyme inhibitors and selected compounds from the chemical entities of biological interest

BACKGROUND

Recent COVID-19 outbreak has prompted the search of novel therapeutic agents to treat the disease. The initial step of the infection involves the binding of the virus through the viral spike protein with the host angiotensin converting enzyme 2 (ACE2). In this study, the interaction of some ACE or ACE2 inhibitors and their analogues as well as selected compounds with the viral spike protein as a strategy to hinder viral-ACE2 interaction were investigated. SARS-CoV-2 spike protein as well as the ligands were retrieved from protein databank and ChEBI database respectively. The molecules were prepared before initiating the virtual screening using PyRx software. Discovery studio was used to further visualize the binding interactions between the compounds and the protein.

RESULTS

The ACE inhibitors and their analogues fosinopril (1-), fosinopril and moexipril have the best binding affinity to the protein with binding energies < - 7.0 kcal/mol while non-flavonoid stilben-4-ol binds with free binding energy of - 7.1 kcal/mol. Others compounds which belong to either the flavonoids, terpenes and alkaloid classes also have binding energies  < - 7.0 kcal/mol. Such high binding energies were enhanced via hydrogen bond (h-bond) interactions in addition to other interactions observed between the compounds and the amino acid residues of the protein.

CONCLUSIONS

The ACE inhibitors and their analogues as well as the selected compounds could serve as inhibitors of the spike protein as well as lead in drug discovery processes to target the SARS-CoV-2 virus.

Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro

The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C-S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma.

Structurally modified compounds of hydroxychloroquine, remdesivir and tetrahydrocannabinol against main protease of SARS-CoV-2, a possible hope for COVID-19: Docking and molecular dynamics simulation studies

Now a days, more than 200 countries faces the health crisis due to epidemiological disease COVID-19 caused by SARS-CoV-2 virus. It will cause a very high impact on world's economy and global health sector. Earlier the structure of main protease (M^pro) protein was deposited in the RCSB protein repository. Hydroxychloroquine (HCQ) and remdesivir were found to effective in treatment of COVID-19 patients. Here we have performed docking and molecule dynamic (MD) simulation study of HCQ and remdesivir with M^pro protein which gave promising results to inhibit M^pro protein in SARS-CoV-2. On the basis of results obtained we designed structurally modified 18 novel derivatives of HCQ, remdesivir and tetrahydrocannabinol (THC) and carried out docking studies of all the derivatives. From the docking studies six molecules DK4, DK7, DK10, DK16, DK17 and DK19 gave promising results and can be use as inhibitor for M^pro of SARS-CoV-2 to control COVID-19 very effectively. Further, molecular dynamics simulation of one derivative of HCQ and one derivative of tetrahydrocannabinol showing excellent docking score was performed along with the respective parent molecules. The two derivatives gave excellent docking score and higher stability than the parent molecule as validated with molecular dynamics (MD) simulation for the binding affinities towards M^pro of SARS-CoV-2 thus represented as strong inhibitors at very low concentration.

A dossier on COVID-19 chronicle

The dissemination of the 2019 novel coronavirus (2019-nCoV) is presenting the planet with a new health emergency response or threat to health. The virus emerged in bats and was disseminated to humans in December 2019 via still unknown intermediate species in Wuhan, China. It is disseminated by inhalation or breaks out with infected droplets and the incubation period is between 2 and 14 days. The symptoms usually include high body temperature, cough, sore throat, dyspnea, low energy or tiredness, and weakness. The condition is moderate in most people; but in the elderly and those with comorbidities, it advances to pneumonia, acute respiratory distress syndrome (ARDS), and multiple organ failure. Popular research work includes normal/low WBC with upraised C-reactive protein (CRP). Treatment is generally supportive and requires home seclusion of suspected persons and rigorous infection control methods at hospitals. The Covid-19 has lower fatality than SARS and MERS. Among the proposed therapeutic regimen, hydroxychloroquine, chloroquine, remdisevir, azithromycin, toclizumab, and cromostat mesylate have shown promising results, and the limited benefit was seen with lopinavir-ritonavir treatment in hospitalized adult patients with severe COVID-19. Early development of the SARS-CoV-2 vaccine started based on the full-length genome analysis of severe acute respiratory syndrome coronavirus. Several subunit vaccines, peptides, nucleic acids, plant-derived, and recombinant vaccines are under pipeline. Research work, development of new medicines and vaccines, and efforts to reduce disease morbidity and mortality must be encouraged to improve our position in the fight against this disease and to protect human life.

Progression and Trends in Virus from Influenza A to COVID-19: An Overview of Recent Studies

Influenza is a highly known contagious viral infection that has been responsible for the death of many people in history with pandemics. These pandemics have been occurring every 10 to 30 years in the last century. The most recent global pandemic prior to COVID-19 was the 2009 influenza A (H1N1) pandemic. A decade ago, the H1N1 virus caused 12,500 deaths in just 19 months globally. Now, again, the world has been challenged with another pandemic. Since December 2019, the first case of a novel coronavirus (COVID-19) infection was detected in Wuhan. This infection has risen rapidly throughout the world; even the World Health Organization (WHO) announced COVID-19 as a worldwide emergency to ensure human health and public safety. This review article aims to discuss important issues relating to COVID-19, including clinical, epidemiological, and pathological features of COVID-19 and recent progress in diagnosis and treatment approaches for the COVID-19 infection. We also highlight key similarities and differences between COVID-19 and influenza A to ensure the theoretical and practical details of COVID-19.

Disposable face masks and reusable face coverings as non-pharmaceutical interventions (NPIs) to prevent transmission of SARS-CoV-2 variants that cause coronavirus disease (COVID-19): Role of new sustainable NPI design innovations and predictive mathematical modelling

Best-published evidence supports the combined use of vaccines with non-pharmaceutical interventions (NPIs), to reduce the relative risk of contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19; this will enable a safe transition to achieving herd immunity. Albeit complex, the strategic public health goal is to bundle NPIs to keep the basic reproduction number R₀ below one. However, validation of these NPIs is conducted using random clinical trials, which is challenging in a swiftly moving pandemic given the need for recruiting large participant cohort over a longitudinal analysis period. This review highlights emerging innovations for potentially improving the design, functionality and improved waste management of disposable face masks such as filtering facepiece (FFPs) respirators, medical masks, and reusable face coverings to help prevent COVID-19. It describes use of different mathematical models under varying scenarios to inform efficacy of single and combined use of NPIs as important counter-measures to break the cycle of COVID-19 infection including new SARS-CoV-2 variants. Demand for face masks during COVID-19 pandemic keeps increasing, especially for FFPs worn by medical workers. Collaborative and well-conducted randomised controlled trials across borders are required to generate robust data to inform common and consistent policies for COVID-19 and future pandemic planning and management; however, current use of systematic reviews of best available evidence can be considered to guide interim policies.

Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies

The current outbreak of novel coronavirus (COVID-19) infections urges the need to identify potential therapeutic agents. Therefore, the repurposing of FDA-approved drugs against today's diseases involves the use of de-risked compounds with potentially lower costs and shorter development timelines. In this study, the recently resolved X-ray crystallographic structure of COVID-19 main protease (Mpro) was used to generate a pharmacophore model and to conduct a docking study to capture antiviral drugs as new promising COVID-19 main protease inhibitors. The developed pharmacophore successfully captured five FDA-approved antiviral drugs (lopinavir, remdesivir, ritonavir, saquinavir and raltegravir). The five drugs were successfully docked into the binding site of COVID-19 Mpro and showed several specific binding interactions that were comparable to those tying the co-crystallized inhibitor X77 inside the binding site of COVID-19 Mpro. Three of the captured drugs namely, remdesivir, lopinavir and ritonavir, were reported to have promising results in COVID-19 treatment and therefore increases the confidence in our results. Our findings suggest an additional possible mechanism of action for remdesivir as an antiviral drug inhibiting COVID-19 Mpro. Additionally, a combination of structure-based pharmacophore modeling with a docking study is expected to facilitate the discovery of novel COVID-19 Mpro inhibitors.

Medicinal plant compounds as promising inhibitors of coronavirus (COVID-19) main protease: an in silico study

The novel Coronavirus (COVID-19) has spread rapidly across the globe and has involved more than 215 countries and territories. Due to a lack of effective therapy or vaccine, urgent and concerted efforts are needed to identify therapeutic targets and medications. COVID-19 main protease represents a major target for drug treatment to inhibit viral function. The present study sought to evaluate medicinal plant compounds as potential inhibitors of the COVID-19 main protease using molecular docking and molecular dynamic analysis. The PDB files of COVID-19 main protease and some medicinal plant compounds were retrieved from the Protein Data Bank (http://www.rcsb.org) and Pubchem server, respectively. The Gromacs software was used for simulation studies, and molecular docking analysis was done using Autodock 4.2. The COVID-19 main protease simulation, compared with some phytochemicals docked to the COVID-19 main protease, were analyzed. Glabridin, catechin, and fisetin had the greatest tendency to interact with the COVID-19 main protease by hydrogen and hydrophobic interactions. Docking of these phytochemicals to COVID-19 main protease led to an increase in the radius of gyration (Rg), decrease in the Root mean square fluctuation (RMSF), and induced variation in COVID-19 main protease secondary structure. The high tendency interaction of glabridin, catechin, and fisetin to COVID-19 main protease induced conformational changes on this enzyme. These interactions can lead to enzyme inhibition. This simulated study indicates that these phytochemicals may be considered as potent inhibitors of the viral protease; however, more investigations are required to explore their potential medicinal use.Communicated by Ramaswamy H. Sarma.

Structural insights on the interaction potential of natural leads against major protein targets of SARS-CoV-2: Molecular modelling, docking and dynamic simulation studies

Though significant efforts are in progress for developing drugs and vaccines against COVID-19, limited therapeutic agents are available currently. Thus, it is essential to undertake COVID-19 research and to identify therapeutic interventions in which computational modeling and virtual screening of lead molecules provide significant insights. The present study aimed to predict the interaction potential of natural lead molecules against prospective protein targets of SARS-CoV-2 by molecular modeling, docking, and dynamic simulation. Based on the literature survey and database search, fourteen molecular targets were selected and the three targets which lack the native structures were computationally modeled. The drug-likeliness and pharmacokinetic features of ninety-two natural molecules were predicted. Four lead molecules with ideal drug-likeliness and pharmacokinetic properties were selected and docked against fourteen targets, and their binding energies were compared with the binding energy of the interaction between Chloroquine and Hydroxychloroquine to their usual targets. The stabilities of selected docked complexes were confirmed by MD simulation and energy calculations. Four natural molecules demonstrated profound binding to most of the prioritized targets, especially, Hyoscyamine and Tamaridone to spike glycoprotein and Rotiorinol-C and Scutifoliamide-A to replicase polyprotein-1ab main protease of SARS-CoV-2 showed better binding energy, conformational and dynamic stabilities compared to the binding energy of Chloroquine and its usual target glutathione-S-transferase. The aforementioned lead molecules can be used to develop novel therapeutic agents towards the protein targets of SARS-CoV-2, and the study provides significant insight for structure-based drug development against COVID-19.

Computational evidence for nitro derivatives of quinoline and quinoline N-oxide as low-cost alternative for the treatment of SARS-CoV-2 infection

A new and more aggressive strain of coronavirus, known as SARS-CoV-2, which is highly contagious, has rapidly spread across the planet within a short period of time. Due to its high transmission rate and the significant time–space between infection and manifestation of symptoms, the WHO recently declared this a pandemic. Because of the exponentially growing number of new cases of both infections and deaths, development of new therapeutic options to help fight this pandemic is urgently needed. The target molecules of this study were the nitro derivatives of quinoline and quinoline N-oxide. Computational design at the DFT level, docking studies, and molecular dynamics methods as a well-reasoned strategy will aid in elucidating the fundamental physicochemical properties and molecular functions of a diversity of compounds, directly accelerating the process of discovering new drugs. In this study, we discovered isomers based on the nitro derivatives of quinoline and quinoline N-oxide, which are biologically active compounds and may be low-cost alternatives for the treatment of infections induced by SARS-CoV-2.

Demystifying Excess Immune Response in COVID-19 to Reposition an Orphan Drug for Down-Regulation of NF-κB: A Systematic Review

The immunological findings from autopsies, biopsies, and various studies in COVID-19 patients show that the major cause of morbidity and mortality in COVID-19 is excess immune response resulting in hyper-inflammation. With the objective to review various mechanisms of excess immune response in adult COVID-19 patients, Pubmed was searched for free full articles not related to therapeutics or co-morbid sub-groups, published in English until 27.10.2020, irrespective of type of article, country, or region. Joanna Briggs Institute's design-specific checklists were used to assess the risk of bias. Out of 122 records screened for eligibility, 42 articles were included in the final review. The review found that eventually, most mechanisms result in cytokine excess and up-regulation of Nuclear Factor-κB (NF-κB) signaling as a common pathway of excess immune response. Molecules blocking NF-κB or targeting downstream effectors like Tumour Necrosis Factor α (TNFα) are either undergoing clinical trials or lack specificity and cause unwanted side effects. Neutralization of upstream histamine by histamine-conjugated normal human immunoglobulin has been demonstrated to inhibit the nuclear translocation of NF-κB, thereby preventing the release of pro-inflammatory cytokines Interleukin (IL) 1β, TNF-α, and IL-6 and IL-10 in a safer manner. The authors recommend repositioning it in COVID-19.

Insights of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) pandemic: a current review

COVID-19, a pandemic of the 21st century caused by novel coronavirus SARS-CoV-2 was originated from China and shallowed world economy and human resource. The medical cures via herbal treatments, antiviral drugs, and vaccines still in progress, and studying rigorously. SARS-CoV-2 is more virulent than its ancestors due to evolution in the spike protein(s), mediates viral attachment to the host's membranes. The SARS-CoV-2 receptor-binding spike domain associates itself with human angiotensin-converting enzyme 2 (ACE-2) receptors. It causes respiratory ailments with irregularities in the hepatic, nervous, and gastrointestinal systems, as reported in humans suffering from COVID-19 and reviewed in the present article. There are several approaches, have been put forward by many countries under the world health organization (WHO) recommendations and some trial drugs were introduced for possible treatment of COVID-19, such as Lopinavir or Ritonavir, Arbidol, Chloroquine (CQ), Hydroxychloroquine (HCQ) and most important Remdesivir including other like Tocilizumab, Oritavancin, Chlorpromazine, Azithromycin, Baricitinib, etc. RT-PCR is the only and early detection test available besides the rapid test kit (serodiagnosis) used by a few countries due to unreasonable causes. Development of vaccine by several leader of pharmaceutical groups still under trial or waiting for approval for mass inoculation. Management strategies have been evolved by the recommendations of WHO, specifically important to control COVID-19 situations, in the pandemic era. This review will provide a comprehensive collection of studies to support future research and enhancement in our wisdom to combat COVID-19 pandemic and to serve humanity.

Carbon nanotubes for rapid capturing of SARS-COV-2 virus: revealing a mechanistic aspect of binding based on computational studies

We investigate the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus. Two essential components of the SARS-CoV-2 structure i.e.6LU7 (main protease of SARS-CoV-2) and 6LZG (spike receptor-binding domain complexed with its receptor ACE2) were used for computational studies. MWCNTs of different morphologies (zigzag, armchair and chiral) were synthesized through a thermal chemical vapour deposition process as a function of pyrolysis temperature. A direct correlation between radius to volume ratio of the synthesized MWCNTs and the binding energies for all three (zigzag, armchair and chiral) conformations were observed in our computational studies. Our result suggests that MWCNTs interact with the active sites of the main protease along with the host angiotensin-converting enzyme2 (ACE2) receptors. Furthermore, it is also observed that MWCNTs have significant binding affinities towards SARS-CoV-2. However, the highest free binding energy of -87.09 kcal mol-1 with 6LZG were shown by the armchair MWCNTs with SARS-CoV-2 through the simulated molecular dynamic trajectories, which could alter the SARS-CoV-2 structure with higher accuracy. The radial distribution function also confirms the density variation as a function of distance from a reference particle of MWCNTs for the study of interparticle interactions of the MWCNT and SARS-CoV-2. Due to these interesting attributes, such MWCNTs could find potential application in personal protective equipment (PPE) and diagnostic kits.

Curse of La Corona: unravelling the scientific and psychological conundrums of the 21st century pandemic

Microbes possess a tremendous potential to interact with their surroundings and have continued to shape the future of all life forms existing on earth. Of all the groups of microbes, viruses are the most nefarious creatures which cannot be solely classified as living or non-living but still pose the greatest threats to the biosphere. Viruses are minuscule, diverse and are probably the only entities that exhibit non-mutualistic association with other lifeforms while retaining their ability to infect and hijack any of the existing living being on the planet. The latest global devastation, caused by novel SARS-CoV-2, is unparalleled in the last century. This review encompasses the mysterious origin of this virus by tracking its lineage, which may help to decode the conundrum of SARS-CoV-2 and shed more light on its epidemiology. The implications and the challenge posed by this virus to the scientific community to the medical community and the economy at large are reflected. Also discussed is the paradigm shift brought upon by the COVID-19 pandemic on the human psyche and their behaviour.

Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations

The outbreak of a new coronavirus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) has caused a global COVID-19 (coronavirus disease 2019) pandemic, resulting in millions of infections and thousands of deaths around the world. There is currently no drug or vaccine for COVID-19, but it has been revealed that some commercially available drugs are promising, at least for treating symptoms. Among them, remdesivir, which can block the activity of RNA-dependent RNA polymerase (RdRp) in old SARS-CoV and MERS-CoV viruses, has been prescribed to COVID-19 patients in many countries. A recent experiment showed that remdesivir binds to SARS-CoV-2 with an inhibition constant of μM, but the exact target has not been reported. In this work, combining molecular docking, steered molecular dynamics, and umbrella sampling, we examined its binding affinity to two targets including the main protease (Mpro), also known as 3C-like protease, and RdRp. We showed that remdesivir binds to Mpro slightly weaker than to RdRp, and the corresponding inhibition constants, consistent with the experiment, fall to the μM range. The binding mechanisms of remdesivir to two targets differ in that the electrostatic interaction is the main force in stabilizing the RdRp-remdesivir complex, while the van der Waals interaction dominates in the Mpro-remdesivir case. Our result indicates that remdesivir can target not only RdRp but also Mpro, which can be invoked to explain why this drug is effective in treating COVID-19. We have identified residues of the target protein that make the most important contribution to binding affinity, and this information is useful for drug development for this disease.

Identification of Potential Inhibitors of 3CL Protease of SARS-CoV-2 From ZINC Database by Molecular Docking-Based Virtual Screening

The rapid outbreak of Coronavirus Disease 2019 (COVID-19) that was first identified in Wuhan, China is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The 3CL protease (3CLpro) is the main protease of the SARS-CoV-2, which is responsible for the viral replication and therefore considered as an attractive drug target since to date there is no specific and effective vaccine available against this virus. In this paper, we reported molecular docking-based virtual screening (VS) of 2000 compounds obtained from the ZINC database and 10 FDA-approved (antiviral and anti-malaria) on 3CLpro using AutoDock Vina to find potential inhibitors. The screening results showed that the top four compounds, namely ZINC32960814, ZINC12006217, ZINC03231196, and ZINC33173588 exhibited high affinity at the 3CLpro binding pocket. Their free energy of binding (FEB) were -12.3, -11.9, -11.7, and -11.2 kcal/mol while AutoDock Vina scores were -12.61, -12.32, -12.01, and -11.92 kcal/mol, respectively. These results were better than the co-crystallized ligand N3, whereby its FEB was -7.5 kcal/mol and FDA-approved drugs. Different but stable interactions were obtained between the four identified compounds with the catalytic dyad residues of the 3CLpro. In conclusion, novel 3CLpro inhibitors from the ZINC database were successfully identified using VS and molecular docking approach, fulfilling the Lipinski rule of five, and having low FEB and functional molecular interactions with the target protein. The findings suggests that the identified compounds may serve as potential leads that act as COVID-19 3CLpro inhibitors, worthy for further evaluation and development.

Are losartan and imatinib effective against SARS-CoV2 pathogenesis? A pathophysiologic-based in silico study

Proposing a theory about the pathophysiology of cytokine storm in COVID19, we were to find the potential drugs to treat this disease and to find any effect of these drugs on the virus infectivity through an in silico study. COVID-19-induced ARDS is linked to a cytokine storm phenomenon not explainable solely by the virus infectivity. Knowing that ACE2, the hydrolyzing enzyme of AngII and SARS-CoV2 receptor, downregulates when the virus enters the host cells, we hypothesize that hyperacute AngII upregulation is the eliciting factor of this ARDS. We were to validate this theory through reviewing previous studies to figure out the role of overzealous activation of AT1R in ARDS. According to this theory losartan may attenuate ARDS in this disease. Imatinib, has previously been elucidated to be promising in modulating lung inflammatory reactions and virus infectivity in SARS and MERS. We did an in silico study to uncover any probable other unconsidered inhibitory effects of losartan and imatinib against SARS-CoV2 pathogenesis. Reviewing the literature, we could find that over-activation of AT1R could explain precisely the mechanism of cytokine storm in COVID19. Our in silico study revealed that losartan and imatinib could probably: (1) decline SARS-CoV2 affinity to ACE2. (2) inhibit the main protease and furin, (3) disturb papain-like protease and p38MAPK functions. Our reviewing on renin-angiotensin system showed that overzealous activation of AT1R by hyper-acute excess of AngII due to acute downregulation of ACE2 by SARS-CoV2 explains precisely the mechanism of cytokine storm in COVID-19. Besides, based on our in silico study we concluded that losartan and imatinib are promising in COVID19.

Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine and Pyronaridine: In vitro Activity Against SARS-CoV-2 and Potential Mechanisms

SARS-CoV-2 is a newly identified virus that has resulted in over 1.3 M deaths globally and over 59 M cases globally to date. Small molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola virus and demonstrated activity against SARS-CoV-2 in vivo . Most notably the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small molecule drugs that are active against Ebola virus would seem a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg virus in vitro in HeLa cells and of mouse adapted Ebola virus in mouse in vivo . We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7 and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC 50 values of 180 nM and IC 50 198 nM, respectively. We have also tested them in a pseudovirus assay and used microscale thermophoresis to test the binding of these molecules to the spike protein. They bind to spike RBD protein with K d values of 339 nM and 647 nM, respectively. Human C max for pyronaridine and quinacrine is greater than the IC 50 hence justifying in vivo evaluation. We also provide novel insights into their mechanism which is likely lysosomotropic.

Molecular targets and system biology approaches for drug repurposing against SARS-CoV-2

BACKGROUND

COVID-19, a pandemic declared by WHO, has infected about 39.5 million and killed about 1.1 million people throughout the world. There is the urgent need of more studies to identify the novel drug targets and the drug candidates against it to handle the situation.

MAIN BODY

To virtually screen various drugs against SARS-CoV-2, the scientists need the detail information about the various drug targets identified till date. The present review provides the information about almost all the drug targets, including structural and non-structural proteins of virus as well as host cell surface receptors, that can be used for virtual screening of drugs. Moreover, this review also focuses on the different network analysis tools that have been used for the identification of new drug targets and candidate repurposable drugs against SARS-CoV-2.

CONCLUSION

This review provides important insights of various drug targets and the network analysis tools to young bioinformaticians and will help in creating pace to the drug repurposing strategy for COVID-19 disease.

Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation

In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. The 3C-Like proteinase (3CL^pro) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as an important drug target due to its role in viral replication. The lack of a potent 3CL^pro inhibitor and the availability of the X-ray crystal structure of 3CL^pro (PDB-ID 6LU7) motivated us to perform computational studies to identify commercially available potential inhibitors. A combination of modeling studies was performed to identify potential 3CL^pro inhibitors from the protease inhibitor database MEROPS (https://www.ebi.ac.uk/merops/index.shtml). Binding energy evaluation identified key residues for inhibitor design. We found 15 potential 3CL^pro inhibitors with higher binding affinity than that of an α-ketoamide inhibitor determined via X-ray structure. Among them, saquinavir and three other investigational drugs aclarubicin, TMC-310911, and faldaprevir could be suggested as potential 3CL^pro inhibitors. We recommend further experimental investigation of these compounds.

Stopping the COVID-19 Pandemic: A Review on the Advances of Diagnosis, Treatment, and Control Measures

With the continued spread of COVID-19 across the world, rapid diagnostic tools, readily available respurposable drugs, and prompt containment measures to control the SARS-CoV-2 infection are of paramount importance. Examples of recent advances in diagnostic tests are CRISPR technology, IgG assay, spike protein detection, and use of artificial intelligence. The gold standard reverse transcription polymerase chain (RT-PCR) has also been upgraded with point-of-care rapid tests. Supportive treatment, mechanical ventilation, and extracorporeal membrane oxygenation (ECMO) remain the primary choice, while therapeutic options include antivirals, antiparasitics, anti-inflammatories, interferon, convalescent plasma, monoclonal antibody, hyperimmunoglobulin, RNAi, and mesenchymal stem cell therapy. Different types of vaccines such as RNA, DNA, and lentiviral, inactivated, and viral vector are in clinical trials. Moreover, rapidly deployable and easy-to-transport innovative vaccine delivery systems are also in development. As countries have started easing down on the lockdown measures, the chance for a second wave of infection demands strict and rational control policies to keep fatalities minimized. An improved understanding of the advances in diagnostic tools, treatments, vaccines, and control measures for COVID-19 can provide references for further research and aid better containment strategies.

Recognition of Natural Products as Potential Inhibitors of COVID-19 Main Protease (Mpro): In-Silico Evidences

SARS-CoV-2 (2019-nCoV) emerged in 2019 and proliferated rapidly across the globe. Scientists are attempting to investigate antivirals specific to COVID-19 treatment. The 2019-nCoV and SARS-CoV utilize the same receptor of the host which is COVID-19 of the main protease (Mpro).COVID-19 caused by SARS-CoV-2 is burdensome to overcome by presently acquired antiviral candidates. So the objective and purpose of this work was to investigate the plants with reported potential antiviral activity. With the aid of in silico techniques such as molecular docking and druggability studies, we have proposed several natural active compounds including glycyrrhizin, bicylogermecrene, tryptanthrine, β-sitosterol, indirubin, indican, indigo, hesperetin, crysophanic acid, rhein, berberine and β-caryophyllene which can be encountered as potential herbal candidate exhibiting anti-viral activity against SARS-CoV-2. Promising docking outcomes have been executed which evidenced the worthy of these selected herbal remedies for future drug development to combat coronavirus disease.

Phytochemicals containing biologically active polyphenols as an effective agent against Covid-19-inducing coronavirus

The outbreak of Covid-19 disease caused by SARS-CoV-19, along with the lack of targeted medicaments and vaccines, forced the scientific world to search for new antiviral formulations. In this review, we describe the current knowledge about plant extracts containing polyphenols that inhibit Covid-19. Many plant-derived natural compounds (polyphenols) might provide a starting point for the research on the use of plant extracts in coronavirus treatment and prevention. Antivirus polyphenolic drugs can inhibit coronavirus enzymes, which are essential for virus replication and infection. This group of natural substances (betulinic acid, indigo, aloeemodine, luteolin, and quinomethyl triterpenoids, quercitin or gallates) is a potential key to designing antiviral therapies for inhibiting viral proteases. The known pharmacophore structures of bioactive substances can be useful in the elaboration of new anti-Covid-19 formulations. The benefit of using preparations containing phytochemicals is their high safety for patients and no side effects.

An overview of COVID-19 with an emphasis on computational approach for its preventive intervention

SARS-CoV-2, a novel Betacoronavirus, has attracted global attention because of its extremely high infection rate and large number of human deaths. It possesses a positive-sense, single-stranded RNA of ~ 30 kb nucleotides as its genetic material. It is responsible for COVID-19 which has been declared a pandemic by WHO. Having reported for the first time in Wuhan, China, the virus infected over 21.48 million people and caused over 0.77 million deaths till mid-august 2020. SARS-CoV-2 contains the spike protein site that gets activated by an enzyme furin which is found in the lung, liver, and small intestine of humans. It shows the potentiality of virus for attacking multiple organs and their failures. Due to the absence of vaccines, the cure is restricted to supportive care including repurposed drugs. In silico approaches may offer an alternative screening to optimize hits to lead stages. It can provide important related to drug resistance, their lineages and evolution. This approach may also help to find an effective vaccine against COVID-19. This review focuses on the in silico aspects of genomics, proteomics, pathogenesis, phylogenetic analysis and viral receptor binding analysis in Betacoronavirus.

Carotane sesquiterpenes from Ferula vesceritensis: in silico analysis as SARS-CoV-2 binding inhibitors

Two sesquiterpenes, 8α-anisate-dauc-4-ene-3,9-dione (webiol anisate) (1) and 10α-acetoxy-6α-benzoate-jaeschkeanadiol (2) as well as, ten known analogues (3-10), and two sesquiterpene coumarins (11-12) were isolated from an organic root extract of Ferula vesceritensis (Fam. Apiaceae). Chemical structures were elucidated based on IR, 1D- and 2D-NMR and HRMS, spectroscopic analyses. With molecular overlap observed between two protease inhibitors that are being examined as anti-COVID-19 drugs, and sesquiterpenes isolated here, metabolite molecular docking calculations were made using the main protease (Mpro), which is required for viral multiplication as well as RNA-dependent RNA polymerase (RdRp). In silico binding-inhibition analysis predicted that select F. vesceritensis sesquiterpenes can bind to these enzymes required for viral replication. Structures of the isolated constituents were also consistent with the chemo-systematic grouping of F. vesceritensis secondary metabolites with other Ferula species.

An evidence-based systematic review on emerging therapeutic and preventive strategies to treat novel coronavirus (SARS-CoV-2) during an outbreak scenario

A novel coronavirus infection coronavirus disease 2019 (COVID-19) emerged from Wuhan, Hubei Province of China, in December 2019 caused by SARS-CoV-2 is believed to be originated from bats in the local wet markets. Later, animal to human and human-to-human transmission of the virus began and resulting in widespread respiratory illness worldwide to around more than 180 countries. The World Health Organization declared this disease as a pandemic in March 2020. There is no clinically approved antiviral drug or vaccine available to be used against COVID-19. Nevertheless, few broad-spectrum antiviral drugs have been studied against COVID-19 in clinical trials with clinical recovery. In the current review, we summarize the morphology and pathogenesis of COVID-19 infection. A strong rational groundwork was made keeping the focus on current development of therapeutic agents and vaccines for SARS-CoV-2. Among the proposed therapeutic regimen, hydroxychloroquine, chloroquine, remdisevir, azithromycin, toclizumab and cromostat mesylate have shown promising results, and limited benefit was seen with lopinavir-ritonavir treatment in hospitalized adult patients with severe COVID-19. Early development of SARS-CoV-2 vaccine started based on the full-length genome analysis of severe acute respiratory syndrome coronavirus. Several subunit vaccines, peptides, nucleic acids, plant-derived, recombinant vaccines are under pipeline. This article concludes and highlights ongoing advances in drug repurposing, therapeutics and vaccines to counter COVID-19, which collectively could enable efforts to halt the pandemic virus infection.

Artificial Intelligence for COVID-19 Drug Discovery and Vaccine Development

SARS-COV-2 has roused the scientific community with a call to action to combat the growing pandemic. At the time of this writing, there are as yet no novel antiviral agents or approved vaccines available for deployment as a frontline defense. Understanding the pathobiology of COVID-19 could aid scientists in their discovery of potent antivirals by elucidating unexplored viral pathways. One method for accomplishing this is the leveraging of computational methods to discover new candidate drugs and vaccines in silico. In the last decade, machine learning-based models, trained on specific biomolecules, have offered inexpensive and rapid implementation methods for the discovery of effective viral therapies. Given a target biomolecule, these models are capable of predicting inhibitor candidates in a structural-based manner. If enough data are presented to a model, it can aid the search for a drug or vaccine candidate by identifying patterns within the data. In this review, we focus on the recent advances of COVID-19 drug and vaccine development using artificial intelligence and the potential of intelligent training for the discovery of COVID-19 therapeutics. To facilitate applications of deep learning for SARS-COV-2, we highlight multiple molecular targets of COVID-19, inhibition of which may increase patient survival. Moreover, we present CoronaDB-AI, a dataset of compounds, peptides, and epitopes discovered either in silico or in vitro that can be potentially used for training models in order to extract COVID-19 treatment. The information and datasets provided in this review can be used to train deep learning-based models and accelerate the discovery of effective viral therapies.

GSK-3 Inhibition as a Therapeutic Approach Against SARs CoV2: Dual Benefit of Inhibiting Viral Replication While Potentiating the Immune Response

The SARS-CoV2 (COVID-19) pandemic and uncertainties in developing a vaccine have created an urgent need for new therapeutic approaches. A key question is whether it is possible to make rational predictions of new therapies based on the presently available scientific and medical information. In this regard, I have noticed an omission in the present analysis in the literature related to the exploitation of glycogen synthase kinase 3 (GSK-3) as a therapeutic approach. This is based on two key observations, that GSK-3 inhibitors can simultaneously block SARs viral replication, while boosting CD8+ adaptive T-cell and innate natural killer (NK) responses. Firstly, it is already clear that GSK-3 phosphorylation of SARs CoV1 N protein on key serine residues is needed for viral replication such that small molecule inhibitors (SMIs) of GSK-3 can inhibit viral replication. In comparing protein sequences, I show here that the key sites in the N protein of SARs CoV1 N for replication are conserved in SARs CoV2. This strongly suggests that GSK-3 SMIs will also inhibit SARs Cov2 replication. Secondly, we and others have previously documented that GSK-3 SMIs markedly enhance CD8+ cytolytic T-cell (CTL) and NK cell anti-viral effector functions leading to a reduction in both acute and chronic viral infections in mice. My hypothesis is that the repurposing of low-cost inhibitors of GSK-3 such as lithium will limit SARS-CoV2 infections by both reducing viral replication and potentiating the immune response against the virus. To date, there has been no mention of this dual connection between GSK-3 and SARs CoV2 in the literature. To my knowledge, no other drugs exist with the potential to simultaneously target both viral replication and immune response against SARs CoV2.

Biocides and Novel Antimicrobial Agents for the Mitigation of Coronaviruses

In December, 2019, a highly infectious and rapidly spreading new pneumonia of unknown cause was reported to the Chinese WHO Country Office. A cluster of these cases had appeared in Wuhan, a city in the Hubei Province of China. These infections were found to be caused by a new coronavirus which was given the name "2019 novel coronavirus" (2019-nCoV). It was later renamed "severe acute respiratory syndrome coronavirus 2," or SARS-CoV-2 by the International Committee on Taxonomy of Viruses on February 11, 2020. It was named SARS-CoV-2 due to its close genetic similarity to the coronavirus which caused the SARS outbreak in 2002 (SARS-CoV-1). The aim of this review is to provide information, primarily to the food industry, regarding a range of biocides effective in eliminating or reducing the presence of coronaviruses from fomites, skin, oral/nasal mucosa, air, and food contact surfaces. As several EPA approved sanitizers against SARS-CoV-2 are commonly used by food processors, these compounds are primarily discussed as much of the industry already has them on site and is familiar with their application and use. Specifically, we focused on the effects of alcohols, povidone iodine, quaternary ammonium compounds, hydrogen peroxide, sodium hypochlorite (NaOCl), peroxyacetic acid (PAA), chlorine dioxide, ozone, ultraviolet light, metals, and plant-based antimicrobials. This review highlights the differences in the resistance or susceptibility of different strains of coronaviruses, or similar viruses, to these antimicrobial agents.

Computational screening for potential drug candidates against the SARS-CoV-2 main protease

Background: SARS-CoV-2 is the causal agent of the current coronavirus disease 2019 (COVID-19) pandemic. They are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly, and pathogenicity. The approximately 33.8 kDa M pro protease of SARS-CoV-2 is a non-human homologue and is highly conserved among several coronaviruses, indicating that M pro could be a potential drug target for Coronaviruses. Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 M pro protease (6LU7), and also screened 50,000 natural compounds from the ZINC Database dataset against this protease target. Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 11 best selected ligands, namely ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as beta-carboline, alkaloids, and polyflavonoids, and all displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as other known ligands. Conclusions: Our results suggest that these 11 molecules could be effective against SARS-CoV-2 protease and may be subsequently tested in vitro and in vivo to develop novel drugs against this virus.