Promising phytochemicals of traditional Indian herbal steam inhalation therapy to combat COVID-19 - An in silico study

Eucalyptus Oils Phytochemical Composition in Correlation with Their Newly Explored Anti-SARS-CoV-2 Potential: in Vitro and in Silico Approaches

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the latest arisen contagious respiratory pathogen related to the global outbreak of atypical pneumonia pandemic (COVID-19). The essential oils (EOs) of Eucalyptus camaldulensis, E. ficifolia F. Muell., E. citriodora Hook, E. globulus Labill, E. sideroxylon Cunn. ex Woolls, and E. torquata Luehm. were investigated for its antiviral activity against SARS-CoV-2. The EOs phytochemical composition was determined using GC/MS analysis. Correlation with the explored antiviral activity was also studied using multi-variate data analysis and Pearson's correlation. The antiviral MTT and cytopathic effect inhibition assays revealed very potent and promising anti SARS-CoV-2 potential for E. citriodora EO (IC50 = 0.00019 µg/mL and SI = 26.27). The multivariate analysis revealed α-pinene, α-terpinyl acetate, globulol, γ -terpinene, and pinocarvone were the main biomarkers for E. citriodora oil. Pearson's correlation revealed that globulol is the top positively correlated compound in E. citriodora oil to its newly explored potent anti SARS-CoV-2 potential. A molecular simulation was performed on globulol via docking in the main active sites of both SARS-CoV-2 viral main protease (Mpro) and spike protein (S). In silico predictive ADMET study was also developed to investigate the pharmacokinetic profile and predict globulol toxicity. The obtained in silico, in vitro and Pearson's correlation results were aligned showing promising SARS-CoV-2 inhibitory activity of E. citriodora and globulol. This study is a first record for E. citriodora EO as a novel lead exhibiting potent in vitro, and in silico anti SARS-CoV-2 potential and suggesting its component globulol as a promising candidate for further extensive in silico, in vitro and in vivo anti-COVID studies.

In silico analysis unravels the promising anticariogenic efficacy of fatty acids against dental caries causing Streptococcus mutans

Globally, dental caries is a prevalent oral disease caused by cariogenic bacteria, primarily Streptococcus mutans. It establishes caries either through sucrose-dependent (via glycosyltransferases) or through sucrose-independent (via surface adhesins Antigen I/II) mechanism. Sortase A (srtA) attaches virulence-associated adhesins to host tissues. Because of their importance in the formation of caries, targeting these proteins is decisive in the development of new anticariogenic drugs. High-throughput virtual screening with LIPID MAPS -a fatty acid database was performed. The selected protein-ligand complexes were subjected to molecular dynamics simulation (MDs). The Binding Free Energy of complexes was predicted using MM/PBSA. Further, the drug-likeness and pharmacokinetic properties of ligands were also analyzed. Out of 46,200 FAs scrutinized virtually against the three protein targets (viz., GtfC, Ag I/II and srtA), top 5 FAs for each protein were identified as the best hit based on interaction energies viz., hydrogen bond numbers and hydrophobic interaction. Further, two common FAs (LMFA01050418 and LMFA01040045) that showed high binding affinity against Ag I/II and srtA were selected for MDs analysis. A 100ns MDs unveiled a stable conformation. Results of Rg signified that FAs does not induce significant structural & conformational changes. SASA indicated that the complexes maintain higher thermodynamic stability during MDs. The predicted binding free energy (MM/PBSA) of complexes elucidated their stable binding interaction. ADME analysis suggested the FAs are biologically feasible as therapeutic candidates. Overall, the presented in silico data is the first of its kind in delineating FAs as promising anticaries agents of future.Communicated by Ramaswamy H. Sarma.

Diet-induced animal model anti-obesity, phytochemical profiling, and in silico analysis of culinary plant gokhru (Pedalium murex L.) mucilage

Plant-based diets (PBDs) are renowned for managing and developing bioactive chemical inhibitors to combat obesity, a well-known global public health concern. There are currently no published research studies examining the effects of food plant mucilage dietary supplements on animal models of obesity induced by high-fat diets (HFD). The present research investigated the anti-obesity properties of the culinary plant Pedalium murex L. mucilage (PMM) in obese albino male rats models fed HFD. PMM's HR-LCMS phytochemical profiling and in silico evaluation of anti-obesity and drug-likeness using Schrodinger's Glide, QikProp, and GROMACS modules were also investigated. In vivo, anti-obesity model animal rat's daily dietary intake, common blood biochemical parameters, and histological examination of the liver and kidney tissues for the development of macrovesicular and microvesicular steatosis were all performed. Among the 46 Phytochemicals profiled, 7(14)-Bisabolene-2, 3, 10,11tetrol, Moschamine, and N-Feruloyltyramine show prominent anti-obesity activity and drug-like characteristics in silico. Rats given PMM showed significantly lower serum levels of total cholesterol (TC), low-density lipoprotein (LDL), and triglycerides (TGs), increased levels of high-density lipoprotein (HDL), as well as macro-and microvesicular steatosis, lobular inflammation of the liver and kidney tissues. This suggests that PMM is an effective natural anti-obesity therapeutic ingredient or dietary supplement with a high concentration of anti-obesity phytochemicals that mainly satisfies the needs for such natural anti-obesity medicine or a supplement.Communicated by Ramaswamy H. Sarma.

Covalent Inhibitors from Saudi Medicinal Plants Target RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2

COVID-19, a disease caused by SARS-CoV-2, has caused a huge loss of human life, and the number of deaths is still continuing. Despite the lack of repurposed drugs and vaccines, the search for potential small molecules to inhibit SARS-CoV-2 is in demand. Hence, we relied on the drug-like characters of ten phytochemicals (compounds 1-10) that were previously isolated and purified by our research team from Saudi medicinal plants. We computationally evaluated the inhibition of RNA-dependent RNA polymerase (RdRp) by compounds 1-10. Non-covalent (reversible) docking of compounds 1-10 with RdRp led to the formation of a hydrogen bond with template primer nucleotides (A and U) and key amino acid residues (ASP623, LYS545, ARG555, ASN691, SER682, and ARG553) in its active pocket. Covalent (irreversible) docking revealed that compounds 7, 8, and 9 exhibited their irreversible nature of binding with CYS813, a crucial amino acid in the palm domain of RdRP. Molecular dynamic (MD) simulation analysis by RMSD, RMSF, and Rg parameters affirmed that RdRP complexes with compounds 7, 8, and 9 were stable and showed less deviation. Our data provide novel information on compounds 7, 8, and 9 that demonstrated their non-nucleoside and irreversible interaction capabilities to inhibit RdRp and shed new scaffolds as antivirals against SARS-CoV-2.

Evaluation of Rapanone and Nectandrin B as novel inhibitors for targeting the metastatic regulator protein BACH1 using breast cancer cell line Mcf-7

Cancer formation is defined as the unrestrained proliferation of cells due to various factors acting as a causing agent. A limited number of over-expressed transcription factors are contributed to the development of numerous types of cancer. The metastatic regulator protein BTB And CNC Homology 1 (BACH1) is Cap 'N' Collar (CNC) and it belongs to a basic region leucine zipper (bZIP) family. The presence of the least level concentration of intracellular heme BACH1 forms heterodimers with musculo aponeurotic fibrosarcoma (sMAF) proteins and inhibits or induces the target gene expression. Based on the previous studies, BACH1 plays a critical player in the conditions of senescence and oxidative stress, cycling of cell life, heme degradation pathway and cancer, especially in metastasis. Discovering new anti-cancer drugs (identification of bioactive compounds) stages finally needs to inhibit the target protein. This present study is aimed to screen and identify stability, binding affinity and analysis of pharmacokinetics of selected compounds through structural screening, ADMET, DFT and MESP. From this study, it is revealed that Rapanone and Nectandrin B have the potential to alter the degree of gene expression via binding with the BACH1 allosteric region which will further change the degree of expression of BACH1 downstream target genes involved in the regulation of cancer progression particularly in metastasis. The two plant origin compounds Rapanone and Nectandrin B might be novel candidates for developing anti-cancer drugs. The predicted compounds were further validated through in-vitro experimental approaches.Communicated by Ramaswamy H. Sarma.

Herbal concoction Unveiled: A computational analysis of phytochemicals' pharmacokinetic and toxicological profiles using novel approach methodologies (NAMs)

Herbal medications have an extensive history of use in treating various diseases, attributed to their perceived efficacy and safety. Traditional medicine practitioners and contemporary healthcare providers have shown particular interest in herbal syrups, especially for respiratory illnesses associated with the SARS-CoV-2 virus. However, the current understanding of the pharmacokinetic and toxicological properties of phytochemicals in these herbal mixtures is limited. This study presents a comprehensive computational analysis utilizing novel approach methodologies (NAMs) to investigate the pharmacokinetic and toxicological profiles of phytochemicals in herbal syrup, leveraging in-silico techniques and prediction tools such as PubChem, SwissADME, and Molsoft's database. Although molecular dynamics, docking, and broader system-wide analyses were not considered, future studies hold potential for further investigation in these areas. By combining drug-likeness with molecular simulation, researchers identify diverse phytochemicals suitable for complex medication development examining their pharmacokinetic-toxicological profiles in phytopharmaceutical syrup. The study focuses on herbal solutions for respiratory infections, with the goal of adding to the pool of all-natural treatments for such ailments. This research has the potential to revolutionize environmental and alternative medicine by leveraging in-silico models and innovative analytical techniques to identify novel phytochemicals with enhanced therapeutic benefits and explore network-based and systems biology approaches for a deeper understanding of their interactions with biological systems. Overall, our study offers valuable insights into the computational analysis of the pharmacokinetic and toxicological profiles of herbal concoction. This paves the way for advancements in environmental and alternative medicine. However, we acknowledge the need for future studies to address the aforementioned topics that were not adequately covered in this research.

Combination of bendamustine-azacitidine against Syk target of breast cancer: an in silico study

Breast cancer (BC) is the most serious and second leading cause of death in women worldwide. When breast cancer is diagnosed and treated early, the chance of long-term survival is up to 90%. On the other hand, 90% of BC patient deaths are due to metastasis and a lack of effective early diagnosis. The existing conventional chemotherapy provides negative feedback due to transportation barriers towards the action sites, multidrug resistance, poor bio-availability, non-specific delivery and systemic side effects on the healthy tissue. Syk protein Kinase has been reported in BC, as a tumor modulator, providing a pro-survival signal and also by restricting epithelial-mesenchymal transition, enhancing cell-cell interactions and inhibiting migration. In the present study, we explored the possibility of targeting BC by attenuating Syk protein Kinase. Hence, we have conjugated the hydrophobic Bendamustine (BEN) and hydrophilic Azacitidine (AZA) anticancer drugs to evaluate their efficacy against BC. The native drugs (BEN and AZA) and designed drug-drug conjugate (BEN-AZA) were docked with Syk protein. Then, the docked complex was performed for Binding Free Energy and Molecular Dynamics Simulations. Furthermore, DFT and ADME properties were carried out. The results revealed that the designed drug-drug conjugate has a better docking score, ΔGbind and admirable stability throughout the simulation when compared with native drugs. In DFT and ADME analyses, the designed drug-drug conjugate has shown good stereo electronic features and pharmaceutical relevant parameters than that of native drugs. The overall results suggested that the designed drug-drug conjugate may be a suitable candidate for BC treatment.Communicated by Ramaswamy H. Sarma.

Pulmonary drug delivery: an effective and convenient delivery route to combat COVID-19

The recent outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China has spread rapidly around the world, leading to a widespread and urgent effort to develop and use comprehensive approaches in the treatment of COVID-19. While oral therapy is accepted as an effective and simple method, since the primary site of infection and disease progression of COVID-19 is mainly through the lungs, inhaled drug delivery directly to the lungs may be the most appropriate route of administration. To prevent or treat primary SARS-CoV-2 infections, it is essential to target the virus port of entry in the respiratory tract and airway epithelium, which requires rapid and high-intensity inhibition or control of viral entry or replication. To achieve success in this field, inhalation therapy is the most attractive treatment approach due to efficacy/safety profiles. In this review article, pulmonary drug delivery as a unique treatment option in lung diseases will be briefly reviewed. Then, possible inhalation therapies for the treatment of symptoms of COVID-19 will be discussed and the results of clinical trials will be presented. By pulmonary delivery of the currently approved drugs for COVID-19, efficacy of the treatment would be improved along with reducing systemic side effects.

Phytochemicals, Biological Activities, Molecular Mechanisms, and Future Prospects of Plantago asiatica L

Plantago asiatica L. has been used as a vegetable and nutritious food in Asia for thousands of years. According to recent phytochemical and pharmacological research, the active compositions of the plant contribute to various health benefits, such as antioxidant, anti-inflammatory, antibacterial, antiviral, and anticancer. This article reviews the 87 components of the plant and their structures, as well as their biological activities and molecular research progress, in detail. This review provides valuable reference material for further study, production, and application of P. asiatica, as well as its components in functional foods and therapeutic agents.

Computational identification of potential inhibitory compounds in Indian medicinal and aromatic plant species against major pathogenicity determinants of SARS-CoV-2

SARS-CoV-2 (COVID-19) viral pandemic has been reported across 223 countries and territories. Globalized vaccination programs alongside administration of repurposed drugs will assumingly confer a stronger and longer individual specific immune protection. However, considering possible recurrence of the disease via new variants, a conveniently deliverable phytopharmaceutical drug might be the best option for COVID-19 treatment. In the current study, the efforts have been made to identify potential leads for inhalation therapy as nasal swabs have been reported to transfer viral load prominently. In that direction, 2363 Essential oil (EOs) compounds from Indian medicinal and aromatic plants were screened through docking analysis and potential candidates were shortlisted that can interfere with viral pathogenicity. The main protease (M^pro) of SARS-CoV-2 interacted closely with jatamansin (JM), 6,7-dehydroferruginol (FG) and beta-sitosterol (BS), while Papain-like Protease (PL^pro) with friedelane-3-one (F3O) and lantadene D (LD) independently. Reduced Lantadene A (LAR) exhibited preferable interaction with RNA-dependent-RNA-polymerase (RdRp) whereas Lantadene A (LA) with RdRp and spike-glycoprotein (SG-pro) both target proteins. When compared against highest binding affinity conformations of well-known inhibitors of targets, these prioritized compounds conferred superior or comparable SARS-CoV-2 protein inhibition. Additionally, promising results were noted from pharmacokinetics prediction for all shortlisted compounds. Besides, molecular dynamics simulation for 100 ns in two replicates and binding free energy analysis revealed the stability of complexes with optimum compactness. To the best of our knowledge, the current investigation is a unique initial attempt whereby EO compounds have been computationally screened, irrespective of their known medicinal properties to fight COVID-19 infection.Communicated by Ramaswamy H. Sarma.

Study of potentiality of dexamethasone and its derivatives against Covid-19

In December 2019, COVID-19 epidemic was reported in Wuhan, China, and subsequently the infection has spread all over the world and became pandemic. The death toll associated with the pandemic is increasing day by day in a high rate. Herein, an effort has been made to identify the potentiality of commercially available drugs and also their probable derivatives for creation of better opportunity to make more powerful drugs against coronavirus. This study involves the in-silico interactions of dexamethasone and its derivatives against the multiple proteins of SARS-CoV-2 with the help of various computational methods. Descriptor parameters revealed their non-toxic effect in the human body. Ultimately docking studies and molecular dynamic simulation on those target protein by dexamethasone and its derivatives showed a high binding energy. Dexamethasone showed -9.8 kcal/mol and its derivative D5 showed -12.1 kcal/mol binding energy. Those scores indicate that dexamethasone has more therapeutic effect on SARS CoV-2 than other currently used drugs. Derivatives give the clue for the synthesis of a novel drug to remove SARS CoV-2. Until then, dexamethasone will be used as a potential inhibitor of SARS CoV-2.Communicated by Ramaswamy H. Sarma.

Neurological disorders of COVID-19: insights to applications of natural products from plants and microorganisms

In addition to the typical respiratory manifestations, various disorders including involvement of the nerve system have been detected in COVID-19 ranging from 22 to 36%. Although growing records are focusing on neurological aspects of COVID-19, the pathophysiological mechanisms and related therapeutic methods remain obscure. Considering the increased concerns of SARS-CoV-2 potential for more serious neuroinvasion conditions, the present review attempts to focus on the neuroprotective effects of natural compounds as the principle source of therapeutics inhibiting multiple steps of the SARS-CoV-2 infection cycle. The great majority of the natural products with anti-SARS-CoV-2 activity mainly inhibit the attachment, entry and gene expression rather than the replication, assembly, or release. Although microbial-derived natural products comprise 38.5% of the known natural products with neuroprotective effects following viral infection, the neuroprotective potential of the majority of microorganisms is still undiscovered. Among natural products, chrysin, huperzine A, ginsenoside Rg1, pterostilbene, and terrein have shown potent in vitro neuroprotective activity and can be promising for new or repurpose drugs for neurological complications of SARS-CoV-2.

Scientific production on medicinal plants and their efficacy against Covid-19: A review and scientometric analysis based on VOSviewer

Historically, numerous plants have been used to alleviate various diseases, particularly viral diseases (bronchitis, influenza virus and dengue virus). This review evaluated their therapeutic potential against Covid-19 and mapped the 10 most studied plants during the pandemic. The standardized protocol for systematic reviews (PRISMA-P) was developed in this study. All studies involving medicinal plants and their potential against Covid-19 infection were also considered. Two specific search fields “traditional medicine and Covid-19” and “medicinal plants and Covid-19” with appearance in the title, abstract and keywords were used to search for information. Only papers (review and original) published between 2020 and October 2021 were included. Short communications, letters to the editor, books and book chapters were excluded. A total of 24,046 articles were recorded among the four databases and an increase of 69% in publications for the 2021 search date, a higher percentage compared to the previous year (31%). China was the country with the highest production with 28% (2725 papers). The analysis of variance showed that the number of studies of Nigella sativa L. (1.62 ± 0.21; p = 0.02), Glycyrrhiza glabra L. (1.50 ± 0.32; p = 0.03), Zingiber officinale Roscoe (1.51 ± 0.32; p = 0.03) were statistically significant with respect to the other species. This is probably because these species show compounds with high antiviral spectrum. Despite the pharmacological potential found in medicinal plants, more large-scale clinical trials are still needed to demonstrate the efficacy of phytocompounds against viral diseases.

An exhaustive comprehension of the role of herbal medicines in Pre- and Post-COVID manifestations

ETHNOPHARMACOLOGICAL RELEVANCE

The coronavirus disease (COVID-19) has relentlessly spread all over the world even after the advent of vaccines. It demands management, treatment, and prevention as well with utmost safety and effectiveness. It is well researched that herbal medicines or natural products have shown promising outcomes to strengthen immunity with antiviral potential against SARS-COV-2.

AIM OF THE REVIEW

Our objective is to provide a comprehensive insight into the preventive and therapeutic effects of herbal medicines and products (Ayurvedic) for pre-and post-COVID manifestations.

MATERIAL AND METHOD

The database used in the text is collected and compiled from Scopus, PubMed, Nature, Elsevier, Web of Science, bioRxiv, medRxiv, American Chemical Society, and clinicaltrials.gov up to January 2022. Articles from non-academic sources such as websites and news were also retrieved. Exploration of the studies was executed to recognize supplementary publications of research studies and systematic reviews. The keywords, such as "SARS-COV-2, coronavirus, COVID-19, herbal drugs, immunity, herbal immunomodulators, infection, herbal antiviral drugs, and WHO recommendation" were thoroughly searched. Chemical structures were drawn using the software Chemdraw Professional 15.0.0.160 (PerkinElmer Informatics, Inc.).

RESULT

A plethora of literature supports that the use of herbal regimens not only strengthen immunity but can also treat SARS-COV-2 infection with minimal side effects. This review summarizes the mechanistic insights into herbal therapy engaging interferons and antibodies to boost the response against SARS-COV-2 infection, several clinical trials, and in silico studies (computational approaches) on selected natural products including, Ashwagandha, Guduchi, Yashtimadhu, Tulsi, etc. as preventive and therapeutic measures against COVID. We have also emphasized the exploitation of herbal medicine-based pharmaceutical products along with perspectives for unseen upcoming alike diseases.

CONCLUSION

According to the current state of art and cutting-edge research on herbal medicines have showed a significant promise as modern COVID tools. Since vaccination cannot be purported as a long-term cure for viral infections, herbal/natural medicines can only be considered a viable alternative to current remedies, as conceived from our collected data to unroot recurring viral infections.

The SARS-CoV-2 main protease (Mpro): Structure, function, and emerging therapies for COVID-19

The main proteases (M^pro), also termed 3‐chymotrypsin‐like proteases (3CL^pro), are a class of highly conserved cysteine hydrolases in β‐coronaviruses. Increasing evidence has demonstrated that 3CL^pros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus‐caused infectious diseases, including COVID‐19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) main protease M^pro (also known as 3CL^pro), as well as recent advances in discovering and developing SARS‐CoV‐2 3CL^pro inhibitors. To better understand the characteristics of SARS‐CoV‐2 3CL^pro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CL^pro inhibitors (including marketed drugs, peptidomimetic, and non‐peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CL^pro inhibitors as novel anti‐coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS‐CoV‐2 3CL^pro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CL^pro inhibitors as novel anti‐coronavirus agents.

Pseudoscience and fraudulent products for COVID-19 management

As of now, the COVID-19 pandemic has become uncontrolled and is spreading widely throughout the world. Additionally, new variants of the mutated viral variants have been found in some countries that are more dangerous than the original strain. Even vaccines cannot produce complete protective immunity against the newer strains of SARS-CoV-2. Due to such a dreadful situation, lots of fear and depression have been created among the public. People are looking for the treatment of the disease at any cost and there is a race in the market to provide treatment and make money, whether it is effective or not! In such a condition, many fraud products, remedies, and myths have come into the market, which is falsely claimed to be effective for the disease and can harm the patients. Hence, FDA has banned such products and remedies. In this review, we have compiled all such fraudulent and pseudosciences identified for COVID-19. Currently, in the pandemic time, health agencies are approving the repurposed medicines based on the small-scale clinical data for emergency uses that become ineffective (most of the cases) after large randomized clinical studies. Proper vigilance strategies need to be defined by the regulatory agencies of the nation and routine awareness programs shall be arranged for educating the people and healthcare workers on routine updates.

Potential Multifunctional Bioactive Compounds from Dysosma versipellis Explored by Bioaffinity Ultrafiltration-HPLC/MS with Topo I, Topo II, COX-2 and ACE2

Background

Dysosma versipellis (D. versipellis) has been traditionally used as a folk medicine for ages. However, the specific phytochemicals responsible for their correlated anti-inflammatory, anti-proliferative and antiviral activities remain unknown.

Purpose

This study aimed to explore the specific active components in D. versipellis responsible for its potential anti-inflammatory, anti-proliferative, and antiviral effects, and further elucidate the corresponding mechanisms of action.

Methods

Bioaffinity ultrafiltration coupled to liquid chromatography–mass spectrometry (UF-LC/MS) was firstly hired to fast screen for the anti-inflammatory, anti-proliferative and antiviral compounds from rhizomes of D. versipellis, and then further validation was conducted using in vitro inhibition assays and molecular docking.

Results

A total of 12, 12, 9 and 12 phytochemicals with considerable affinities to Topo I, Topo II, COX-2 and ACE2 were fished out, respectively. The anti-proliferative assay in vitro indicated that podophyllotoxin and quercetin exhibited comparably strong inhibitory rates on A549 and HT-29 cells compared with 5-FU and etoposide. Meanwhile, kaempferol displayed prominent dose-dependent inhibition against COX-2 with IC₅₀ value at 0.36 ± 0.02 μM lower than indomethacin at 0.73 ± 0.07 μM. Furthermore, quercetin exerted stronger inhibitory effect against ACE2 with IC₅₀ value at 104.79 ± 8.26 μM comparable to quercetin 3-O-glucoside at 135.25 ± 6.54 μM.

Conclusion

We firstly showcased an experimental investigation on the correlations between bioactive phytochemicals of D. versipellis and their multiple drug targets reflecting its potential pharmacological activities, and further constructed a multi-target and multi-component network to decipher its empirical traditional applications. It could not only offer a reliable and valuable experimental basis to better comprehend the curative effects of D. versipellis but also provide more new insights and strategies for other traditional medicinal plants.

Pharmacogenetics and Precision Medicine Approaches for the Improvement of COVID-19 Therapies

Many drugs are being administered to tackle coronavirus disease 2019 (COVID-19) pandemic situations without establishing clinical effectiveness or tailoring safety. A repurposing strategy might be more effective and successful if pharmacogenetic interventions are being considered in future clinical studies/trials. Although it is very unlikely that there are almost no pharmacogenetic data for COVID-19 drugs, however, from inferring the pharmacokinetic (PK)/pharmacodynamic(PD) properties and some pharmacogenetic evidence in other diseases/clinical conditions, it is highly likely that pharmacogenetic associations are also feasible in at least some COVID-19 drugs. We strongly mandate to undertake a pharmacogenetic assessment for at least these drug–gene pairs (atazanavir–UGT1A1, ABCB1, SLCO1B1, APOA5; efavirenz–CYP2B6; nevirapine–HLA, CYP2B6, ABCB1; lopinavir–SLCO1B3, ABCC2; ribavirin–SLC28A2; tocilizumab–FCGR3A; ivermectin–ABCB1; oseltamivir–CES1, ABCB1; clopidogrel–CYP2C19, ABCB1, warfarin–CYP2C9, VKORC1; non-steroidal anti-inflammatory drugs (NSAIDs)–CYP2C9) in COVID-19 patients for advancing precision medicine. Molecular docking and computational studies are promising to achieve new therapeutics against SARS-CoV-2 infection. The current situation in the discovery of anti-SARS-CoV-2 agents at four important targets from in silico studies has been described and summarized in this review. Although natural occurring compounds from different herbs against SARS-CoV-2 infection are favorable, however, accurate experimental investigation of these compounds is warranted to provide insightful information. Moreover, clinical considerations of drug–drug interactions (DDIs) and drug–herb interactions (DHIs) of the existing repurposed drugs along with pharmacogenetic (e.g., efavirenz and CYP2B6) and herbogenetic (e.g., andrographolide and CYP2C9) interventions, collectively called multifactorial drug–gene interactions (DGIs), may further accelerate the development of precision COVID-19 therapies in the real-world clinical settings.

In silico evaluation of Vitis amurensis Rupr. polyphenol compounds for their inhibition potency against CoVID-19 main enzymes Mpro and RdRp

The rapid transmission of the pneumonia (COVID-19) emerged as an entire worldwide health concern and it was declared as pandemic by the World Health Organization (WHO) as a consequence of the increasing reported infections number. COVID-19 disease is caused by the novel SARS-CoV-2 virus, and unfortunatly no drugs are currently approved against this desease. Accordingly, it is of outmost importance to review the possible therapeutic effects of naturally-occuring compounds that showed approved antiviral activities. The molecular docking approach offers a rapid prediction of a possible inhibition of the main enzymes M^pro and RdRp that play crucial role in the SARS-CoV-2 replication and transcription. In the present work, we review the anti-viral activities of polyphenol compounds (phenolic acids, flavonoids and stilbene) derived from the traditional Chinese medicinal Vitis amurensis. Recent molecular docking studies reported the possible binding of these polyphenols on SARS-CoV-2 enzymes M^pro and RdRp active sites and showed interesting inhibitory effects. This antiviral activity was explained by the structure-activity relationships of the studied compounds. Also, pharmacokinetic analysis of the studied molecules is simulated in the present work. Among the studied polyphenol compounds, only five, namely caffeic acid, ferulic acid, quercetin, naringenin and catechin have drug-likeness characteristics. These five polyphenols derived from Vitis amurensis are promising drug candidates for the COVID-19 treatment.

Phytocompounds from Anvillea radiata as promising anti-Covid-19 drugs: in silico studies and in vivo safety assessment

As an alternative strategy in combating the COVID-19 pandemic, phytoconstituents from medicinal plants are getting attention worldwide. The current investigation focused on the efficacy of the essential phytocompounds identified in Anvillea radiata to target the main protease (M^pro) of SARS-COV-2 through molecular docking and dynamic analyses; in addition to the safety assessment of this herb in vivo. In silico, the 6LU7 structure of M^pro was prepared as a target by Discovery Studio 2020. The virtual screening of phytocompounds from Anvillea radiata was performed through iGEMDOCK program, followed by an evaluation of the potential inhibitors based on the docking scores calculated using AutoDock Vina and MGL Tools programs, as well as complexes stability assessment through MD simulation. In vivo toxicity studies of Anvillea radiata aqueous extract were also conducted in Wistar rats. Among the phytocompounds evaluated in this study, 3,5-Dicaffeoylquinic acid, Spinacetin, 9α-Epoxyparthenolide, Hispidulin, Quercetin, jaceosidin, Nepetin, and isorhamnetin were predicted to have the highest binding affinity for the Main protease (M^pro) target of SARS-CoV-2. The aqueous extract of Anvillea radiata did not induce any signs of toxicity. 3,5-Dicaffeoylquinic acid, Spinacetin, 9α-Epoxyparthenolide, jaceosidin, and isorhamnetin from Anvillea radiata were selected as potential inhibitors of SARS-Cov-2 to develop new drugs anti-COVID-19.

The emerging role of miRNAs in the pathogenesis of COVID-19: Protective effects of nutraceutical polyphenolic compounds against SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause immunosuppression and cytokine storm, leading to lung damage and death. The clinical efficacy of anti-SARS-CoV-2 drugs in preventing viral entry into host cells and suppressing viral replication remains inadequate. MicroRNAs (miRNAs) are crucial to the immune response to and pathogenesis of coronaviruses, such as SARS-CoV-2. However, the specific roles of miRNAs in the life cycle of SARS-CoV-2 remain unclear. miRNAs can participate in SARS-CoV-2 infection and pathogenesis through at least four possible mechanisms: 1. host cell miRNA expression interfering with SARS-CoV-2 cell entry, 2. SARS-CoV-2-derived RNA transcripts acting as competitive endogenous RNAs (ceRNAs) that may attenuate host cell miRNA expression, 3. host cell miRNA expression modulating SARS-CoV-2 replication, and 4. SARS-CoV-2-encoded miRNAs silencing the expression of host protein-coding genes. SARS-CoV-2-related miRNAs may be used as diagnostic or prognostic biomarkers for predicting outcomes among patients with SARS-CoV-2 infection. Furthermore, accumulating evidence suggests that dietary polyphenolic compounds may protect against SARS-CoV-2 infection by modulating host cell miRNA expression. These findings have major implications for the future diagnosis and treatment of COVID-19.

Less COVID-19 deaths in southern and insular Italy explained by forest bathing, Mediterranean environment, and antiviral plant volatile organic compounds

The coronavirus disease 2019 (COVID-19) is causing major sanitary and socioeconomic issues, yet some locations are less impacted than others. While densely populated areas are likely to favor viral transmission, we hypothesize that other environmental factors could explain lower cases in some areas. We studied COVID-19 impact and population statistics in highly forested Mediterranean Italian regions versus some northern regions where the amount of trees per capita is much lower. We also evaluated the affinity of Mediterranean plant-emitted volatile organic compounds (VOCs) isoprene, α-pinene, linalool and limonene for COVID-19 protein targets by molecular docking modeling. Results show that while mean death number increased about 4 times from 2020 to 2021, the percentage of deaths per population (0.06-0.10%) was lower in the greener Mediterranean regions such as Sardinia, Calabria and Basilica versus northern regions with low forest coverage, such as Lombardy (0.33%) and Emilia Romagna (0.29%). Data also show that the pandemic severity cannot be explained solely by population density. Modeling reveals that plant organic compounds could bind and interfere with the complex formed by the receptor binding domain of the coronavirus spike protein with the human cell receptor. Overall, our findings are likely explained by sea proximity and mild climate, Mediterranean diet and the abundance of non-deciduous Mediterranean plants which emit immunomodulatory and antiviral compounds. Potential implications include 'forest bathing' as a therapeutic practice, designing nasal sprays containing plant volatile organic compounds, and preserving and increasing forest coverage.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10311-021-01309-5.

Screening S protein - ACE2 blockers from natural products: Strategies and advances in the discovery of potential inhibitors of COVID-19

The Coronavirus disease, 2019 (COVID-19) is caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which poses a major threat to human life and health. Given its continued development, limiting the spread of COVID-19 in the population remains a challenging task. Currently, multiple therapies are being tried around the world to deal with SARS-CoV-2 infection, and a variety of studies have shown that natural products have a significant effect on COVID-19 patients. The combination of SARS-CoV-2 S protein with Angiotensin converting enzyme II(ACE2) of host cell to promote membrane fusion is an initial critical step for SARS-CoV-2 infection. Therefore, screening natural products that inhibit the binding of SARS-CoV-2 S protein and ACE2 also provides a feasible strategy for the treatment of COVID-19. Establishment of high throughput screening model is an important basis and key technology for screening S protein-ACE2 blockers. Based on this, the molecular structures of SARS-CoV-2 and ACE2 and their processes in the life cycle of SARS-CoV-2 and host cell infection were firstly reviewed in this paper, with emphasis on the methods and techniques of screening S protein-ACE2 blockers, including Virtual Screening (VS), Surface Plasmon Resonance (SPR), Biochromatography, Biotin-avidin with Enzyme-linked Immunosorbent assay and Gene Chip Technology. Furthermore, the technical principle, advantages and disadvantages and application scope were further elaborated. Combined with the application of the above screening technologies in S protein-ACE2 blockers, a variety of natural products, such as flavonoids, terpenoids, phenols, alkaloids, were summarized, which could be used as S protein-ACE2 blockers, in order to provide ideas for the efficient discovery of S protein-ACE2 blockers from natural sources and contribute to the development of broad-spectrum anti coronavirus drugs.

Repurposing of Phytomedicine-Derived Bioactive Compounds with Promising Anti-SARS-CoV-2 Potential: Molecular Docking, MD Simulation and Drug-Likeness/ ADMET Studies

In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein–ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules.

An Evaluation of the Potential of Essential Oils against SARS-CoV-2 from In Silico Studies through the Systematic Review Using a Chemometric Approach

Essential oils (EOs) and their compounds have attracted particular attention for their reported beneficial properties, especially their antiviral potential. However, data regarding their anti-SARS-CoV-2 potential are scarce in the literature. Thus, this study aimed to identify the most promising EO compounds against SARS-CoV-2 based on their physicochemical, pharmacokinetic, and toxicity properties. A systematic literature search retrieved 1669 articles; 40 met the eligibility criteria, and 35 were eligible for analysis. These studies resulted in 465 EO compounds evaluated against 11 human and/or SARS-CoV-2 target proteins. Ninety-four EO compounds and seven reference drugs were clustered by the highest predicted binding affinity. Furthermore, 41 EO compounds showed suitable drug-likeness and bioactivity score indices (≥0.67). Among these EO compounds, 15 were considered the most promising against SARS-CoV-2 with the ADME/T index ranging from 0.86 to 0.81. Some plant species were identified as EO potential sources with anti-SARS-CoV-2 activity, such as Melissa officinalis Arcang, Zataria multiflora Boiss, Eugenia brasiliensis Cambess, Zingiber zerumbet Triboun & K.Larsen, Cedrus libani A.Rich, and Vetiveria zizanoides Nash. Our work can help fill the gap in the literature and guide further in vitro and in vivo studies, intending to optimize the finding of effective EOs against COVID-19.

Extracellular pH, osmolarity, temperature and humidity could discourage SARS-CoV-2 cell docking and propagation via intercellular signaling pathways

The COVID-19 pandemic and its virus variants continue to pose a serious and long-lasting threat worldwide. To combat the pandemic, the world's largest COVID-19 vaccination campaign is currently ongoing. As of July 19th 2021, 26.2% of the world population has received at least one dose of a COVID-19 vaccine (1.04 billion), and one billion has been fully vaccinated, with very high vaccination rates in countries like Israel, Malta, and the UEA. Conversely, only 1% of people in low-income countries have received at least one dose with examples of vaccination frequency as low as 0.07% in the Democratic Republic of Congo. It is thus of paramount importance that more research on alternate methods to counter cell infection and propagation is undertaken that could be implemented in low-income countries. Moreover, an adjunctive therapeutic intervention would help to avoid disease exacerbation in high-rate vaccinated countries too. Based on experimental biochemical evidence on viral cell fusion and propagation, herein we identify (i) extracellular pH (epH), (ii) temperature, and (iii) humidity and osmolarity as critical factors. These factors are here in discussed along with their implications on mucus thick layer, proteases, abundance of sialic acid, vascular permeability and exudate/edema. Heated, humidified air containing sodium bicarbonate has long been used in the treatment of certain diseases, and here we argue that warm inhalation of sodium bicarbonate might successfully target these endpoints. Although we highlight the molecular/cellular basis and the signalling pathways to support this intervention, we underscore the need for clinical investigations to encourage further research and clinical trials. In addition, we think that such an approach is also important in light of the high mutation rate of this virus originating from a rapid increase.

Currently Applied Extraction Processes for Secondary Metabolites from Lippia turbinata and Turnera diffusa and Future Perspectives

The poleo (Lippia turbinata Griseb.) and damiana (Turnera diffusa Wild) are two of the most valued species in the Mexican semidesert due to their medicinal uses. The conventional essential oil extraction process is hydrodistillation, and for the extraction of antioxidants, the use of organic solvents. However, these techniques are time-consuming and degrade thermolabile molecules, and the efficiency of the process is dependent on the affinity of the solvent for bioactive compounds. Likewise, they generate solvent residues such as methanol, hexane, petroleum ether, toluene, chloroform, etc. Therefore, in recent years, ecofriendly alternatives such as ohmic heating, microwaves, ultrasound, and supercritical fluids have been studied. These methodologies allow reducing the environmental impact and processing times, in addition to increasing yields at a lower cost. Currently, there is no up-to-date information that provides a description of the ecofriendly trends for the recovery process of essential oils and antioxidants from Lippia turbinata and Turnera diffusa. This review includes relevant information on the most recent advancements in these processes, including conditions and methodological foundation.

Consumption of Phenolic-Rich Food and Dietary Supplements as a Key Tool in SARS-CoV-19 Infection

The first cases of COVID-19, which is caused by the SARS-CoV-2, were reported in December 2019. The vertiginous worldwide expansion of SARS-CoV-2 caused the collapse of health systems in several countries due to the high severity of the COVID-19. In addition to the vaccines, the search for active compounds capable of preventing and/or fighting the infection has been the main direction of research. Since the beginning of this pandemic, some evidence has highlighted the importance of a phenolic-rich diet as a strategy to reduce the progression of this disease, including the severity of the symptoms. Some of these compounds (e.g., curcumin, gallic acid or quercetin) already showed capacity to limit the infection of viruses by inhibiting entry into the cell through its binding to protein Spike, regulating the expression of angiotensin-converting enzyme 2, disrupting the replication in cells by inhibition of viral proteases, and/or suppressing and modulating the host's immune response. Therefore, this review intends to discuss the most recent findings on the potential of phenolics to prevent SARS-CoV-2.

In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19

COVID-19 is one of the members of the coronavirus family that can easily assail humans. As of now, 10 million people are infected and above two million people have died from COVID-19 globally. Over the past year, several researchers have made essential advances in discovering potential drugs. Up to now, no efficient drugs are available on the market. The present study aims to identify the potent phytocompounds from different medicinal plants (Zingiber officinale, Cuminum cyminum, Piper nigrum, Curcuma longa, and Allium sativum). In total, 227 phytocompounds were identified and screened against the proteins S-ACE2 and M ^pro through structure-based virtual screening approaches. Based on the binding affinity score, 30 active phytocompounds were selected. Amongst, the binding affinity for beta-sitosterol and beta-elemene against S-ACE2 showed -12.0 and -10.9 kcal/mol, respectively. Meanwhile, the binding affinity for beta-sitosterol and beta-chlorogenin against M ^pro was found to be -9.7 and -8.4 kcal/mol, respectively. Further, the selected compounds proceeded with molecular dynamics simulation, prime MM-GBSA analysis, and ADME/T property checks to understand the stability, interaction, conformational changes, binding free energy, and pharmaceutical relevant parameters. Moreover, the hotspot residues such as Lys31 and Lys353 for S-ACE2 and catalytic dyad His41 and Cys145 for M ^pro were actively involved in the inhibition of viral entry. From the in silico analyses, we anticipate that this work could be valuable to ongoing novel drug discovery with potential treatment for COVID-19.

Indian Ethnomedicinal Phytochemicals as Promising Inhibitors of RNA-Binding Domain of SARS-CoV-2 Nucleocapsid Phosphoprotein: An In Silico Study

SARS-CoV-2, an etiological agent of COVID-19, has been the reason for the unexpected global pandemic, causing severe mortality and imposing devastative effects on public health. Despite extensive research work put forward by scientist around globe, so far, no suitable drug or vaccine (safe, affordable, and efficacious) has been identified to treat SARS-CoV-2. As an alternative way of improvising the COVID-19 treatment strategy, that is, strengthening of host immune system, a great deal of attention has been given to phytocompounds from medicinal herbs worldwide. In a similar fashion, the present study deliberately focuses on the phytochemicals of three Indian herbal medicinal plants viz., Mentha arvensis, Coriandrum sativum, and Ocimum sanctum for their efficacy to target well-recognized viral receptor protein through molecular docking and dynamic analyses. Nucleocapsid phosphoprotein (N) of SARS-CoV-2, being a pivotal player in replication, transcription, and viral genome assembly, has been recognized as one of the most attractive viral receptor protein targets for controlling the viral multiplication in the host. Out of 127 phytochemicals screened, nine (linarin, eudesmol, cadinene, geranyl acetate, alpha-thujene, germacrene A, kaempferol-3-O-glucuronide, kaempferide, and baicalin) were found to be phenomenal in terms of exhibiting high binding affinity toward the catalytic pocket of target N-protein. Further, the ADMET prediction analysis unveiled the non-tumorigenic, noncarcinogenic, nontoxic, non-mutagenic, and nonreproductive nature of the identified bioactive molecules. Furthermore, the data of molecular dynamic simulation validated the conformational and dynamic stability of the docked complexes. Concomitantly, the data of the present study validated the anti-COVID efficacy of the bioactives from selected medicinal plants of Indian origin.

An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19

The recent outbreak of the deadly coronavirus disease 19 (COVID-19) pandemic poses serious health concerns around the world. The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic molecules. Computer-aided drug design has helped to expedite the drug discovery and development process by minimizing the cost and time. In this review article, we highlight two important categories of computer-aided drug design (CADD), viz., the ligand-based as well as structured-based drug discovery. Various molecular modeling techniques involved in structure-based drug design are molecular docking and molecular dynamic simulation, whereas ligand-based drug design includes pharmacophore modeling, quantitative structure-activity relationship (QSARs), and artificial intelligence (AI). We have briefly discussed the significance of computer-aided drug design in the context of COVID-19 and how the researchers continue to rely on these computational techniques in the rapid identification of promising drug candidate molecules against various drug targets implicated in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The structural elucidation of pharmacological drug targets and the discovery of preclinical drug candidate molecules have accelerated both structure-based as well as ligand-based drug design. This review article will help the clinicians and researchers to exploit the immense potential of computer-aided drug design in designing and identification of drug molecules and thereby helping in the management of fatal disease.

Computational guided identification of potential leads from Acacia pennata (L.) Willd. as inhibitors for cellular entry and viral replication of SARS-CoV-2

BACKGROUND

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in 2019 and is still an on-going pandemic. SARS-CoV-2 uses a human protease called furin to aid in cellular entry and its main protease (M^pro) to achieve viral replication. By targeting these proteins, scientists are trying to identify phytoconstituents of medicinal plants as potential therapeutics for COVID-19. Therefore, our study was aimed to identify promising leads as potential inhibitors of SARS-CoV-2 M^pro and furin using the phytocompounds reported to be isolated from Acacia pennata (L.) Willd.

RESULTS

A total of 29 phytocompounds were reported to be isolated from A. pennata. Molecular docking simulation studies revealed 9 phytocompounds as having the top 5 binding affinities towards SARS-CoV-2 M^pro and furin. Among these phytocompounds, quercetin-3-O-α-L-rhamnopyranoside (C_18), kaempferol 3-O-α-L-rhamnopyranosyl-(1 → 4)-β-D-glucopyranoside (C_4), and isovitexin (C_5) have the highest drug score. However, C_18 and C_4 were not selected for further studies due to bioavailability issues and low synthetic accessibility. Based on binding affinity, molecular properties, drug-likeness, toxicity parameters, ligand interactions, bioavailability, synthetic accessibility, structure-activity relationship, and comparative analysis of our experimental findings with other studies, C_5 was identified as the most promising phytocompound. C_5 interacted with the active site residues of SARS-CoV-2 M^pro (GLU166, ARG188, GLN189) and furin (ASN295, ARG298, HIS364, THR365). Many phytocompounds that interacted with these amino acid residues were reported by other studies as potential inhibitors of SARS-CoV-2 M^pro and furin. The oxygen atom at position 18, the -OH group at position 19, and the 6-C-glucoside were identified as the pharmacophores in isovitexin (also known as apigenin-6-C-glucoside). Other in-silico studies reported apigenin as a potential inhibitor of SARS-CoV-2 M^pro and apigenin-o-7-glucuronide was reported to show stable conformation during MD simulations with SARS-CoV-2 M^pro.

CONCLUSION

The present study found isovitexin as the most promising phytocompound to potentially inhibit the cellular entry and viral replication of SARS-CoV-2. We also conclude that compounds having oxygen atom at position 18 (C-ring), -OH group at position 19 (A-ring), and 6-C-glucoside attached to the A-ring at position 3 on a C₆-C₃-C₆ flavonoid scaffold could offer the best alternative to develop new leads against SARS-CoV-2.