A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem)

Shikonin modulates activated fibroblast apoptosis in silicosis fibrosis via the PI3K/Akt signaling pathway: A network pharmacology approach

BACKGROUND

Silicosis is a lung disease caused by the inhalation of free crystalline silica and is characterized mainly by lung inflammation and progressive pulmonary fibrosis. Shikonin, a biologically active compound isolated from the traditional Chinese medicine Comfrey, has been shown to have significant antifibrotic effects. However, the molecular mechanisms underlying the antifibrotic effects of SHK in silicosis remain unclear.

METHODS

This study used a combination of network pharmacology, molecular docking, molecular dynamics simulation, and in vitro experimental validation to investigate the potential targets of SHK in silicosis.

RESULTS

Network pharmacology analysis identified 208 cross genes associated with disease drugs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis show that these intersecting genes are significantly associated with the PI3K/Akt signaling pathway. Protein protein interaction (PPI) network analysis further revealed 10 core crossover genes, namely ALB, Akt1, STAT3, CASP3, EGFR, MMP9, Bcl-2, ESR1, HSP90AA1, and NF-κB1. Among them, Akt1 and Bcl-2 have the strongest binding ability to SHK. The in vitro experimental results showed that SHK can significantly inhibit the activation of fibroblasts and promote apoptosis of activated fibroblasts through the PI3K/Akt signaling pathway.

CONCLUSION

SHK alleviates silica induced silicosis fibrosis by inhibiting the transformation of fibroblasts into myofibroblasts through the PI3K/Akt signaling pathway.

On the potential activity of hyaluronic acid as an antimicrobial agent: experimental and computational validations

This century has seen the rise of antibiotic resistance as a significant public health problem. In addition, oxidative stress may also be a factor in selecting resistant strains of bacteria. The current study analyzed microbially produced hyaluronic acid's antibacterial activity and antioxidant activity. It had significant antibacterial action against strains of Staphylococcus aureus and Escherichia coli, with the IC50 value obtained being 487.65 µg mL-1 for antioxidant assay. Our molecular docking investigations of hyaluronic acid on tyrosyl-tRNA synthetase (Staphylococcus aureus: -6.13 kcal/mol, Escherichia coli: -5.79 kcal/mol) and topoisomerase II DNA gyrase (Staphylococcus aureus: -5.02 kcal/mol, Escherichia coli: -4.90 kcal/mol) confirmed the ligands' possible binding mode to the appropriate targets' sites. We also employed molecular dynamics simulation and showed that HA binds more strongly with 1JIL (-85.455 ± 12.623 kJ/mol) compared to 2YXN (-49.907 ± 64.191 kJ/mol), 5CDP (-47.285 ± 13.925 kJ/mol), and 6RKS (-45.306 ± 21.338 kJ/mol). We also report that the ligand forms several hydrogen bonds in molecular simulation, implying regular interaction with key residues of the enzymes. The results in this study indicate the potential use of HA in the vast field of applications having both asthetic and medicinal values.

Computational prediction of phytochemical inhibitors against the cap-binding domain of Rift Valley fever virus

Rift Valley fever is a zoonotic disease that can spread through livestock and mosquitoes, and its symptoms include retinitis, photophobia, hemorrhagic fever and neurological effects. The World Health Organization has identified Rift Valley fever as one of the viral infections that has potential to cause a future epidemic. Hence, efforts are urgently needed toward development of therapeutics and vaccine against this infectious disease. Notably, the causative virus namely, the Rift Valley fever virus (RVFV), utilizes the cap-snatching mechanism for viral transcription, rendering its cap-binding domain (CBD) as an effective antiviral target. To date, there are no published studies towards identification of potential small molecule inhibitors for the CBD of RVFV. Here, we employ a virtual screening workflow comprising of molecular docking and molecular dynamics (MD) simulation, to identify 5 potential phytochemical inhibitors of the CBD of RVFV. These 5 phytochemical inhibitors can be sourced from Indian medicinal plants, Ferula assa-foetida, Glycyrrhiza glabra and Leucas cephalotes, used in traditional medicine. In sum, the 5 phytochemical inhibitors of the CBD of RVFV identified by this purely computational study are promising drug lead molecules which can be considered for detailed experimental validation against RVFV infection.

Antiviral Activity, Pharmacoinformatics, Molecular Docking, and Dynamics Studies of Azadirachta indica Against Nipah Virus by Targeting Envelope Glycoprotein: Emerging Strategies for Developing Antiviral Treatment

The Nipah virus (NiV) belongs to the Henipavirus genus is a serious public health concern causing numerous outbreaks with higher fatality rate. Unfortunately, there is no effective medication available for NiV. To investigate possible inhibitors of NiV infection, we used in silico techniques to discover treatment candidates in this work. As there are not any approved treatments for NiV infection, the NiV-enveloped attachment glycoprotein was set as target for our study, which is responsible for binding to and entering host cells. Our in silico drug design approach included molecular docking, post-docking molecular mechanism generalised born surface area (MM-GBSA), absorption, distribution, metabolism, excretion/toxicity (ADME/T), and molecular dynamics (MD) simulations. We retrieved 418 phytochemicals associated with the neem plant (Azadirachta indica) from the IMPPAT database, and molecular docking was used to ascertain the compounds' binding strength. The top 3 phytochemicals with binding affinities of -7.118, -7.074, and -6.894 kcal/mol for CIDs 5280343, 9064, and 5280863, respectively, were selected for additional study based on molecular docking. The post-docking MM-GBSA of those 3 compounds was -47.56, -47.3, and -43.15 kcal/mol, respectively. As evidence of their efficacy and safety, all the chosen drugs had favorable toxicological and pharmacokinetic (Pk) qualities. We also performed MD simulations to confirm the stability of the ligand-protein complex structures and determine whether the selected compounds are stable at the protein binding site. All 3 phytochemicals, Quercetin (CID: 5280343), Cianidanol (CID: 9064), and Kaempferol (CID: 5280863), appeared to have outstanding binding stability to the target protein than control ribavirin, according to the molecular docking, MM-GBSA, and MD simulation outcomes. Overall, this work offers a viable approach to developing novel medications for treating NiV infection.

Cheminformatics-based identification of phosphorylated RET tyrosine kinase inhibitors for human cancer

Background

Rearranged during transfection (RET), an oncogenic protein, is associated with various cancers, including non-small-cell lung cancer (NSCLC), papillary thyroid cancer (PTC), pancreatic cancer, medullary thyroid cancer (MTC), breast cancer, and colorectal cancer. Dysregulation of RET contributes to cancer development, highlighting the importance of identifying lead compounds targeting this protein due to its pivotal role in cancer progression. Therefore, this study aims to discover effective lead compounds targeting RET across different cancer types and evaluate their potential to inhibit cancer progression.

Methods

This study used a range of computational techniques, including Phase database creation, high-throughput virtual screening (HTVS), molecular docking, molecular mechanics with generalized Born surface area (MM-GBSA) solvation, assessment of pharmacokinetic (PK) properties, and molecular dynamics (MD) simulations, to identify potential lead compounds targeting RET.

Results

Initially, a high-throughput virtual screening of the ZINC database identified 2,550 compounds from a pool of 170,269. Subsequent molecular docking studies revealed 10 compounds with promising negative binding scores ranging from -8.458 to -7.791 kcal/mol. MM-GBSA analysis further confirmed the potential of four compounds to exhibit negative binding scores. MD simulations demonstrated the stability of CID 95842900, CID 137030374, CID 124958150, and CID 110126793 with the target receptors.

Conclusion

These findings suggest that these selected four compounds have the potential to inhibit phosphorylated RET (pRET) tyrosine kinase activity and may represent promising candidates for the treatment of various cancers.

Role of dietary supplements in the continuous battle against COVID-19

A sudden outbreak of the COVID-19 pandemic was a big blow to the world community on every level. Created by a novel coronavirus, SARS-CoV-2, which was previously unknown to the human immune system. The expert opinion almost immediately united on the fact that the most effective way of fighting the pandemic would be by building immunity artificially via a mass immunization program. However, it took about a year for the approval of the first vaccine against COVID-19. In the meantime, a big part of the general population started adapting nutritious diet plans and dietary supplements to boost natural immunity as a potential prophylactic strategy against SARS-CoV-2 infection. Whether they originate from mainstream medicine, such as synthetic supplements, or traditional herbal remedies in the form of single or poly-herbs, these supplements may comprise various components that exhibit immunomodulatory, anti-inflammatory, antioxidant, and antimicrobial characteristics. There is a substantial body of predictions and expert opinions suggesting that enhancing one's diet with dietary supplements containing additional nutrients and bioactive compounds like vitamins, minerals, amino acids, fatty acids, phytochemicals, and probiotics can enhance the immune system's ability to develop resistance against COVID-19, although none of them have any conclusive evidence nor officially recommended by World Health Organization (WHO). The current review critically acclaims the gap between public perception-based preference and real evidence-based study to weigh the actual benefit of dietary supplements in relation to COVID-19 prevention and management.

The use of Nibima and Immunim, two Ghanaian herbal medicines in the management of mild COVID-19: A case report

Key Clinical Message

Nibima and Immunim manages mild COVID-19 in 7 days.

Abstract

Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can lead to severe complications and deaths. The search for phytotherapeutic agents to augment the fight against the current COVID-19 pandemic is therefore of highest priority. A 52-year-old female with no history of chronic illness presented to our clinic facility with a 3 days loss of smell and headache which persisted after self-medication. The patient tested positive for COVID-19 in the SARS-CoV-2 Ag test as well as the Typhoid rapid antibody test. Routine laboratory tests were not remarkable. A 60 mL three times daily dose of Nibima and 5 mL in 40 mL of warm water dose of Immunim were given to the patient for 7 days. Patient recovered sense of smell and regained appetite but cough although reduced persisted. She also tested negative for COVID-19 after 7 days treatment. This case is the first documented case of COVID-19 management with herbal medicines in Ghana. We strongly suggest a larger control trial on these products to ascertain these findings to repurpose them as viable treatments for COVID-19.

Unveiling the azo-reductase mechanism in Pseudomonas putida for efficient decolorization of textile Reactive dyes: an in-silico study

The textile industry utilizing affordable azo dyes is a high threat to aquatic life and causes environmental problems due to their toxicity. Biodegradation of azo dyes employing microbes and enzymes has proved to be an efficient method for treating industrial effluent. This study used the novel microbial consortium to decolorize reactive azo dyes (Reactive Red 120; Reactive Black 5 and Reactive Blue 13), and its azo-reductase activity was evaluated. The metagenomic analysis of the consortium identified azo-reductase-producing bacterial species. The molecular docking revealed that PpAzoR from Pseudomonas putida had the highest binding affinities for all the three dyes such as Reactive Black 5 (-9.3 kcal/mol), Reactive Blue 13 (-9.8 kcal/mol) and Reactive Red 120 (-10.7 kcal/mol). The structural rigidity and stability of the docked complex were confirmed through MD simulations evaluated across multiple descriptors from the simulation trajectories. Further, MMPBSA analysis validated the results that binding of the ligands, i.e. dye molecules Reactive Black (RB5), Reactive Blue (RB13) and Reactive Red (RR120) binding with the Azoreductase (PpAzoR) to the screened Azo-dyes was spontaneous. Based on molecular dynamics simulations for 100 ns, RR 120 showed the highest binding affinity (-411.336 ± 46.799 KJ/mol), followed by RB5 (-288.012 ± 33.371 KJ/mol). The dyes (RR120 and RB5) exhibited stable interactions with the target azoreductase (PpAzoR). The present study provides insights that PpAzoR shows the highest decolorization potency, which could be interpreted as a potential dye-degrading protein based on dye-degrading assay findings.

Identification of novel natural product inhibitors of BRD4 using high throughput virtual screening and MD simulation

Bromodomains are evolutionarily conserved structural motifs that recognize acetylated lysine residues on histone tails. They play a crucial role in shaping chromatin architecture and regulating gene expression in various biological processes. Mutations in bromodomains containing proteins lead to multiple human diseases, which makes them attractive target for therapeutic intervention. Extensive studies have been done on BRD4 as a target for several cancers, such as Acute Myeloid Leukemia (AML) and Burkitt Lymphoma. Several potential inhibitors have been identified against the BRD4 bromodomain. However, most of these inhibitors have drawbacks such as non-specificity and toxicity, decreasing their appeal and necessitating the search for novel non-toxic inhibitors. This study aims to address this need by virtually screening natural compounds from the NPASS database against the Kac binding site of BRD4-BD1 using high throughput molecular docking followed by similarity clustering, pharmacokinetic screening, MD simulation and MM-PBSA binding free energy calculations. Using this approach, we identified five natural product inhibitors having a similar or better binding affinity to the BRD4 bromodomain compared to JQ1 (previously reported inhibitor of BRD4). Further systematic analysis of these inhibitors resulted in the top three hits: NPC268484 (Palodesangren-B), NPC295021 (Candidine) and NPC313112 (Buxifoliadine-D). Collectively, our in silico results identified some promising natural products that have the potential to act as potent BRD4-BD1 inhibitors and can be considered for further validation through future in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.

Profiling the Antidiabetic Potential of Compounds Identified from Fractionated Extracts of Entada africana toward Glucokinase Stimulation: Computational Insight

Glucokinase plays an important role in regulating the blood glucose level and serves as an essential therapeutic target in type 2 diabetes management. Entada africana is a medicinal plant and highly rich source of bioactive ligands with the potency to develop new target drugs for glucokinase such as diabetes and obesity. Therefore, the study explored a computational approach to predict identified compounds from Entada africana following its intermolecular interactions with the allosteric binding site of the enzymes. We retrieved the three-dimensional (3D) crystal structure of glucokinase (PDB ID: 4L3Q) from the online protein data bank and prepared it using the Maestro 13.5, Schrödinger Suite 2022-3. The compounds identified were subjected to ADME, docking analysis, pharmacophore modeling, and molecular simulation. The results show the binding potential of the identified ligands to the amino acid residues, thereby suggesting an interaction of the amino acids with the ligand at the binding site of the glucokinase activator through conventional chemical bonds such as hydrogen bonds and hydrophobic interactions. The compatibility of the molecules was highly observed when compared with the standard ligand, thereby leading to structural and functional changes. Therefore, the bioactive components from Entada africana could be a good driver of glucokinase, thereby paving the way for the discovery of therapeutic drugs for the treatment of diabetes and its related complications.

Integrated computational and experimental approach for novel anti-leishmanial molecules by targeting Dephospho-coenzyme A kinase

Coenzyme A acts as a necessary cofactor for many enzymes and is a part of many biochemical processes. One of the critical enzymes involved in Coenzyme A synthesis is Dephospho-coenzyme A-kinase (DPCK). In this study, we have used integrated computational and experimental approaches for promising inhibitors of DPCK using the natural products available in the ZINC database for anti-leishmanial drug development. The top hit compounds chosen after molecular docking were Veratramine, Azulene, Hupehenine, and Hederagenin. The free binding energy of Veratramine, Azulene, Hupehenine, and Hederagenin was estimated. Besides the favourable binding point, the ligands also showed good hydrogen bonding and other interactions with key residues of the enzyme's active site. The natural compounds were also experimentally investigated for their effect on the L. donovani promastigotes and murine macrophage (J774A.1). A good antileishmanial activity by the compounds on the promastigotes was observed as estimated by the MTT assay. The in-vitro experiments revealed that Hupehenine (IC₅₀ = 7.34 ± 0.37 μM) and Veratramine (IC₅₀ = 12.46 ± 2.28 μM) exhibited better inhibition than Hederagenin (IC₅₀ = 23.36 ± 0.54 μM) and Azulene (IC₅₀ = 24.42 ± 3.28 μM). This work has identified novel anti-leishmanial molecules possibly acting through the inhibition of DPCK.

Molecular dynamics and absolute binding free energy studies of piperine derivatives as potential inhibitors of SARS-CoV-2 main protease

The work presents a library of piperine derivatives as potential inhibitors of the main protease protein (Mpro) functionality using Docking Studies, Molecular Dynamics (MD) Simulations and Absolute Binding Free-Energy calculations. 342 ligands were selected for this work and docked with Mpro protein. Among all the ligands studied, PIPC270, PIPC299, PIPC252, PIPC63, PIPC311 were the top five docked conformations having significant hydrogen bonding and hydrophobic interactions inside the active pocket of Mpro. These top five ligands were subjected to MD simulations for 100 ns using GROMACS. Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), Solvent Accessible Surface Area (SASA) and hydrogen bond analysis revealed that the ligands bounded to protein remain stable without significant deviations during the course of MD simulations. Absolute binding free energy (ΔGb) was calculated for theses complexes and found that the ligand PIPC299 shows the prevalent binding affinity with binding free-energy of about -113.05 Kcal/mol. Thus, these molecules can be further tested by in vitro and in vivo studies on Mpro. This study lays a path to explore the new functionality of piperine derivatives as novel drug like molecules.Communicated by Ramaswamy H. Sarma.

IMPPAT 2.0: An Enhanced and Expanded Phytochemical Atlas of Indian Medicinal Plants

Compilation, curation, digitization, and exploration of the phytochemical space of Indian medicinal plants can expedite ongoing efforts toward natural product and traditional knowledge based drug discovery. To this end, we present IMPPAT 2.0, an enhanced and expanded database compiling manually curated information on 4010 Indian medicinal plants, 17,967 phytochemicals, and 1095 therapeutic uses. Notably, IMPPAT 2.0 compiles associations at the level of plant parts and provides a FAIR-compliant nonredundant in silico stereo-aware library of 17,967 phytochemicals from Indian medicinal plants. The phytochemical library has been annotated with several useful properties to enable easier exploration of the chemical space. We have also filtered a subset of 1335 drug-like phytochemicals of which majority have no similarity to existing approved drugs. Using cheminformatics, we have characterized the molecular complexity and molecular scaffold based structural diversity of the phytochemical space of Indian medicinal plants and performed a comparative analysis with other chemical libraries. Altogether, IMPPAT 2.0 is a manually curated extensive phytochemical atlas of Indian medicinal plants that is accessible at https://cb.imsc.res.in/imppat/.

SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, which has seriously affected human health worldwide. The discovery of therapeutic agents is extremely urgent, and the viral structural proteins are particularly important as potential drug targets. SARS-CoV-2 envelope (E) protein is one of the main structural proteins of the virus, which is involved in multiple processes of the virus life cycle and is directly related to pathogenesis process. In this review, we present the amino acid sequence of the E protein and compare it with other two human coronaviruses. We then explored the role of E protein in the viral life cycle and discussed the pathogenic mechanisms that E protein may be involved in. Next, we summarize the potential drugs against E protein discovered in the current studies. Finally, we described the possible effects of E protein mutation on virus and host. This established a knowledge system of E protein to date, aiming to provide theoretical insights for mitigating the current COVID-19 pandemic and potential future coronavirus outbreaks.

Bioactive Azadirachta indica and Melia azedarach leaves extracts with anti-SARS-CoV-2 and antibacterial activities

The leaves of Azadirachta indica L. and Melia azedarach L., belonging to Meliaceae family, have been shown to have medicinal benefits and are extensively employed in traditional folk medicine. Herein, HPLC analysis of the ethyl acetate fraction of the total methanolic extract emphasized the enrichment of both A. indica L., and M. azedarach L. leaves extracts with phenolic and flavonoids composites, respectively. Besides, 4 limonoids and 2 flavonoids were isolated using column chromatography. By assessing the in vitro antiviral activities of both total leaves extracts against Severe Acute Respiratory Syndrome Corona virus 2 (SARS-CoV-2), it was found that A. indica L. and M. azedarach L. have robust anti-SARS-CoV-2 activities at low half-maximal inhibitory concentrations (IC50) of 8.451 and 6.922 μg/mL, respectively. Due to the high safety of A. indica L. and M. azedarach L. extracts with half-maximal cytotoxic concentrations (CC50) of 446.2 and 351.4 μg/ml, respectively, both displayed extraordinary selectivity indices (SI>50). A. indica L. and M. azedarach L. leaves extracts could induce antibacterial activities against both Gram-negative and positive bacterial strains. The minimal inhibitory concentrations of A. indica L. and M. azedarach L. leaves extracts varied from 25 to 100 mg/mL within 30 min contact time towards the tested bacteria. Our findings confirm the broad-spectrum medicinal value of A. indica L. and M. azedarach L. leaves extracts. Finally, additional in vivo investigations are highly recommended to confirm the anti-COVID-19 and antimicrobial activities of both plant extracts.

Role of ethno-phytomedicine knowledge in healthcare of COVID-19: advances in traditional phytomedicine perspective

Background

Since the outbreak of the COVID-19 virus, ethnomedicinal plants have been used in diverse geographical locations for their purported prophylactic and pharmacological effects. Medicinal plants have been relied on by people around the globe for centuries, as 80% of the world’s population rely on herbal medicines for some aspect of their primary health care needs, according to the World Health Organization.

Main body

This review portrays advances in traditional phytomedicine by bridging the knowledge of ethno-phytomedicine and COVID-19 healthcare. Ethnomedicinal plants have been used for symptoms related to COVID-19 as antiviral, anti-infective, anti-inflammatory, anti-oxidant, antipyretic, and lung–gut immune boosters. Traditionally used medicinal plants have the ability to inhibit virus entry and viral assembly, bind to spike proteins, membrane proteins, and block viral replications and enzymes. The efficacy of traditional medicinal plants in the terms of COVID-19 management can be evaluated by in vitro, in vivo as well as different in silico techniques (molecular docking, molecular dynamics simulations, machine learning, etc.) which have been applied extensively to the quest and design of effective biotherapeutics rapidly. Other advances in traditional phytomedicines against COVID-19 are controlled clinical trials, and notably the roles in the gut microbiome. Targeting the gut microbiome via medicinal plants as prebiotics is also found to be an alternative and potential strategy in the search for a COVID-19 combat strategy.

Conclusions

Since medicinal plants are the sources of modern biotherapeutics development, it is essential to build collaborations among ethnobotanists, scientists, and technologists toward developing the most efficient and the safest adjuvant therapeutics against the pandemic of the twenty-first century, COVID-19.

Elucidation of the inhibitory activity of ivermectin with host nuclear importin α and several SARS-CoV-2 targets

Ivermectin (IVM) is an FDA-approved drug that has shown antiviral activity against a wide variety of viruses in recent years. IVM inhibits the formation of the importin-α/β1 heterodimeric complex responsible for the translocation and replication of various viral species proteins. Also, IVM hampers SARS-CoV-2 replication in vitro; however, the molecular mechanism through which IVM inhibits SARS-CoV-2 is not well understood. Previous studies have explored the molecular mechanism through which IVM inhibits importin-α and several potential targets associated with COVID-19 by using docking approaches and MD simulations to corroborate the docked complexes. This study explores the energetic and structural properties through which IVM inhibits importin-α and five targets associated with COVID-19 by using docking and MD simulations combined with the molecular mechanics generalized Born surface area (MMGBSA) approach. Energetic and structural analysis showed that the main protease 3CLpro reached the most favorable affinity, followed by importin-α and Nsp9, which shared a similar relationship. Therefore, in vitro activity of IVM can be explained by acting as an inhibitor of importin-α, dimeric 3CLpro, and Nsp9, but mainly over dimeric 3CLpro.Communicated by Ramaswamy H. Sarma.

Modern drug discovery applications for the identification of novel candidates for COVID-19 infections

In early December 2019, a large pneumonia epidemic occurred in Wuhan, China. The World Health Organization is concerned about the outbreak of another coronavirus with the powerful, rapid, and contagious transmission. Anyone with minor symptoms like fever and cough or travel history to contaminated places might be suspected of having COVID-19. COVID-19 therapy focuses on treating the disease's symptoms. So far, no such therapeutic molecule has been shown effective in treating this condition. So the treatment is mostly supportive and plasma. Globally, numerous studies and researchers have recently started fighting this virus. Vaccines and chemical compounds are also being investigated against infection. COVID-19 was successfully diagnosed using RNA detection and very sensitive RT-PCR (reverse transcription-polymerase chain reaction). The evolution of particular vaccinations is required to reduce illness severity and spread. Numerous computational analyses and molecular docking have predicted various target compounds that might stop this condition. This paper examines the main characteristics of coronavirus and the computational analyses necessary to avoid infection.

Herbal medications and natural products for patients with covid-19 and diabetes mellitus: Potentials and challenges

BACKGROUND

The presence of diabetes mellitus (DM) among COVID-19 patients is associated with increased hospitalization, morbidity, and mortality. Evidence has shown that hyperglycemia potentiates SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection and plays a central role in severe COVID-19 and diabetes comorbidity. In this review, we explore the therapeutic potentials of herbal medications and natural products in the management of COVID-19 and DM comorbidity and the challenges associated with the preexisting or concurrent use of these substances.

METHODS

Research papers that were published from January 2016 to December 2021 were retrieved from PubMed, ScienceDirect, and Google Scholar databases. Papers reporting clinical evidence of antidiabetic activities and any available evidence of the anti-COVID-19 potential of ten selected natural products were retrieved and analyzed for discussion in this review.

RESULTS

A total of 548 papers (73 clinical trials on the antidiabetic activities of the selected natural products and 475 research and review articles on their anti-COVID-19 potential) were retrieved from the literature search for further analysis. A total of 517 articles (reviews and less relevant research papers) were excluded. A cumulative sum of thirty-one (31) research papers (20 clinical trials and 10 others) met the criteria and have been discussed in this review.

CONCLUSION

The findings of this review suggest that phenolic compounds are the most promising phytochemicals in the management of COVID-19 and DM comorbidity. Curcumin and propolis have shown substantial evidence against COVID-19 and DM in humans and are thus, considered the best potential therapeutic options.

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study

COVID-19 pandemic has emerged as a global threat with its highly contagious and mutating nature. Several existing antiviral drugs has been worked on, without proper results and meanwhile the virus is mutating rapidly to create more infectious variant. In order to find some alternatives, phytocompounds can be opted as good one. In this study, three hundred phytocompounds were screened virtually against two viral proteins namely main protease and spike protein. Molecular docking and dynamic simulation study was used to find binding affinity, structural stability and flexibility of the complex. Pharmacokinetic properties were studied through ADMET analysis. To understand energy variation of the complex structure free energy landscape analysis was performed. Among three hundred phytocompounds virtual screening, three phytocompounds were selected for detailed molecular interaction analysis. Oleanderolide, Proceragenin A and Balsaminone A, showed strong binding affinity against both the target proteins and reflected conformational stability throughout the MD run. Oleanderolide, proceragenin A and balsaminone A has docking score -9.4 kcal/mol, -8.6 kcal/mol, and -8.1 kcal/mol respectively against main protease and same -8.3 kcal/mol docking score against spike protein. These three phytocompounds has high gastrointestinal absorption capacity. They were unexplored till now for their antiviral activity. Their promising in silico results suggests that they can be promoted in the long run for development of new antiviral drugs.

Therapeutic role of traditionally used Indian medicinal plants and spices in combating COVID-19 pandemic situation

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is a big challenge and burning issue to the scientific community and doctors worldwide. Globally, COVID-19 has created a health disaster and adversely affects the economic growth. Although some vaccines have already emerged, no therapeutic medication has yet been approved by FDA for the treatment of COVID-19 patients. Traditionally, we have been using different medicinal plants like neem, tulsi, tea, and many spices like garlic, ginger, turmeric, black seed, onion, etc. for the treatment of flu-like diseases. In this paper, we are highlighting the recent research progress in the identification of natural products from the Indian medicinal plants and spices that have potential inhibition properties against SARS-CoV-2. This study will provide an initiative to stimulate further research by providing useful guidance to the medicinal chemists for designing new protease inhibitors effective against SARS-CoV-2 in future.

The Antimicrobial Potential of the Neem Tree Azadirachta indica

Azadirachta indica (A. Juss), also known as the neem tree, has been used for millennia as a traditional remedy for a multitude of human ailments. Also recognized around the world as a broad-spectrum pesticide and fertilizer, neem has applications in agriculture and beyond. Currently, the extensive antimicrobial activities of A. indica are being explored through research in the fields of dentistry, food safety, bacteriology, mycology, virology, and parasitology. Herein, some of the most recent studies that demonstrate the potential of neem as a previously untapped source of novel therapeutics are summarized as they relate to the aforementioned research topics. Additionally, the capacity of neem extracts and compounds to act against drug-resistant and biofilm-forming organisms, both of which represent large groups of pathogens for which there are limited treatment options, are highlighted. Updated information on the phytochemistry and safety of neem-derived products are discussed as well. Although there is a growing body of exciting evidence that supports the use of A. indica as an antimicrobial, additional studies are clearly needed to determine the specific mechanisms of action, clinical efficacy, and in vivo safety of neem as a treatment for human pathogens of interest. Moreover, the various ongoing studies and the diverse properties of neem discussed herein may serve as a guide for the discovery of new antimicrobials that may exist in other herbal panaceas across the globe.

West African medicinal plants and their constituent compounds as treatments for viral infections, including SARS-CoV-2/COVID-19

OBJECTIVES

The recent emergence of the COVID-19 pandemic (caused by SARS-CoV-2) and the experience of its unprecedented alarming toll on humanity have shone a fresh spotlight on the weakness of global preparedness for pandemics, significant health inequalities, and the fragility of healthcare systems in certain regions of the world. It is imperative to identify effective drug treatments for COVID-19. Therefore, the objective of this review is to present a unique and contextualised collection of antiviral natural plants or remedies from the West African sub-region as existing or potential treatments for viral infections, including COVID-19, with emphasis on their mechanisms of action.

EVIDENCE ACQUISITION

Evidence was synthesised from the literature using appropriate keywords as search terms within scientific databases such as Scopus, PubMed, Web of Science and Google Scholar.

RESULTS

While some vaccines and small-molecule drugs are now available to combat COVID-19, access to these therapeutic entities in many countries is still quite limited. In addition, significant aspects of the symptomatology, pathophysiology and long-term prognosis of the infection yet remain unknown. The existing therapeutic armamentarium, therefore, requires significant expansion. There is evidence that natural products with antiviral effects have been used in successfully managing COVID-19 symptoms and could be developed as anti-COVID-19 agents which act through host- and virus-based molecular targets.

CONCLUSION

Natural products could be successfully exploited for treating viral infections/diseases, including COVID-19. Strengthening natural products research capacity in developing countries is, therefore, a key strategy for reducing health inequalities, improving global health, and enhancing preparedness for future pandemics.

The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects

The novel coronavirus that caused COVID-19 pandemic is SARS-CoV-2. Although various vaccines are currently being used to prevent the disease's severe consequences, there is still a need for medications for those who become infected. The SARS-CoV-2 has a variety of proteins that have been studied extensively since the virus's advent. In this review article, we looked at chemical to molecular aspects of the various structures studied that have pharmaceutical activity and attempted to find a link between drug activity and compound structure. For example, designing of the compounds which bind to the allosteric site and modify hydrogen bonds or the salt bridges can disrupt SARS-CoV2 RBD–ACE2 complex. It seems that quaternary ammonium moiety and quinolin-1-ium structure could act as a negative allosteric modulator to reduce the tendency between spike-ACE2. Pharmaceutical structures with amino heads and hydrophobic tails can block envelope protein to prevent making mature SARS-CoV-2. Also, structures based on naphthalene pharmacophores or isosteres can form a strong bond with the PLpro and form a π-π and the Mpro's active site can be occupied by octapeptide compounds or linear compounds with a similar fitting ability to octapeptide compounds. And for protein RdRp, it is critical to consider pH and pKa so that pKa regulation of compounds to comply with patients is very effective, thus, the presence of tetrazole, phenylpyrazole groups, and analogs of pyrophosphate in the designed drugs increase the likelihood of the RdRp active site inhibition. Finally, it can be deduced that designing hybrid drug molecules along with considering the aforementioned characteristics would be a suitable approach for developing medicines in order to accurate targeting and complete inhibition this virus.

Functionalized non-woven surfaces for combating the spread of the COVID-19 pandemic

The worldwide outbreak of SARS-CoV-2 infection has necessitated mandatory use of face masks, personal protective equipment and intake of a healthy diet for immunity boosting. As per WHO's recommendation, continuous use of masks has been proven effective in decreasing the SARS-CoV-2 infection rate. The present study reports on the bacterial filtration efficacy (BFE) of a novel 4-ply functionalized non-woven face mask. We synthesized a polypropylene-based fabric with inner layers of melt-blown fine fibres coated with polylactic acid and immune-boosting herbal phytochemicals. Experimental studies on the synthesized face mask demonstrated a BFE of greater than 99% against Staphylococcus aureus (a bacterium species frequently found in mammalian respiratory tract). A thorough computational analysis using LibDock algorithm demonstrated an effective docking performance of herbal phytochemicals against harmful virus structures. More importantly, the face mask also showed sufficient and stable breathability as per regulatory standards. A breathing resistance of 30 Pa at an aerosol flow rate of 30 l h⁻¹ was reported under standard temperature and pressure conditions, indicating a high potential for real-world applications.

An Insight into the Dermatological Applications of Neem: A Review on Traditional and Modern Aspect

BACKGROUND

Dermatological disorders are cutaneous infirmities which are frequently occurring and increasing at an alarming rate. These range from mild itching/redness (dermatitis) to fatal skin cancers and has posed a major health concern. Azadirachta indica A. Juss (commonly known as neem), a member of Meliaceae family, is an Indian medicinal plant which has been known for its health promoting effects since ancient times.

OBJECTIVE

The review highlights the traditional practices, pharmacological aspects, and formulatory approach of neem for the treatment of dermatological disorders. Further, recent patents and novel delivery systems (developed and in pipeline) improving skin delivery and therapeutic profile of neem are discussed.

RESULTS

Neem is a traditional medicinal plant that has been employed for the prevention and treatment of numerous ailments covering systemic and topical disorders. Scientific studies have validated the traditional claims of neem and attributed these health benefits to the presence of more than 300 structurally diverse and complex compounds. It possesses anti-inflammatory, antibacterial, analgesic, antiviral, antifungal, immunomodulatory and antioxidant activities which substantiate its use as skin therapy. Various novel formulations and associated patents that improved the permeability of neem based products across skin could be found in literature.

CONCLUSION

Critical appraisal of available literature revealed that neem possesses anti-microbial, anti-inflammatory, antioxidant and antiseptic properties. Thus it has the potential to be developed as a single effective therapy for the management of multimodal skin disorders. Further, pharmaceutical tailoring of neem by implication of novel carriers could enhance its penetrability across skin.

Natural Products as Potential Antiviral Drugs: The Specific Case of Marine Biotoxins

To fight against various viral infections researchers turned to new chemical structures resulting from natural medicinal plants and more recently from "marine origin" as sources of active molecules against viral infections. The present manuscript describes complex marine origin drugs, their chemical complex structure, their therapeutic use, and their antiviral properties. Emphasis is placed more particularly on the properties of ionic channels (Na+, K+, Ca2+) blockers compounds from marine origin, named Dinotoxins, derived from "dinoflagellates microalgae". These compounds are of particular pharmaceutical interest since ionic channels blockers could be used to fight against a wide diversity of viruses, including SARS-CoV2 virus.

Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PLpro and Mpro/ 3CLpro: molecular docking and simulation studies of three pertinent medicinal plant natural components

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - coronavirus disease 2019 (COVID-19) has raised a severe global public health issue and creates a pandemic situation. The present work aims to study the molecular -docking and dynamic of three pertinent medicinal plants i.e. Eurycoma harmandiana, Sophora flavescens and Andrographis paniculata phyto-compounds against SARS-COV-2 papain-like protease (PL^pro) and main protease (M^pro)/3-chymotrypsin-like protease (3CL^pro). The interaction of protein targets and ligands was performed through AutoDock-Vina visualized using PyMOL and BIOVIA-Discovery Studio 2020. Molecular docking with canthin-6-one 9-O-beta-glucopyranoside showed highest binding affinity and less binding energy with both PL^pro and M^pro/3CL^pro proteases and was subjected to molecular dynamic (MD) simulations for a period of 100ns. Stability of the protein-ligand complexes was evaluated by different analyses. The binding free energy calculated using MM-PBSA and the results showed that the molecule must have stable interactions with the protein binding site. ADMET analysis of the compounds suggested that it is having drug-like properties like high gastrointestinal (GI) absorption, no blood-brain barrier permeability and high lipophilicity. The outcome revealed that canthin-6-one 9-O-beta-glucopyranoside can be used as a potential natural drug against COVID-19 protease.

Herbal medicine use for the management of COVID-19: A review article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause pandemic of coronavirus disease 2019 (COVID-19). For many thousands of years, herbal products and dietary plants have been prescribed for various diseases by traditional healers. Thus, the aim of this review is to present main herbal products, their source, characteristics, and potential antiviral actions concerning COVID-19. Publications on herbal products related to antiviral effects were searched from different databases, such as Web of Science, Google Scholar, Medline, Scopus, and PubMed, until August 2021, using English key terms. According to different studies, there are so many important medicinal plants with antiviral activity, which can be used for viral infections or can be prescribed as supportive treatment. lack of information on the safety profile and amount of dose for different diseases is some of the limitations of medicinal plants. herbal medicine can interfere with COVID-19 pathogenesis by inhibiting SARS-CoV-2 replication and entry to host cells. Some of the antiviral medicinal plant species are citrus Spp., orange (C. Sinensis), Allium sativum, Allium cepa, Mentha piperita, and nigella sativa are the most desirable herbal drink or fruit that can introduce effective adjuvant components in COVID-19 management.

A survey on computational methods in discovering protein inhibitors of SARS-CoV-2

The outbreak of acute respiratory disease in 2019, namely Coronavirus Disease-2019 (COVID-19), has become an unprecedented healthcare crisis. To mitigate the pandemic, there are a lot of collective and multidisciplinary efforts in facilitating the rapid discovery of protein inhibitors or drugs against COVID-19. Although many computational methods to predict protein inhibitors have been developed [ 1– 5], few systematic reviews on these methods have been published. Here, we provide a comprehensive overview of the existing methods to discover potential inhibitors of COVID-19 virus, so-called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). First, we briefly categorize and describe computational approaches by the basic algorithms involved in. Then we review the related biological datasets used in such predictions. Furthermore, we emphatically discuss current knowledge on SARS-CoV-2 inhibitors with the latest findings and development of computational methods in uncovering protein inhibitors against COVID-19.

Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLpro)

The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome - novel Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-2003. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-CoV-2. The high-resolution crystal structure of the main protease of SARS-CoV-2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open-source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for the main protease helped in exploring the conformational variation in the drug-binding site of the main protease leading to the efficient binding of more relevant drug molecules. The drugs obtained as top hits from the ensemble docking possessed anti-bacterial and anti-viral properties. This in silico ensemble docking approach would support the identification of potential candidates for repurposing against COVID-19.Communicated by Ramaswamy H. Sarma.

Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19

Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.

Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation

Coronavirus disease-2019 (COVID-19) is a global health emergency and the matter of serious concern, which has been declared a pandemic by WHO. Till date, no potential medicine/ drug is available to cure the infected persons from SARS-CoV-2. This deadly virus is named as novel 2019-nCoV coronavirus and caused coronavirus disease, that is, COVID-19. The first case of SARS-CoV-2 infection in human was confirmed in the Wuhan city of the China. COVID-19 is an infectious disease and spread from man to man as well as surface to man . In the present work, in silico approach was followed to find potential molecule to control this infection. Authors have screened more than one million molecules available in the ZINC database and taken the best two compounds based on binding energy score. These lead molecules were further studied through docking against the main protease of SARS-CoV-2. Then, molecular dynamics simulations of the main protease with and without screened compounds were performed at room temperature to determine the thermodynamic parameters to understand the inhibition. Further, molecular dynamics simulations at different temperatures were performed to understand the efficiency of the inhibition of the main protease in the presence of the screened compounds. Change in energy for the formation of the complexes between the main protease of novel coronavirus and ZINC20601870 as well ZINC00793735 at room temperature was determined on applying MM-GBSA calculations. Docking and molecular dynamics simulations showed their antiviral potential and may inhibit viral replication experimentally. Communicated by Ramaswamy H. Sarma.

Potential alternatives to current cholinesterase inhibitors: an in silico drug repurposing approach

Acetylcholinesterase/Butyrylcholinesterase inhibitors are considered an effective method for treating Alzheimer's disease (AD). In this current work, we have computationally analyzed 11 new small molecule drugs used in various neurological diseases and Donepezil, a known inhibitor of acetylcholinesterase, as a positive control. We investigated these drugs for possible fundamental interactions with acetylcholinesterase and butyrylcholinesterase as both are critical in the pathophysiology of Alzheimer's disease. We have selected FDA approved compounds for repurposing as possible inhibitors of these enzymes and novel therapeutic option for Alzheimer's disease. We selected the top two molecules for each protein for their binding energies, interactions, and Donepezil, the most commonly used drug for AD treatment. Molecular simulation and dynamics studies of the top 2 drugs in each case and free energy analysis helped us reach further conclusions about the best possible drugs for repurposing. Brexipirazole and Deutetrabenazine produce encouraging results as butyrylcholinesterase and acetylcholinesterase inhibitors, respectively.

Computational Chemistry to Repurposing Drugs for the Control of COVID-19

Thus far, in 2021, 219 countries with over 175 million people have been infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is a positive sense, single-stranded RNA virus, and is the causal agent for coronavirus disease (COVID-19). Due to the urgency of the situation, virtual screening as a computational modeling method offers a fast and effective modality of identifying drugs that may be effective against SARS-CoV-2. There has been an overwhelming abundance of molecular docking against SARS-CoV-2 in the last year. Due to the massive volume of computational studies, this systematic review has been created to evaluate and summarize the findings of existing studies. Herein, we report on computational articles of drugs which target, (1) viral protease, (2) Spike protein-ACE 2 interaction, (3) RNA-dependent RNA polymerase, and (4) other proteins and nonstructural proteins of SARS-CoV-2. Based on the studies presented, there are 55 identified natural or drug compounds with potential anti-viral activity. The next step is to show anti-viral activity in vitro and translation to determine effectiveness into human clinical trials.

Needleless electrospun phytochemicals encapsulated nanofibre based 3-ply biodegradable mask for combating COVID-19 pandemic

The emergence of COVID-19 pandemic has severely affected human health and world economies. According to WHO guidelines, continuous use of face mask is mandatory for personal protection for restricting the spread of bacteria and virus. Here, we report a 3-ply cotton-PLA-cotton layered biodegradable face-mask containing encapsulated phytochemicals in the inner-filtration layer. The nano-fibrous PLA filtration layer was fabricated using needleless electrospinning of PLA & phytochemical-based herbal-extracts. This 3-layred face mask exhibits enhanced air permeability with a differential pressure of 35.78 Pa/cm² and superior bacterial filtration efficiency of 97.9% compared to conventional face masks. Close-packed mesh structure of the nano-fibrous mat results in effective adsorption of particulate matter, aerosol particles, and bacterial targets deep inside the filtration layer. The outer hydrophobic layer of mask exhibited effective blood splash resistance up to a distance of 30 cm, ensuring its utilization for medical practices. Computational analysis of constituent phytochemicals using the LibDock algorithm predicted inhibitory activity of chemicals against the protein structured bacterial sites. The computational analysis projected superior performance of phytochemicals considering the presence of stearic acid, oleic acid, linoleic acid, and Arachidic acid exhibiting structural complementarity to inhibit targeted bacterial interface. Natural cotton fibers and PLA bio-polymer demonstrated promising biodegradable characteristics in the presence of in-house cow-dung based biodegradation slurry. Addition of jaggery to the slurry elevated the biodegradation performance, resulting in increment of change of weight from 07% to 12%. The improved performance was attributed to the increased sucrose content in biodegradation slurry, elevating the bacterial growth in the slurry. An innovative face mask has shown promising results for utilization in day-to-day life and medical frontline workers, considering the post-pandemic environmental impacts.

Mechanistic Aspects of Medicinal Plants and Secondary Metabolites against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

BACKGROUND AND OBJECTIVE

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a highly pathogenic virus, is responsible for a respiratory disease termed coronavirus disease 2019 (COVID-19). SARS-CoV-2 genome encodes various structural and non-structural proteins, which are necessary for viral entry and replication. Among these proteins, papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase, a serine protease, and spike protein are potential targets of herbal remedies and phytocompounds for inhibition of viral infection and replication. There is at present no confirmed cure for the COVID-19. Various plants and their components have been introduced against SARS-Co-2. A number of review articles have also been published on them. This article is focusing on the mechanistic aspects of these plants and their derivatives on SARS-CV-2.

METHOD

The material in this review article was prepared from significant scientific databases, including Web of Science, PubMed, Science Direct, Scopus and Google Scholar.

RESULTS

Different medicinal plants and their phytocompounds interact with important structural and non-structural of SARS-CoV-2 proteins. Natural compounds form strong bonds with the active site of SARS-CoV-2 protease and make large conformational changes. These phytochemicals are potential inhibitors of structural and non-structural of SARS-CoV-2 proteins such as Spike protein, PLpro, and 3CLpro. Some important anti-SARS-CoV-2 actions of medicinal plants and their metabolites are inhibition of the virus replication or entry, blocking the angiotensin-converting enzyme 2 (ACE-2) receptor and "Transmembrane protease, serine 2 (TMPRSS2)" regulation of inflammatory mediators, inhibition of endothelial activation, toll-like receptors (TLRs) and activation of the nuclear factor erythroid-derived 2-related factor 2 (Nrf2). Some of these important natural immune boosters that are helpful for prevention and curing various symptoms related to COVID-19 include Allium sativum, Nigella sativa, Glycyrrhiza glabra Zingiber officinalis, Ocimum sanctum, Withania somnifera, Tinospora cordifolia, and Scutellaria baicalensis. Also, Kaempferol, Quercetin, Baicalin, Scutellarin, Glycyrrhizin, Curcumin, Apigenin, Ursolic acid, and Chloroquine are the best candidates for treating the symptoms associated with SARS-CoV-2 infection.

CONCLUSION

Medicinal plants and/or their bioactive compounds with inhibitory effects against SARS-CoV-2 support the human immune system and help in fighting against COVID-19 and rejuvenating the immune system.

Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors

The COVID-19 epidemic is one of the most influential epidemics in history. Understanding the impact of coronaviruses (CoVs) on host cells is very important for disease treatment. The SARS-CoV-2 envelope (E) protein is a small structural protein involved in many aspects of the viral life cycle. The E protein promotes the packaging and reproduction of the virus, and deletion of this protein weakens or even abolishes the virulence. This review aims to establish new knowledge by combining recent advances in the study of the SARS-CoV-2 E protein and by comparing it with the SARS-CoV E protein. The E protein amino acid sequence, structure, self-assembly characteristics, viroporin mechanisms and inhibitors are summarized and analyzed herein. Although the mechanisms of the SARS-CoV-2 and SARS-CoV E proteins are similar in many respects, specific studies on the SARS-CoV-2 E protein, for both monomers and oligomers, are still lacking. A comprehensive understanding of this protein should prompt further studies on the design and characterization of effective targeted therapeutic measures.

Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2

The novel coronavirus (SARS-CoV-2) outbreak has started taking away the millions of lives worldwide. Identification of known and approved drugs against novel coronavirus disease (COVID-19) seems to be an urgent need for the repurposing of the existing drugs. So, here we examined a safe strategy of using approved drugs of SuperDRUG2 database against modeled membrane protein (M-protein) of SARS-CoV-2 which is essential for virus assembly by using molecular docking-based virtual screening. A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We therefore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds. The complexes of M-protein with the selected drugs were simulated for 50 ns and ranked according to their binding free energies. The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein. We therefore additionally identified four Colchicine derivatives which can bind efficiently with M-protein and have better pharmacokinetic properties. We recommend that these drugs can be tested further through in vitro studies against SARS-CoV-2 M-protein.

Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.

Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.

Natural Products Modulating Angiotensin Converting Enzyme 2 (ACE2) as Potential COVID-19 Therapies

The 2019 coronavirus disease (COVID-19) is a potentially fatal multisystemic infection caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Currently, viable therapeutic options that are cost effective, safe and readily available are desired, but lacking. Nevertheless, the pandemic is noticeably of lesser burden in African and Asian regions, where the use of traditional herbs predominates, with such relationship warranting a closer look at ethnomedicine. From a molecular viewpoint, the interaction of SARS-CoV-2 with angiotensin converting enzyme 2 (ACE2) is the crucial first phase of COVID-19 pathogenesis. Here, we review plants with medicinal properties which may be implicated in mitigation of viral invasion either via direct or indirect modulation of ACE2 activity to ameliorate COVID-19. Selected ethnomedicinal plants containing bioactive compounds which may prevent and mitigate the fusion and entry of the SARS-CoV-2 by modulating ACE2-associated up and downstream events are highlighted. Through further experimentation, these plants could be supported for ethnobotanical use and the phytomedicinal ligands could be potentially developed into single or combined preventive therapeutics for COVID-19. This will benefit researchers actively looking for solutions from plant bioresources and help lessen the burden of COVID-19 across the globe.

Spices and herbs: Potential antiviral preventives and immunity boosters during COVID-19

A severe acute respiratory syndrome is an unusual type of contagious pneumonia that is caused by SARS coronavirus. At present, the whole world is trying to combat this coronavirus disease and scientific communities are putting rigorous efforts to develop vaccines. However, there are only a few specific medical treatments for SARS-CoV-2. Apart from other public health measures taken to prevent this virus, we can boost our immunity with natural products. In this article, we have highlighted the potential of common spices and herbs as antiviral agents and immunity boosters. A questionnaire-based online survey has been conducted on home remedies during COVID-19 among a wide range of peoples (n-531) of different age groups (13-68 years) from various countries. According to the survey, 71.8% of people are taking kadha for combating infection and boosting immunity. Most people (86.1%) think that there is no side effect of kadha while 13.9% think vice versa. A total of 93.6% of people think that spices are helpful in curing coronavirus or other viral infection as well as boosting immunity. Most people are using tulsi drops, vitamin C, and chyawanprash for boosting their immunity. Therefore, we conclude from the survey and available literature that spices and herbs play a significant role against viral infections.

Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies

Outbreak of Coronavirus (SARS-CoV-2) has thrown a big challenge to the globe by snatching millions of human lives from the world. In this study, inhibitory efficiency of ten anti-HIV compounds from different Indian medicinal plant parts have been virtually screened against Mpro, PLpro and RdRp proteins of SARS-CoV-2. The molecular docking study reflected that among these compounds, Proptine (PTP) has the highest binding affinity for the three cases. Introduction of PTP molecules within the binding pocket of these proteins showed a large structural and conformational changes on the structure of proteins which is revealed from molecular dynamics (MD) simulation studies. RMSD, RMSF and analysis of thermodynamic parameters also revealed that PTP makes a huge impact on the structures of the respective proteins which will pave an opportunity for doing advanced experimental research to evaluate the potential drug to combat COVID-19.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13721-021-00309-3.

Therapeutic Potentials of Antiviral Plants Used in Traditional African Medicine With COVID-19 in Focus: A Nigerian Perspective

The coronavirus disease 2019 (COVID-19) pandemic is caused by an infectious novel strain of coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was earlier referred to as 2019-nCoV. The respiratory disease is the most consequential global public health crisis of the 21st century whose level of negative impact increasingly experienced globally has not been recorded since World War II. Up till now, there has been no specific globally authorized antiviral drug, vaccines, supplement or herbal remedy available for the treatment of this lethal disease except preventive measures, supportive care and non-specific treatment options adopted in different countries via divergent approaches to halt the pandemic. However, many of these interventions have been documented to show some level of success particularly the Traditional Chinese Medicine while there is paucity of well reported studies on the impact of the widely embraced Traditional African Medicines (TAM) adopted so far for the prevention, management and treatment of COVID-19. We carried out a detailed review of publicly available data, information and claims on the potentials of indigenous plants used in Sub-Saharan Africa as antiviral remedies with potentials for the prevention and management of COVID-19. In this review, we have provided a holistic report on evidence-based antiviral and promising anti-SARS-CoV-2 properties of African medicinal plants based on in silico evidence, in vitro assays and in vivo experiments alongside the available data on their mechanistic pharmacology. In addition, we have unveiled knowledge gaps, provided an update on the effort of African Scientific community toward demystifying the dreadful SARS-CoV-2 micro-enemy of man and have documented popular anti-COVID-19 herbal claims emanating from the continent for the management of COVID-19 while the risk potentials of herb-drug interaction of antiviral phytomedicines when used in combination with orthodox drugs have also been highlighted. This review exercise may lend enough credence to the potential value of African medicinal plants as possible leads in anti-COVID-19 drug discovery through research and development.

The use of medicinal plants to prevent COVID-19 in Nepal

BACKGROUND

Medicinal plants are the fundamental unit of traditional medicine system in Nepal. Nepalese people are rich in traditional medicine especially in folk medicine (ethnomedicine), and this system is gaining much attention after 1995. The use of medicinal plants has increased during the COVID-19 pandemic as a private behavior (not under the control of government). A lot of misinterpretations of the use of medicinal plants to treat or prevent COVID-19 have been spreading throughout Nepal which need to be managed proactively. In this context, a research was needed to document medicinal plants used, their priority of use in society, their cultivation status, and the source of information people follow to use them. This study aimed to document the present status of medicinal plant use and make important suggestion to the concerned authorities.

METHODS

This study used a web-based survey to collect primary data related to medicinal plants used during COVID-19. A total of 774 respondents took part in the survey. The study calculated the relative frequencies of citation (RFC) for the recorded medicinal plants. The relationship between plants recorded and different covariates (age, gender education, occupation, living place, and treatment methods) was assessed using Kruskal-Wallis test and Wilcoxon test. The relationship between the information sources people follow and the respondent characteristics was assessed using chi-square test.

RESULTS

The study found that the use of medicinal plants has increased during COVID-19 and most of the respondents recommended medicinal plants to prevent COVID-19. This study recorded a total of 60 plants belonging to 36 families. The leaves of the plants were the most frequently used. The Zingiber officinale was the most cited species with the frequency of citation 0.398. Most of the people (45.61%) were getting medicinal plants from their home garden. The medicinal plants recorded were significantly associated with the education level, location of home, primary treatment mode, gender, and age class. The information source of plants was significantly associated with the education, gender, method of treatment, occupation, living with family, and location of home during the lockdown caused by COVID-19.

CONCLUSIONS

People were using more medicinal plants during COVID-19 claiming that they can prevent or cure COVID-19. This should be taken seriously by concerned authorities. The authorities should test the validity of these medicinal plants and control the flow of false information spread through research and awareness programs.