Potential role of medicinal plants and their constituents in the mitigation of SARS-CoV-2: identifying related therapeutic targets using network pharmacology and molecular docking analyses

In-silico and in-vitro studies to identify potential inhibitors of SARS-CoV-2 spike protein from Omani medicinal plants

In the quest for novel therapeutic agents against SARS-CoV-2, the proposed study explores the potential of traditional Omani medicinal plants, focusing on the efficacy of natural ligands against the virus's Spike protein. Among 437 identified medicinal plants across Oman, 47 species that are documented for their traditional use in treating respiratory infections, with 30 species' ligands available were chosen for analysis. Molecular docking was performed using Autodock Vina on these ligands, yielding 406 unique ligands post-duplication removal. The binding affinities of target-ligand complexes were precisely determined, ranking them by interaction strength. This process identified Corilagin, a phytochemical from the Acalypha indica plant (locally known as Aeyan Al Aqrada), as the most promising inhibitor. Subsequent analyses using GROMACS for molecular dynamics simulation confirmed its binding stability and interaction dynamics of the Corilagin-protein complex. The in-vitro studies further validated Corilagin's inhibitory effect on SARS-CoV-2, demonstrating a remarkable 92 % inhibition at 0.5 mM concentration. Dilution studies to ascertain the IC50 value revealed Corilagin's high potency at a micromolar level (IC50 = 2.15 ± 0.13 μM), underscoring its potential as a drug candidate for SARS-CoV-2 treatment. These findings highlight the significance of ethnomedicine and in-silico methodologies in drug discovery, offering promising directions for future antiviral research.

Phytochemistry, pharmacological applications, and therapeutic effects of green synthesized nanomaterials using Cichorium species-a comprehensive review

Cichorium is a genus of potential medicinal herbs that finds widespread cultivation in regions spanning Asia and Europe. Belonging to the Asteraceae family, these plants are typically biennial or perennial in nature. Among the various explored varieties of chicory plants, the most commonly studied ones include Cichorium intybus, Cichorium endivia, and Cichorium pumilum. In Ayurveda, chicory has long been used as a remedy for many health problems. This versatile plant is renowned for its efficacy in managing conditions such as gallstones, gastroenteritis, sinus ailments, and the treatment of skin abrasions and wounds. Numerous bioactives, including polysaccharides, caffeic acid, flavonoids, coumarins, steroids, alkaloids, organic acids, triterpenoids, sesquiterpenoids, and essential oils, are present, according to a thorough phytochemical examination. The phytochemicals isolated from chicory have displayed significant therapeutic activities, including antidiabetic effects, hepatoprotective benefits, anti-obesity properties, and anti-cancer potential, as extensively documented by numerous researchers. The incorporation of these bioactive compounds into one's diet as part of a healthy lifestyle has demonstrated considerable advantages for human well-being. Green synthesis is a recent technology in which plant extracts or phytochemicals are used for synthesizing nanoparticles since plant extracts are generally less toxic and contain capping and reducing agents. This review summarizes current developments in green synthesis employing phytoconstituents from Cichorium species and extracts from various plant parts and their application to scientific problems. In order to preserve lifestyles and cure human diseases, the investigation emphasizes the therapeutic effects of the chemical components and nanoparticles obtained from the extract of Cichorium species.

Olive Leaf Extract Downregulates the Protein Expression of Key SARS-CoV-2 Entry Enzyme ACE-2, TMPRSS2, and Furin

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses ongoing global health challenges due to its propensity for mutations, which can undermine vaccine efficacy. With no definitive treatment available, urgent research into affordable and biocompatible therapeutic agents is extremely urgent. Angiotensin converting enzyme-2 (ACE-2), transmembrane protease serine subtype 2 (TMPRSS2), and Furin enzymes, which allow the virus to enter cells, are particularly important as potential drug targets among scientists. Olive leaf extract (OLE) has garnered attention for its potential against Coronavirus Disease-9 (COVID-19), yet its mechanism remains understudied. In this study, we aimed to investigate the effects of OLE on ACE-2, TMPRSS2, and Furin protein expressions by cell culture study. Total phenol, flavonoid content, and antioxidant capacity were measured by photometric methods, and oleuropein levels were measured by liquid LC-HR-MS. Cell viability was analyzed by ATP levels using a luminometric method. ACE-2, TMPRSS2, and Furin expressions were analyzed by the Western Blotting method. ACE-2, TMPRSS2, and Furin protein expression levels were significantly lower in a dose dependent manner and the highest inhibition was seen at 100 μg/ml OLE. The results showed that OLE may be a promising treatment candidate for COVID-19 disease. However, further studies need to be conducted in cells co-infected with the virus.

In vitro biological evaluation and in silico insights into the antiviral activity of standardized olive leaves extract against SARS-CoV-2

There is still a great global need for efficient treatments for the management of SARS-CoV-2 illness notwithstanding the availability and efficacy of COVID-19 vaccinations. Olive leaf is an herbal remedy with a potential antiviral activity that could improve the recovery of COVID-19 patients. In this work, the olive leaves major metabolites were screened in silico for their activity against SARS-CoV-2 by molecular docking on several viral targets such as methyl transferase, helicase, Plpro, Mpro, and RdRp. The results of in silico docking study showed that olive leaves phytoconstituents exhibited strong potential antiviral activity against SARS-CoV-2 selected targets. Verbacoside demonstrated a strong inhibition against methyl transferase, helicase, Plpro, Mpro, and RdRp (docking scores = -17.2, -20, -18.2, -19.8, and -21.7 kcal/mol.) respectively. Oleuropein inhibited 5rmm, Mpro, and RdRp (docking scores = -15, -16.6 and -18.6 kcal/mol., respectively) respectively. Apigenin-7-O-glucoside exhibited activity against methyl transferase and RdRp (docking score = -16.1 and -19.4 kcal/mol., respectively) while Luteolin-7-O-glucoside inhibited Plpro and RdRp (docking score = -15.2 and -20 kcal/mol., respectively). The in vitro antiviral assay was carried out on standardized olive leaf extract (SOLE) containing 20% oleuropein and IC50 was calculated. The results revealed that 20% SOLE demonstrated a moderate antiviral activity against SARS-CoV-2 with IC50 of 118.3 μg /mL. Accordingly, olive leaf could be a potential herbal therapy against SARS-CoV-2 but more in vivo and clinical investigations are recommended.

Eco-Technological Evaluation of Natural Phytochemicals Potential Drug Molecules Against Main Protease: A Machine Learning Algorithm

Introduction: The global viral pandemic has rapidly spread, leading to many individuals experiencing the infection. Coronaviruses (CoVs) are among many viral families that infect different types of mammals. They can spread to humans and cause gastrointestinal, neurological, and respiratory problems. The present investigation has discovered flavonoid compounds as promising molecular agents with potential antiviral activity against virus proteins, specifically main protease (Mpro). Methodology: A comprehensive in silico screening of natural compounds derived from medicinal plants was performed in the present study. It included parameter assessments such as drug-likeness, pharmacokinetics, molecular docking, toxicity evaluations, bioavailability assessments, and molecular target exploration. In this systematic approach, the primary objective was to identify potential lead compounds. These phytochemicals were investigated as drug candidates to provide a detailed understanding of their molecular properties. Results: The Mpro binding energy values were -10.637, -12.752, -7.813, -15.732, -6.449, -5.578, -8.037, and -8.52 kcal/mol for isoquercetin, narirutin, myricetin, hesperidin, silibinin, baicalein, taxifolin, and petunidin. Molecular simulations were conducted on two flavonoid compounds - hesperidin and narirutin - stable over 100 nanoseconds in the Coronavirus protein. Conclusions: The computational study we conducted is promising, but to validate the action of these compounds, further experimental studies are needed, with a critical component of the research being the conduct of in vitro and in vivo experiments.

Unveiling the Antiviral Properties of Panduratin A through SARS-CoV-2 Infection Modeling in Cardiomyocytes

Establishing a drug-screening platform is critical for the discovery of potential antiviral agents against SARS-CoV-2. In this study, we developed a platform based on human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) to investigate SARS-CoV-2 infectivity, with the aim of evaluating potential antiviral agents for anti-SARS-CoV-2 activity and cardiotoxicity. Cultured myocytes of iPSC-CMs and immortalized human cardiomyocyte cell line (AC-16) were primarily characterized for the expression of cardiac markers and host receptors of SARS-CoV-2. An infectivity model for the wild-type SARS-CoV-2 strain was then established. Infection modeling involved inoculating cells with SARS-CoV-2 at varying multiplicities of infection (MOIs) and then quantifying infection using immunofluorescence and plaque assays. Only iPSC-CMs, not AC16 cells, expressed angiotensin-converting enzyme 2 (ACE-2), and quantitative assays confirmed the dose-dependent infection of iPSC-CMs by SARS-CoV-2, unlike the uninfectable AC16 cells lacking the expression of ACE2. Cytotoxicity was evaluated using MTT assays across a concentration range. An assessment of the plant-derived compound panduratin A (panA) showed cytotoxicity at higher doses (50% cytotoxic concentration (CC50) 10.09 μM) but promising antiviral activity against SARS-CoV-2 (50% inhibition concentration (IC50) 0.8-1.6 μM), suppressing infection at concentrations 10 times lower than its CC50. Plaque assays also showed decreased viral production following panA treatment. Overall, by modeling cardiac-specific infectivity, this iPSC-cardiomyocyte platform enables the reliable quantitative screening of compound cytotoxicity alongside antiviral efficacy. By combining disease pathogenesis and pharmacology, this system can facilitate the evaluation of potential novel therapeutics, such as panA, for drug discovery applications.

Preliminary study on molecular mechanism of COVID-19 intervention by Polygonum cuspidatum through computer bioinformatics

To explore the mechanism of action of Polygonum cuspidatum in intervening in coronavirus disease 2019 using a network pharmacology approach and to preliminarily elucidate its mechanism. The active ingredients and action targets of P cuspidatum were classified and summarized using computer virtual technology and molecular informatics methods. The active ingredients and relevant target information of P cuspidatum were identified using the TCM Systematic Pharmacology Database and Analysis Platform, the TCM Integrated Pharmacology Research Platform v2.0, and the SwissTarget database. The GENECARDS database was used to search for COVID-19 targets. The STRING database was analyzed and combined with Cytoscape 3.7.1 software to construct a protein interaction network map to screen the core targets. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was then performed. The core compound, polydatin, was selected and the core targets were analyzed by computer virtual docking using software such as discovery studio autodock tool. In vitro cell models were constructed to experimentally validate the activity of the core compound, polydatin. By computer screening, we identified 9 active ingredients and their corresponding 286 targets from P cuspidatum. A search of the GENECARDS database for COVID-19 yielded 303 core targets. By mapping the active ingredient targets to the disease targets, 27 overlapping targets could be extracted as potential targets for the treatment of COVID-19 with P cuspidatum. In addition, the enrichment analysis of Kyoto Encyclopedia of Genes and Genomes pathway on core targets showed that the coronavirus disease, MAPK signaling pathway, NF kappa B signaling pathway, and other signaling pathways were highly enriched. Combined with the degree-high target analysis in the protein interaction network, it was found to be mainly concentrated in the NF-kappaB (NF-κB) signaling pathway, indicating that the NF-κB signaling pathway may be an important pathway for P cuspidatum intervention. In vitro assays showed no effect of 0.1 to 10 μM polydatin on cell viability, but an inhibitory effect on the transcriptional activity of NF-κB-RE. Molecular docking showed stable covalent bonding of polydatin molecules with Il-1β protein at residue leu-26, TNF protein ser-60, residue gly-121, and residue ile-258 of ICAM-1 protein, indicating a stable docking result. The treatment of COVID-19 with P cuspidatum is characterized by multi-component, multi-target, and multi-pathway, which can exert a complex network of regulatory effects through the interaction between different targets, providing a new idea and basis for further exploration of the mechanism of action of P cuspidatum in the treatment of COVID-19.

Pharmacological Activities of Rhododendron afghanicum; an Endemic Species of Khyber Pakhtunkhwa, Pakistan

Majority of different kinds of metabolites having therapeutic characteristics are thought to be stored in medicinal plants. So, the present study was aimed to explore the crude extract of leaves and stem of R. afghanicum for phytochemical screening and various pharmacological activities. Toxicological studies at 100 mg/kg showed 60 % mortality where its safe dose level was 90 mg/kg. Phytochemical screening revealed the presence of alkaloids, glycosides, flavonoids and tannins in both extracts. Bacterial strains were susceptible to (RLEt) and (RLM) crude extracts except Staphylococcus aureus. RSM showed maximum anti-inflammatory activity (20.16 %) followed by RSEt (20.14 %) where lowest activity was displayed by RLEt (18.46 %). Phytotoxic activity showed a substantial dose-dependent phyto-inhibition of Lemna minor. An outstanding cytotoxic potential was displayed with LD50 values of 9.46 and 13.03 μg/ml in both stem extracts. RLEt demonstrated a dose-dependent pain relief at 30, 60 and 90 mg/kg which was 31 %, 40 % and 52 % respectively. A considerable spasmolytic action was observed by the shrinkage of jejunum muscle in albino mice. RLEt at 1000 ppm showed (17 mm) and RLM at 1000 ppm showed (16 mm) zone of inhibition against Aspergillus niger. These findings support and corroborate the traditional applications of R. afghanicum for treating digestive, analgesic and inflammatory ailments.

Bioavailability of bioactive compounds in Hibiscus sabdariffa beverage as a potential anti-inflammatory

The absorption and metabolism of bioactive compounds (BCs) in a Hibiscus sabdariffa drink (HbD) were evaluated by the in vivo bioavailability of organic acids (OA) and phenolic compounds (PC's). An acute single-blind clinical study in humans was conducted. Twelve volunteers consumed a HbD and a control drink (CD). Urine and plasma samples were taken after consuming both beverages. OA and PC's of the beverages (HbD and CD) and the biological samples (urine and plasma) were characterized by HPLC-DAD-MS. Thirthy-eight compounds in HbD and four CD were detected and quantified, equivalent to 937.37 mg and 1.22 mg per 60 mL, respectively. Hibiscus acid was the most abundant OA in both drinks. Additionally, hydroxycinnamic acids, flavonoids, anthocyanins, and anthocyanidins were also detected in HbD, although their amount represented 10% of the total BCs. 25 different metabolites were identified, 15 in urine and 23 in plasma. The microbiota extensively biotransformed PCs and their amount was lower than organic acids, particularly hibiscus acid and hydroxycitric acid. The colonic metabolites derived from PCs and organic acids would be behind the anti-inflammatory bioactivity described for Hibiscus sabdariffa L. (Malvaceae family). However, further studies are necessary to evaluate the metabolites responsible for their anti-inflammatory activity.

Forecasting of potential anti-inflammatory targets of some immunomodulatory plants and their constituents using in vitro, molecular docking and network pharmacology-based analysis

Most synthetic immunomodulatory medications are extremely expensive, have many disadvantages and suffer from a lot of side effects. So that, introducing immunomodulatory reagents from natural sources will have great impact on drug discovery. Therefore, this study aimed to comprehend the mechanism of the immunomodulatory activity of some natural plants via network pharmacology together with molecular docking and in vitro testing. Apigenin, luteolin, diallyl trisulfide, silibinin and allicin had the highest percentage of C-T interactions while, AKT1, CASP3, PTGS2, NOS3, TP53 and MMP9 were found to be the most enriched genes. Moreover, the most enriched pathways were pathways in cancer, fluid shear stress and atherosclerosis, relaxin signaling pathway, IL-17 signaling pathway and FoxO signaling pathway. Additionally, Curcuma longa, Allium sativum, Oleu europea, Salvia officinalis, Glycyrrhiza glabra and Silybum marianum had the highest number of P-C-T-P interactions. Furthermore, molecular docking analysis of the top hit compounds against the most enriched genes revealed that silibinin had the most stabilized interactions with AKT1, CASP3 and TP53, whereas luteolin and apigenin exhibited the most stabilized interactions with AKT1, PTGS2 and TP53. In vitro anti-inflammatory and cytotoxicity testing of the highest scoring plants exhibited equivalent outcomes to those of piroxicam.

In-silico studies on wild orange (Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets

One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 aftermath persists to remain fuzzy. The survivors of severe COVID-19infection having defeated the virus are just the starting of an uncharted recovery path. Currently, there is no drug available that is safe to consume to combat this pandemic. However, researchers still struggling to find specific therapeutic solutions. The present study employed an in silico approach to assessing the inhibitory potential of the phytochemicals obtained from GC-MS analysis of Citrus macroptera against inflammatory proteins like COX-2, NMDAR and VCAM-1 which remains in a hyperactive state even after a patient is fully cured of this deadly mRNA virus. An extensive molecular docking investigation of the phyto-compounds at the active binding pockets of the inflammatory proteins revealed the promising inhibitory potential of the phytochemicals. Reasonable physicochemical attributes of the compounds following Lipinski's rule of five, VEBER and PAINS analysis further established them as potential therapeutic candidates against aforesaid inflammatory proteins. MM-GBSA binding free energy estimation revealed that Limonene was the most promising candidate displaying the highest binding efficacy with the concerned VCAM-1 protein included in the present analysis. An interesting finding is the phytochemicals exhibited better binding energy scores with the concerned COX-2, VCAM-1 and NMDA receptor proteins than the conventional drugs that are specifically targeted against them. Our in silico results suggest that all the natural phyto-compounds derived from C. macroptera could be employed in Post covid inflammation complexities after appropriate pre-clinical and clinical trials for further scientific validation.Communicated by Ramaswamy H. Sarma.

In silico screening of phenylethanoid glycosides, a class of pharmacologically active compounds as natural inhibitors of SARS-CoV-2 proteases

Since the advent of Covid-19, several natural products have been investigated regarding their in silico interactions with SARS-CoV-2 proteases - 3CL^pro and PL^pro, two of the most important pharmacological targets for antiviral development. Phenylethanoid glycosides (PG) are a class of natural products present in important medicinal plants and a drug containing this group of active ingredients has been successfully used in the treatment of Covid-19 in China. Thus, a dataset with 567 derivatives of this class was built from reviews published between 1994 and 2020, and their interaction against both SARS-CoV-2 proteases was investigated. The virtual screening was performed by filtering the PGs through the evaluation of scores based on the AutoDock Vina, GOLD/ChemPLP, and GOLD/GoldScore evaluation functions. The bRO5 pharmacokinetic parameters of the PGs ranked in the previous step were analyzed and their interaction with key amino acid residues of the 3CL^pro and PL^pro enzymes was evaluated. Ninety-eight compounds were identified by computational approaches against PL^pro and 80 PGs against 3CL^pro. Of these, four interacted with key catalytic residues of PL^pro, which is an indicative of inhibitory activity, and three compounds interacted with catalytic key residues of 3CL^pro. Of these, five PGs occur in plants of the Traditional Chinese Medicine (TCM), while two are components of plants/formulations currently used in the Covid-19 protocols in China. The data presented here show the potential of PGs as selective inhibitors of SARS-CoV-2 3CL^pro and PL^pro.

Benchmarked molecular docking integrated molecular dynamics stability analysis for prediction of SARS-CoV-2 papain-like protease inhibition by olive secoiridoids

Objectives

We performed a virtual screening of olive secoiridoids of the OliveNet^TM library to predict SARS-CoV-2 PLpro inhibition. Benchmarked molecular docking protocol that evaluated the performance of two docking programs was applied to execute virtual screening. Molecular dynamics stability analysis of the top-ranked olive secoiridoid docked to PLpro was also carried out.

Methods

Benchmarking virtual screening used two freely available docking programs, AutoDock Vina 1.1.2. and AutoDock 4.2.1. for molecular docking of olive secoiridoids to a single PLpro structure. Screening also included benchmark structures of known active and decoy molecules from the DEKOIS 2.0 library. Based on the predicted binding energies, the docking programs ranked the screened molecules. We applied the usual performance evaluation metrices to evaluate the docking programs using the predicted ranks. Molecular dynamics of the top-ranked olive secoiridoid bound to PLpro and computation of MM-GBSA energy using three iterations during the last 50 ps of the analysis of the dynamics in Desmond supported the stability prediction.

Results and discussions

Predictiveness curves suggested that AutoDock Vina has a better predictive ability than AutoDock, although there was a moderate correlation between the active molecules rankings (Kendall's correlation of rank (τ) = 0.581). Interestingly, two same molecules, Demethyloleuropein aglycone, and Oleuroside enriched the top 1 % ranked olive secoiridoids predicted by both programs. Demethyloleuropein aglycone bound to PLpro obtained by docking in AutoDock Vina when analyzed for stability by molecular dynamics simulation for 50 ns displayed an RMSD, RMSF<2 Å, and MM-GBSA energy of -94.54 ± 6.05 kcal/mol indicating good stability. Molecular dynamics also revealed the interactions of Demethyloleuropein aglycone with binding sites 2 and 3 of PLpro, suggesting a potent inhibition. In addition, for 98 % of the simulation time, two phenolic hydroxy groups of Demethyloleuropein aglycone maintained two hydrogen bonds with Asp302 of PLpro, specifying the significance of the groups in receptor binding.

Conclusion

AutoDock Vina retrieved the active molecules accurately and predicted Demethyloleuropein aglycone as the best inhibitor of PLpro. The Arabian diet consisting of olive products rich in secoiridoids benefits from the PLpro inhibition property and reduces the risk of viral infection.

Small molecules in the treatment of COVID-19

The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and Mpro, interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed.

Efficacy of olive leaves extract on the outcomes of hospitalized covid-19 patients: A randomized, triple-blinded clinical trial

Introduction

Since the emergence of the novel coronavirus, herbal medicine has been considered a treatment for COVID-19 patients. This study was done to determine the efficacy of olive leaf extract on the outcomes of COVID-19 patients.

Materials and Methods

This randomized, triple-blinded clinical trial was conducted on hospitalized COVID-19 patients. Using block randomization, eligible patients were allocated to the following groups: intervention A received olive leaf extract (250 mg every 12 hours for five days), intervention B received olive leaf extract (500 mg every 12 hours for five days), and the control group received placebo (every 12 hours for five days). The outcomes (vital signs, laboratory tests, and length of hospitalization) were compared by group.

Results

Of the 150 patients randomized into groups, 141 completed the follow-up and were analyzed. On the fifth day of hospitalization, body temperature (MD=0.34, P<0.001), pulse rate (MD=5.42, P=0.016), respiratory rate (MD=1.66, P=0.001), ESR (MD=13.55, P<0.001), and CRP (MD=15.68, P<0.001) of intervention A were significantly lower than the control group, while oxygen saturation (MD= -1.81, P=0.001) of intervention A was significantly higher than the control group. Furthermore, body temperature (MD=0.30, P=0.001), pulse rate (MD=5.29, P=0.022), respiratory rate (MD=1.41, P=0.006), ESR (MD=14.79, P<0.001), and CRP (MD=16.28, P<0.001) of intervention B were significantly lower than the control group, while oxygen saturation (MD= -2.38, P<0.001) of intervention B was significantly higher than the control group.

Conclusion

Olive leaf extract can improve the clinical status of the patients and decrease the length of hospitalization.

In Vitro Induction of Apoptosis in Isolated Acute Myeloid Leukemia Cells: The Role of Anastatica hierochuntica Methanolic Extract

Anastatica hierochuntica L. (Cruciferae) has been known in Egyptian folk medicine as a remedy for gastrointestinal disorders, diabetes and heart diseases. Despite the wide usage, A. hierochuntica research provides insufficient data to support its traditional practice. The cytotoxicity of A. hierochuntica methanolic extract was investigated on acute myeloid leukemia blasts (AML) and normal human peripheral leucocytes (NHPL). The phytochemical identification of bioactive compounds using ¹H-NMR and LC-ESI-MS was also performed. A. hierochuntica extract caused non-significant cytotoxicity on NHPL, while the cytotoxicity on AML was significant (IC₅₀: 0.38 ± 0.02 μg/mL). The negative expression of p53, upregulation of Caspase-3 and increase in the BAX/BCL-2 ratio were reported at the protein and mRNA levels. The results suggest that A. hierochuntica extract induced AML cell death via the p53-independent mitochondrial intrinsic pathway and further attention should be paid to this plant as a promising natural anticancer agent.

Metabolic profiling of Lantana camara L. using UPLC-MS/MS and revealing its inflammation-related targets using network pharmacology-based and molecular docking analyses

Lantana camara L. is widely used in folk medicine for alleviation of inflammatory disorders, but studies that proved this folk use and that revealed the molecular mechanism of action in inflammation mitigation are not enough. Therefore, this study aimed to identify L. camara phytoconstituents using UPLC-MS/MS and explain their multi-level mechanism of action in inflammation alleviation using network pharmacology analysis together with molecular docking and in vitro testing. Fifty-seven phytoconstituents were identified in L. camara extract, from which the top hit compounds related to inflammation were ferulic acid, catechin gallate, myricetin and iso-ferulic acid. Whereas the most enriched inflammation related genes were PRKCA, RELA, IL2, MAPK 14 and FOS. Furthermore, the most enriched inflammation-related pathways were PI3K-Akt and MAPK signaling pathways. Molecular docking revealed that catechin gallate possessed the lowest binding energy against PRKCA, RELA and IL2, while myricetin had the most stabilized interaction against MAPK14 and FOS. In vitro cytotoxicity and anti-inflammatory testing indicated that L. camara extract is safer than piroxicam and has a strong anti-inflammatory activity comparable to it. This study is a first step in proving the folk uses of L. camara in palliating inflammatory ailments and institutes the groundwork for future clinical studies.

A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19

BACKGROUND

COVID-19 highly caused contagious infections and massive deaths worldwide as well as unprecedentedly disrupting global economies and societies, and the urgent development of new antiviral medications are required. Medicinal herbs are promising resources for the discovery of prophylactic candidate against COVID-19. Considerable amounts of experimental efforts have been made on vaccines and direct-acting antiviral agents (DAAs), but neither of them was fast and fully developed.

PURPOSE

This study examined the computational approaches that have played a significant role in drug discovery and development against COVID-19, and these computational methods and tools will be helpful for the discovery of lead compounds from phytochemicals and understanding the molecular mechanism of action of TCM in the prevention and control of the other diseases.

METHODS

A search conducting in scientific databases (PubMed, Science Direct, ResearchGate, Google Scholar, and Web of Science) found a total of 2172 articles, which were retrieved via web interface of the following websites. After applying some inclusion and exclusion criteria and full-text screening, only 292 articles were collected as eligible articles.

RESULTS

In this review, we highlight three main categories of computational approaches including structure-based, knowledge-mining (artificial intelligence) and network-based approaches. The most commonly used database, molecular docking tool, and MD simulation software include TCMSP, AutoDock Vina, and GROMACS, respectively. Network-based approaches were mainly provided to help readers understanding the complex mechanisms of multiple TCM ingredients, targets, diseases, and networks.

CONCLUSION

Computational approaches have been broadly applied to the research of phytochemicals and TCM against COVID-19, and played a significant role in drug discovery and development in terms of the financial and time saving.

Glycyrrhetinic acid: A potential drug for the treatment of COVID-19 cytokine storm

BACKGROUND

The cytokine storm (CS) triggered by coronavirus disease 2019 (COVID-19) has caused serious harm to health of humanity and huge economic burden to the world, and there is a lack of effective methods to treat this complication.

PURPOSE

In this research, we used network pharmacology and molecular docking to reveal the interaction mechanism in the glycyrrhetinic acid (GA) for the treatment of CS, and validated the effect of GA intervention CS by experiments.

STUDY DESIGN

First, we screened corresponding target of GA and CS from online databases, and obtained the action target genes through the Venn diagram. Then, protein-protein interaction (PPI) network, Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of the action target genes were acquired by R language to predict its mechanism. Next, molecular docking was performed on core targets. Finally, experiments in which GA intervened in lipopolysaccharide (LPS)-induced CS were implemented.

RESULTS

84 action target genes were obtained from online database. The PPI network of target genes showed that TNF, IL6, MAPK3, PTGS2, ESR1 and PPARG were considered as the core genes. The results of GO and KEGG showed that action target genes were closely related to inflammatory and immune related signaling pathways, such as TNF signaling pathway, IL-17 signaling pathway, Human cytomegalovirus infection, PPAR signaling pathway and so on. Molecule docking results prompted that GA had fine affinity with IL6 and TNF proteins. Finally, in vivo and in vitro experimental results showed that GA could significantly inhibit LPS-induced CS.

CONCLUSION

GA has a potential inhibitory effect on CS, which is worthy of further exploration.

Medicinal plant sources and traditional healthcare practices of forest-dependent communities in and around Chunati Wildlife Sanctuary in southeastern Bangladesh

Bangladesh's forest-dependent people rely on medicinal plants for traditional healthcare practices, as plant-based medicines are easily available and cost-effective. This study evaluated and documented ethnomedicinal practices for, and traditional knowledge of, utilising plants to cure ailments. Ethnobotanical indices quantified the use value (UV), frequency of citation, relative frequency of citation (RFC) and the informant consensus factor. Using a semi-structured questionnaire, the study interviewed 231 respondents from 18 villages in and around Chunati Wildlife Sanctuary (CWS). The study documented 134 medicinal plant species from 60 families; tree species were dominant (37.31%). Malvaceae (seven species), Rutaceae and Lamiaceae (six species each) families covered more species. Nearly half of the species (46.02%) were collected from CWS. Both above-ground and below-ground plant parts treated 71 types of ailments under 21 categories, with leaves (66 species) being the most widely used plant part. In total 33 species were used to treat dysentery, 25 species each for fever and jaundice, and 24 species for cuts and wounds. The average UV value was 0.24 and RFC value was 0.47%. Communities were found to utilise medicinal plants more at home than to sell at markets, substantially relying on medicinal plants to meet their domestic needs. Plants used for healthcare and cultural and religious beliefs have a strong connection that plays a vital role in plant conservation. This study identified 42 medicinal plant species that could be considered to treat COVID-19 patients in Bangladesh. The findings suggest that community awareness of sustainable harvesting and commercial cultivation could lead to conservation and use of these invaluable plant species for healthcare, new drugs discovery and sustainable forest management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42398-022-00230-z.

Olive Leaves as a Potential Phytotherapy in the Treatment of COVID-19 Disease; A Mini-Review

Beginning from December 2019, widespread COVID-19 has caused huge financial misfortunes and exceptional wellbeing emergencies across the globe. Discovering an effective and safe drug candidate for the treatment of COVID-19 and its associated symptoms became an urgent global demand, especially due to restricted information that has been discharged with respect to vaccine efficacy and safety in humans. Reviewing the recent research, olive leaves were selected as a potential co-therapy supplement for the treatment and improvement of clinical manifestations in COVID-19 patients. Olive leaves were reported to be rich in phenolic compounds such as oleuropein, hydroxytyrosol, verbascoside, apigenin-7-O-glucoside, and luteolin-7-O-glucoside and also triterpenoids such as maslinic, ursolic, and oleanolic acids that have been reported as anti-SARS-CoV-2 metabolites in recent computational and in vitro studies. In addition, olive leaf extract was previously reported in several in vivo studies for its anti-inflammatory, analgesic, antipyretic, immunomodulatory, and antithrombotic activities which are of great benefit in the control of associated inflammatory cytokine storm and disseminated intravascular coagulation in COVID-19 patients. In conclusion, the described biological activities of olive leaves alongside their biosafety, availability, and low price make them a potential candidate drug or supplement to control COVID-19 infection and are recommended for clinical investigation.

In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer

In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.

The Role of Diet and Supplementation of Natural Products in COVID-19 Prevention

Recently, a discussion has begun on the global management strategy against COVID-19 based on the hypothesis that individuals' macro- and micronutrient status combined with antiviral drugs and herbs can be an ally against the infection. The hypothesis is that people's nutritional and oxidative scavenging capacity may provide fundamental data to predict severe and acute pulmonary distress following SARS-Cov2 infection. Consequently, the scientific community has addressed the role of balanced diets, nutritional supplements, and micronutrients, including folk herbal formulations, in reducing hospitalization and the severity of pulmonary impact in COVID-19 by preventing the most serious forms of the infection. This led to an animated debate on the potential effectiveness of some vitamins, micronutrients, and traditional Chinese medicine in preventing COVID-19, with some authors convinced that plant extracts could act oppositely, exacerbating the effect of the infection. While current research is still far to assess the suggestions and issues raised in this short communication, it is undoubtedly true that determining an individual's current metabolic status, including macro- and micronutrients, is an essential factor in defining any individuals' deficiencies, which will need to be addressed urgently through a proper diet, specific personalized nutritional supplementation, and lifestyle changes.

In-silico efficacy of potential phytomolecules from Ayurvedic herbs as an adjuvant therapy in management of COVID-19

The recent COVID-19 outbreak caused by SARS-CoV-2 virus has sparked a new spectrum of investigations, research and studies in multifarious directions. Efforts are being made around the world for discovery of effective vaccines/drugs against COVID-19. In this context, Ayurveda, an alternative traditional system of medicine in India may work as an adjuvant therapy in compromised patients. We selected 40 herbal leads on the basis of their traditional applications. The phytomolecules from these leads were further screened through in-silico molecular docking against two main targets of SARS-CoV-2 i.e. the spike protein (S; structural protein) and the main protease (MPRO; non-structural protein). Out of the selected 40, 12 phytomolecules were able to block or stabilize the major functional sites of the main protease and spike protein. Among these, Ginsenoside, Glycyrrhizic acid, Hespiridin and Tribulosin exhibited high binding energy with both main protease and spike protein. Etoposide showed good binding energy only with Spike protein and Teniposide had high binding energy only with main protease. The above phytocompounds showed promising binding efficiency with target proteins indicating their possible applications against SARS-CoV-2. However, these findings need to be validated through in vitro and in vivo experiments with above mentioned potential molecules as candidate drugs for the management of COVID-19. In addition, there is an opportunity for the development of formulations through different permutations and combinations of these phytomolecules to harness their synergistic potential.

COVID-19: A review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks

Today, the world population is facing an existential threat by an invisible enemy known as severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) or COVID-19. It is highly contagious and has infected a larger fraction of human population across the globe on various routes of transmission. The detailed knowledge of the SARS-CoV-2 structure and clinical aspects offers an important insight into the evolution of infection, disease progression and helps in executing the different therapies effectively. Herein, we have discussed in detail about the genome structure of SARS-CoV-2 and its role in the proteomic rational spread of different muted species and pathogenesis in infecting the host cells. The mechanisms behind the viral outbreak and its immune response, the availability of existing diagnostics techniques, the treatment efficacy of repurposed drugs and the emerging vaccine trials for the SARS-CoV-2 outbreak also have been highlighted. Furthermore, the possible antiviral effects of various herbal products and their extracted molecules in inhibiting SARS-CoV-2 replication and cellular entry are also reported. Finally, we conclude our opinion on current challenges involved in the drug development, bulk production of drug/vaccines and their storage requirements, logistical procedures and limitations related to dosage trials for larger population.

Jeopardy of COVID-19: Rechecking the Perks of Phytotherapeutic Interventions

The novel coronavirus disease (COVID-19), the reason for worldwide pandemic, has already masked around 220 countries globally. This disease is induced by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). Arising environmental stress, increase in the oxidative stress level, weak immunity and lack of nutrition deteriorates the clinical status of the infected patients. Though several researches are at its peak for understanding and bringing forward effective therapeutics, yet there is no promising solution treating this disease directly. Medicinal plants and their active metabolites have always been promising in treating many clinical complications since time immemorial. Mother nature provides vivid chemical structures, which act multi-dimensionally all alone or synergistically in mitigating several diseases. Their unique antioxidant and anti-inflammatory activity with least side effects have made them more effective candidate for pharmacological studies. These medicinal plants inhibit attachment, encapsulation and replication of COVID-19 viruses by targeting various signaling molecules such as angiotensin converting enzyme-2, transmembrane serine protease 2, spike glycoprotein, main protease etc. This property is re-examined and its potency is now used to improve the existing global health crisis. This review is an attempt to focus various antiviral activities of various noteworthy medicinal plants. Moreover, its implications as prophylactic or preventive in various secondary complications including neurological, cardiovascular, acute kidney disease, liver disease are also pinpointed in the present review. This knowledge will help emphasis on the therapeutic developments for this novel coronavirus where it can be used as alone or in combination with the repositioned drugs to combat COVID-19.

Network Pharmacology-Based Analysis on the Action Mechanism of Oleanolic Acid to Alleviate Osteoporosis

Oleanolic acid (OA) is a triterpenoid commonly found in plants and has shown extensive pharmaceutical activities. This study aimed to investigate the underlying mechanism of antiosteoporosis (OP) action of OA by utilizing the network pharmacology approach and molecular docking methods. First, the targets of OA were identified using the GeneCards, Stitch, and Swisstarget databases, and the targets related to OP were mined using the NCBI, Genecards, and DisGeNet databases. The overlapped targets of OA and OP were regarded as candidate targets, and the String database was used to obtain the protein-protein interactions among the targets. Then, Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway enrichment pathways of the candidate targets were performed using the DAVID database. In addition, the top 16 targets in the protein interaction network were used for molecular docking. Finally, an animal model constructed using d-galactose-induced oxidative stress and a low-calcium diet with accelerated bone loss was used to verify the in vivo effects of OA on osteoporotic mice. A total of 42 candidate targets for OA to treat OP were obtained. According to the protein-protein interaction network, MAPK1 showed the highest connectivity with other proteins. Additionally, GO analysis identified the top 20 biological processes, 9 cellular components, and top 20 molecular functions. Moreover, the candidate targets were mainly involved in 13 signaling pathways such as TNF signaling pathway, insulin resistance, MAPK signaling pathway, apoptosis, and PI3K-Akt signaling pathways. Furthermore, molecular docking revealed that OA has a high degree of connections with 16 key proteins. In addition, the anti-OP effects of OA are further validated through the in vivo model. Altogether, our study elucidated the candidate targets for OA to alleviate OP, explored the protein-protein interactions and related signaling pathways of the targets, and validated the anti-OP effects of OA. It could provide a better understanding of the action mechanism in OA to treat OP.

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.

Can Antiviral Activity of Licorice Help Fight COVID-19 Infection?

The phytotherapeutic properties of Glycyrrhiza glabra (licorice) extract are mainly attributed to glycyrrhizin (GR) and glycyrrhetinic acid (GA). Among their possible pharmacological actions, the ability to act against viruses belonging to different families, including SARS coronavirus, is particularly important. With the COVID-19 emergency and the urgent need for compounds to counteract the pandemic, the antiviral properties of GR and GA, as pure substances or as components of licorice extract, attracted attention in the last year and supported the launch of two clinical trials. In silico docking studies reported that GR and GA may directly interact with the key players in viral internalization and replication such as angiotensin-converting enzyme 2 (ACE2), spike protein, the host transmembrane serine protease 2, and 3-chymotrypsin-like cysteine protease. In vitro data indicated that GR can interfere with virus entry by directly interacting with ACE2 and spike, with a nonspecific effect on cell and viral membranes. Additional anti-inflammatory and antioxidant effects of GR cannot be excluded. These multiple activities of GR and licorice extract are critically re-assessed in this review, and their possible role against the spread of the SARS-CoV-2 and the features of COVID-19 disease is discussed.

Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19

Although several pharmacological agents are under investigation to be repurposed as therapeutic against COVID-19, not much success has been achieved yet. So, the search for an effective and active option for the treatment of COVID-19 is still a big challenge. The Spike protein (S), RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro) are considered to be the primary therapeutic drug target for COVID-19. In this study we have screened the drugbank compound library against the Main Protease. But our search was not limited to just Mpro. Like other viruses, SARS-CoV-2, have also acquired unique mutations. These mutations within the active site of these target proteins may be an important factor hindering effective drug candidate development. In the present study we identified important active site mutations within the SARS-CoV-2 Mpro (Y54C, N142S, T190I and A191V). Further the drugbank database was computationally screened against Mpro and the selected mutants. Finally, we came up with the common molecules effective against the wild type (WT) and all the selected Mpro. The study found Imiglitazar, was found to be the most active compound against the wild type of Mpro. While PF-03715455 (Y54C), Salvianolic acid A (N142S and T190I), and Montelukast (A191V) were found to be most active against the other selected mutants. It was also found that some other compounds such as Acteoside, 4-Amino-N- {4-[2-(2,6-Dimethyl-Phenoxy)-Acetylamino]-3-Hydroxy-1-Isobutyl-5-Phenyl-Pentyl}-Benzamide, PF-00610355, 4-Amino-N-4-[2-(2,6-Dimethyl-Phenoxy)-Acetylamino]-3-Hydroxy-1-Isobutyl-5-Phenyl-Pentyl}-Benzamide and Atorvastatin were showing high efficacy against the WT as well as other selected mutants. We believe that these molecules will provide a better and effective option for the treatment of COVID-19 clinical manifestations.

Druggability of cavity pockets within SARS-CoV-2 spike glycoprotein and pharmacophore-based drug discovery

Aim: Virus spike glycoprotein of SARS-CoV-2 is a good target for drug discovery. Objective: To examine the potential for druggability of spike protein for pharmacophore-based drug discovery and to investigate the binding affinity of natural products with SARS-CoV-2 spike protein. Methods: Druggable cavities were searched though CavityPlus. A pharmacophore was built and used for hit identification. Autodock Vina was used to evaluate the hits' affinities. 10 chemical derivatives were also made from the chemical backbone to optimize the lead compound. Results: 10 druggable cavities were found within the glycoprotein spike. Only one cavity with the highest score at the binding site was selected for pharmacophore extraction. Hit identification resulted in the identification of 410 hits. Discussion: This study provides a druggable region within viral glycoprotein and a candidate compound to block viral entry.

The Common Cichory (Cichorium intybus L.) as a Source of Extracts with Health-Promoting Properties-A Review

Natural products are gaining more interest recently, much of which focuses on those derived from medicinal plants. The common chicory (Cichorium intybus L.), of the Astraceae family, is a prime example of this trend. It has been proven to be a feasible source of biologically relevant elements (K, Fe, Ca), vitamins (A, B1, B2, C) as well as bioactive compounds (inulin, sesquiterpene lactones, coumarin derivatives, cichoric acid, phenolic acids), which exert potent pro-health effects on the human organism. It displays choleretic and digestion-promoting, as well as appetite-increasing, anti-inflammatory and antibacterial action, all owing to its varied phytochemical composition. Hence, chicory is used most often to treat gastrointestinal disorders. Chicory was among the plants with potential against SARS-CoV-2, too. To this and other ends, roots, herb, flowers and leaves are used. Apart from its phytochemical applications, chicory is also used in gastronomy as a coffee substitute, food or drink additive. The aim of this paper is to present, in the light of the recent literature, the chemical composition and properties of chicory.

Network pharmacology-based analysis for unraveling potential cancer-related molecular targets of Egyptian propolis phytoconstituents accompanied with molecular docking and in vitro studies

Cancer is one of the predominant causes of death worldwide. The new trend nowadays is to exploit natural products with the hope of developing new anticancer agents with fewer side effects. Propolis is one of these natural products which showed effectiveness in cancer treatment. The aim of this study is to understand the multi-level mechanism of action of propolis constituents in cancer treatment using an integrated approach of network pharmacology-based analysis, molecular docking and in vitro cytotoxicity testing. An inhouse database of chemical constituents from Egyptian propolis was compiled and assessed for its ADME properties using the QikProp module in the Schrodinger software. STITCH, UniProt, STRING, KEGG and DAVID databases were used for construction of constituent-target gene, gene-pathway, and constituent-target gene-pathway networks with the aid of Cytoscape 3.8.2. The network pharmacology-based analysis showed that the hit propolis constituents related to cancer targets were genistein, luteolin, benzoic acid, quercetin and vanillic acid, whereas the main cancer-associated targets were CYP1A1, CYP19A1, ESR1, NOS3, CASP3 and AKT1. Twenty-four cancer-related pathways were recognized where the most enriched ones were pathways in cancer and estrogen signaling pathway. The most enriched biological processes involved in the mechanism of action of propolis constituents in cancer treatment were negative regulation of the apoptotic process and the metabolic process and negative regulation of cellular glucuronidation. Molecular docking analysis of the top hit compounds against the most enriched target proteins in the constructed networks was carried out using the Maestro interface of the Schrodinger software. Among hit compounds, quercetin and genistein exhibited the most stabilized interaction. Finally, confirmation of the potential anticancer activity of propolis was assured by in vitro cytotoxicity testing of propolis extract on human prostate cancer (DU-145), breast adenocarcinoma (MCF-7) and colorectal adenocarcinoma (Caco-2) cell lines. This study presents deeper insights about propolis molecular mechanisms of action in cancer for the first time using an integrated approach of network pharmacology, molecular docking and in vitro testing.

Biologically guided isolation and ADMET profile of new factor Xa inhibitors from Glycyrrhiza glabra roots using in vitro and in silico approaches

Selective factor Xa inhibitors effectively block coagulation cascade with a broader therapeutic window than multitargeted anticoagulants. They have evolved as a crucial part of prevention and treatment of thromboembolic diseases and in therapeutic protocols involved in many clinical trials in coronavirus disease 2019 (COVID-19) patients. Biologically-guided isolation of specific FXa inhibitors from licorice (Glycyrrhiza glabra) root extract furnished ten flavonoids. By detailed analysis of their 1H, 13C NMR and MS data, the structures of these flavonoids were established as 7,4'-dihydroxyflavone (1), formononetin (2), 3-R-glabridin (3), isoliquiritigenin (4), liquiritin (5), naringenin 5-O-glucoside (6), 3,3',4,4'-tetrahydroxy-2-methoxychalcone (7), liquiritinapioside (8) and the two isomers isoliquiritigenin-4'-O-β-d-apiosylglucoside (9) and isoliquiritigenin-4-O-β-d-apiosylglucoside (10). All the isolated compounds were assessed for their FXa inhibitory activity using in vitro chromogenic assay for the first time. Liquirtin (5) showed the most potent inhibitory effects with an IC50 of 5.15 μM. The QikProp module was implemented to perform ADMET predictions for the screened compounds.

COVID-19, prevention and treatment with herbal medicine in the herbal markets of Salé Prefecture, North-Western Morocco

INTRODUCTION

Coronaviruses are important animal and human pathogens. Towards the end of 2019, the novel coronavirus identified in Wuhan, China, presented as a cluster of symptoms of pneumonia. Its quick spread resulted in a global pandemic. This research documents detailed ethnopharmacological information on the medicinal plant species used by herbalists against coronavirus disease.

METHODS

The study was conducted in Salé Prefecture, from March 1st, 2020 to May 31st, 2020. Semi-structured face to face interviews were held with 30 herbalists and collected; socio-demographic characteristics, the names of local species, and traditional remedies being used. The data were analyzed through the use reports (UR) and medicinal use value (MUV).

RESULTS

In total, 20 plant species from 20 genera and 14 families had been most frequently used by herbalists from Salé Prefecture for the prevention and treatment of COVID 19. The most mentioned plant was Eucalyptus globulus Labill., followed by Azadirachta indica A. Juss,. and Ziziphus lotus (L.) Lam. Moreover, the most commonly used plant parts for herbal preparations were leaves (28.43%) and seeds (17.5%), and the majority of remedies were prepared through infusion.

CONCLUSIONS

The present study is the first contribution to the ethnopharmacological profile of this Prefecture. It is recommended that the constituents of indigenous species be studied to determine the therapeutic effects and mechanisms of action. However, attention must be paid to the conservation of medicinal species, comprehensively documenting traditional medicinal knowledge as well as conducting phytochemical validation of reported plants.

Importance of glutamine 189 flexibility in SARS-CoV-2 main protease: Lesson learned from in silico virtual screening of ChEMBL database and molecular dynamics

The current global pandemic outbreak of COVID-19, caused by the SARS-CoV-2, strikes an invincible damage to both daily life and the global economy. WHO guidelines for COVID-19 clinical management includes infection control and prevention, social distancing and supportive care using supplemental oxygen and mechanical ventilator support. Currently, evolving researches and clinical reports regarding infected patients with SARS-CoV-2 suggest a potential list of repurposed drugs that may produce appropriate pharmacological therapeutic efficacies in treating COVID-19 infected patients. In this study, we performed virtual screening and evaluated the obtained results of US-FDA approved small molecular database library (302 drug molecule) against two important different protein targets in COVID-19. Best compounds in molecular docking were used as a training set for generation of two different pharmacophores. The obtained pharmacophores were employed for virtual screening of ChEMBL database. The filtered compounds were clustered using Finger print model to obtain two compounds that will be subjected to molecular docking simulations against the two targets. Compounds complexes with SARS-CoV-2 main protease and S-protein were studied using molecular dynamics (MD) simulation. MD simulation studies suggest the potential inhibitory activity of ChEMBL398869 against SARS-CoV-2 main protease and restress the importance of Gln189 flexibility in inhibitors recognition through increasing S2 subsite plasticity.

Molecular Docking and Molecular Dynamics Aided Virtual Search of OliveNet™ Directory for Secoiridoids to Combat SARS-CoV-2 Infection and Associated Hyperinflammatory Responses

Molecular docking and molecular dynamics aided virtual search of OliveNet™ directory identified potential secoiridoids that combat SARS-CoV-2 entry, replication, and associated hyperinflammatory responses. OliveNet™ is an active directory of phytochemicals obtained from different parts of the olive tree, Olea europaea (Oleaceae). Olive oil, olive fruits containing phenolics, known for their health benefits, are indispensable in the Mediterranean and Arabian diets. Secoiridoids is the largest group of olive phenols and is exclusive to the olive fruits. Functional food like olive fruits could help prevent and alleviate viral disease at an affordable cost. A systematized virtual search of 932 conformers of 78 secoiridoids utilizing Autodock Vina, followed by precision docking using Idock and Smina indicated that Nüzhenide oleoside (NZO), Oleuropein dimer (OED), and Dihydro oleuropein (DHO) blocked the SARS-CoV-2 spike (S) protein-ACE-2 interface; Demethyloleuropein (DMO), Neo-nüzhenide (NNZ), and Nüzhenide (NZE) blocked the SARS-CoV-2 main protease (Mpro). Molecular dynamics (MD) simulation of the NZO-S-protein-ACE-2 complex by Desmond revealed stability during 50 ns. RMSD of the NZO-S-protein-ACE-2 complex converged at 2.1 Å after 20 ns. During MD, the interaction fractions confirmed multiple interactions of NZO with Lys417, a crucial residue for inhibition of S protein. MD of DMO-Mpro complex proved its stability as the RMSD converged at 1.6 Å. Analysis of interactions during MD confirmed the interaction of Cys145 of Mpro with DMO and, thus, its inhibition. The docking predicted IC50 of NZO and DMO was 11.58 and 6.44 μM, respectively. Molecular docking and dynamics of inhibition of the S protein and Mpro by NZO and DMO correlated well. Docking of the six-hit secoiridoids to IL1R, IL6R, and TNFR1, the receptors of inflammatory cytokines IL1β, IL6, and TNFα, revealed the anti-inflammatory potential except for DHO. Due to intricate structures, the secoiridoids violated Lipinski's rule of five. However, the drug scores of secoiridoids supported their use as drugs. The ADMET predictions implied that the secoiridoids are non-toxic and pose low oral absorption. Secoiridoids need further optimization and are a suitable lead for the discovery of anti-SARS-CoV-2 therapeutics. For the moment, olive secoiridoids presents an accessible mode of prevention and therapy of SARS-CoV-2 infection.

Breeding Buckwheat for Increased Levels of Rutin, Quercetin and Other Bioactive Compounds with Potential Antiviral Effects

Common buckwheat (Fagopyrum esculentum Moench) and Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) are sources of many bioactive compounds, such as rutin, quercetin, emodin, fagopyrin and other (poly)phenolics. In damaged or milled grain under wet conditions, most of the rutin in common and Tartary buckwheat is degraded to quercetin by rutin-degrading enzymes (e.g., rutinosidase). From Tartary buckwheat varieties with low rutinosidase activity it is possible to prepare foods with high levels of rutin, with the preserved initial levels in the grain. The quercetin from rutin degradation in Tartary buckwheat grain is responsible in part for inhibition of α-glucosidase in the intestine, which helps to maintain normal glucose levels in the blood. Rutin and emodin have the potential for antiviral effects. Grain embryos are rich in rutin, so breeding buckwheat with the aim of producing larger embryos may be a promising strategy to increase the levels of rutin in common and Tartary buckwheat grain, and hence to improve its nutritional value.

Discovery of potent inhibitors for SARS-CoV-2's main protease by ligand-based/structure-based virtual screening, MD simulations, and binding energy calculations

COVID-19 has caused lockdowns all over the world in early 2020, as a global pandemic. Both theoretical and experimental efforts are seeking to find an effective treatment to suppress the virus. In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that has crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions. MD simulations support that the catalytic residue, His41, has a neutral side chain with a protonated delta position. An absolute binding energy (ΔG) of -42 kJ mol-1 for the protein-ligand (Mpro-N3) complex has been calculated using the potential-of-mean-force (geometrical) approach. Furthermore, the relative binding energies were computed for the top docking results. Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro as follows: a bioactive compound, ChEMBL275592, which has the best MM/GBSA binding energy; the second-best compound, montelukast, is an approved drug used in the treatment of asthma and allergic rhinitis; the third-best compound, ChEMBL288347, is a bioactive compound. Bromocriptine and saquinavir are other approved drugs that also demonstrate stability in the active site of Mpro, albeit their relative binding energies are low compared to the N3 inhibitor. This study provides useful insights into de novo protein design and novel inhibitor development, which could reduce the cost and time required for the discovery of a potent drug to combat SARS-CoV-2.