Antimicrobial potential of phytocompounds of Acorus calamus: in silico approach

Medicinal plants are used from prehistoric time to cure various life-threatening bacterial diseases. Acorus calamus is an important medicinal plant widely used to cure gastrointestinal, respiratory, kidney and liver disorders. The objective of the current research was to investigate the interaction of major phytoconstituents of Acorus calamus with bacterial (6VJE) and fungal (1EA1) protein targets. Protein-ligand interactions were estimated using the AutoDock software, drug likeness was predicted by using the molinspiration server and toxicity was predicted with the swissADME and protox II servers. MD simulation of phytocompounds with the best profiles was done on the GROMACS software for 100 ns. Molecular docking results showed among all the selected major phytoconstituents, that β-cadinene showed best binding interaction in complex with bacterial (6VJE) and fungal (1EA1) protein targets with binding energy -7.66 ± 0.1 and -7.73 ± 0.15 kcal mol-1, respectively. Drug likeness and toxicity predictions showed that β-cadinene follows all rules of drug likeness and toxicity. MD simulation study revealed that β-cadinene fit in binding pocket of bacterial and fungal targets and found to be stable throughout the duration of the simulation. Based on the observations from this in-silico study it is being proposed that β-cadinene, a major phytocompound of Acorus calamus, can be considered for the treatment of bacterial and fungal infections since the study shows that it might be one of the compounds that contributes majorly to the plant's biological activity. This study needs in vitro and in vivo validation.Communicated by Ramaswamy H. Sarma.

Identification of novel inhibitor phytoconstituents for Influenza A H3N2: an in silico approach

Influenza A virus subtype H3N2 is a highly infectious respiratory virus that is responsible for global seasonal flu epidemics. The current study was designed to investigate the antiviral activity of 150 phytocompounds of North Western Himalayas medicinal plants by molecular docking. Two target proteins of hemagglutinin of influenza virus A (PDB ID 4WE8) and Influenza virus H3N2 nucleoprotein - R416A mutant (PDB ID 7NT8) are selected for this study. Molecular docking was done by AutoDock vina tool, toxicity and drug-likeness prediction was done by protox II and Moleinspiration. MD simulation of best protein-ligand complexes was done by using Gromacs, version 2021.5. Molecular docking and toxicity data revealed that clicoemodin and rumexocide showed the best binding with both target proteins 4WEB & 7NT8. Clicoemodin showed the -7.5 KJ/mol binding energy with 4WE8 and 7NT8. Similarly, rumexoside showed the -7.6 KJ/mol binding energy with 4WE8 and -7.6 KJ/mol with 7NT8. Furthermore, Molecular dynamic simulation and MMPBSA binding free energy validated the stability of protein-ligand complexes. The current study suggested that clicoemodin and rumexocide are the promising inhibitors of H3N2 proteins hemagglutinin of influenza virus A and Influenza virus H3N2 nucleoprotein - R416A mutant, though there is further in vitro and in vivo validation is required.Communicated by Ramaswamy H. Sarma.

A comprehensive review on traditional applications, phytochemistry, pharmacology, and toxicology of Thymus serpyllum

Thymus serpyllum L. from the Lamiaceae family is an underexplored perennial medicinal shrub with traditional usage in treating respiratory and gastrointestinal issues in the upper foothills of India. This review aims to provide a comprehensive assessment of current knowledge concerning the traditional uses, phytochemistry, and pharmacology of T. serpyllum. The primary objective is to collect updated information on this plant and encourage further in vivo and in vitro research to validate local claims. Notably, the essential oil derived from T. serpyllum has gained significant attention as a plant-derived product due to its diverse pharmacological properties, including antioxidative, antimicrobial, anti-inflammatory, and anticancer activities. Ethnomedicinal research revealed a vast scope of T. serpyllum in developing new drugs to address numerous health sector challenges. While T. serpyllum has been used widely, pharmacological studies are not enough. Most studies are either in vivo or in vitro. More studies are required to assess these medicinal claims through well-planned pharmacological experiments. This review will provide the groundwork for future research. While T. serpyllum has been put to considerable conventional use, pharmacological studies are insufficient; most studies are either in vivo or in vitro. More compound isolation, comprehensive pharmacological analysis, and exploration of food applications are vital areas to investigate.

Comparative docking studies of drugs and phytocompounds for emerging variants of SARS-CoV-2

In the last three years, COVID-19 has impacted the world with back-to-back waves leading to devastating consequences. SARS-CoV-2, the causative agent of COVID-19, was first detected in 2019 and since then has spread to 228 countries. Even though the primary focus of research groups was diverted to fight against COVID-19, yet no dedicated drug has been developed to combat the emergent life-threatening medical conditions. In this study, 35 phytocompounds and 43 drugs were investigated for comparative docking analysis. Molecular docking and virtual screening were performed against SARS-CoV-2 spike glycoprotein of 13 variants using AutoDock Vina tool 1.5.6 and Discovery Studio, respectively, to identify the most efficient drugs. Selection of the most suitable compounds with the best binding affinity was done after screening for toxicity, ADME (absorption, distribution, metabolism and excretion) properties and drug-likeliness. The potential candidates were discovered to be Liquiritin (binding affinities ranging between -7.0 and -8.1 kcal/mol for the 13 variants) and Apigenin (binding affinities ranging between -6.8 and -7.3 kcal/mol for the 13 variants) based on their toxicity and consistent binding affinity with the Spike protein of all variants. The stability of the protein-ligand complex was determined using Molecular dynamics (MD) simulation of Apigenin with the Delta plus variant of SARS-CoV-2. Furthermore, Liquiritin and Apigenin were also found to be less toxic than the presently used drugs and showed promising results based on in silico studies, though, confirmation using in vitro studies is required. This in-depth comparative investigation suggests potential drug candidates to fight against SARS-CoV-2 variants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03450-6.

In vitro and in silico antioxidant and anti-inflammatory potential of essential oil of Cymbopogon citratus (DC.) Stapf. of North-Western Himalaya

Cymbopogon citratus (DC.) Stapf is an aromatic perennial herb of Gramineae (Poaceae) family and is known for its application in food and healthcare industry. The present study aimed to evaluate anti-inflammatory and antioxidant potential of C. citratus essential oil (CEO) through in vitro and in silico studies. Chemical characterization of CEO was done using Gas chromatography-mass spectrophotometry (GC-MS) method. In vitro antioxidant activity was evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and ferric ion reducing antioxidant power (FRAP) assays, while egg albumin denaturation method was used to evaluate in vitro anti-inflammatory activity of CEO. Molecular docking investigation of major phytocompounds of CEO was done using Autodock vina software against human peroxiredoxin 5 (PDB ID: 1HD2) and human cyclooxygenase 2 (PDB ID: 5IKQ) proteins, which were further analyzed through molecular dynamics (MD) simulation using YASARA. GC-MS analysis of CEO showed the presence of geranial (48%) neral (34.04%), β-myrcene (9.77%), geraniol (1.88%), linalool (0.84%), isogeranial (0.81%), β-caryophyllene (0.80%), D-limonene (0.51%) as major constituents. CEO showed significant antioxidant activity with DPPH (IC₅₀-47.53 ± 2.16 µg/ml), FRAP (IC₅₀-30.7 ± 0.31 µM), and ABTS assays (IC₅₀-27.87 ± 0.09 µg/ml). CEO also exhibited significant in-vitro anti-inflammatory activity with IC₅₀-29.71 ± 1.95 µg/ml as compared to that of Diclofenac sodium (IC₅₀-36.52 ± 1.95 µg/ml). Molecular docking revealed that β-caryophyllene showed considerable binding potential with human peroxiredoxin 5 receptor (-6.0 kcal/mol) and human cyclooxygenase 2 receptor (-10.1 kcal/mol). Further, MD simulations demonstrated considerable and stable interactions of β-caryophyllene with 1HD2 and 5IKQ proteins up to 100 ns. Drug-likeness and ADME/T features also showed that β-caryophyllene can be used as a potential candidate to replace the synthetic anti-inflammatory drugs with side effects and also act as natural antioxidants.Communicated by Ramaswamy H. Sarma.

In vitro and in silico analysis of Thymus serpyllum essential oil as bioactivity enhancer of antibacterial and antifungal agents

Wild thyme (Thymus serpyllum L.) of family Laminaceae is an unexplored perennial medicinal shrub. Aerial part of this plant is traditionally used for the treatment of respiratory and gastrointestinal problems. The current study was designed to evaluate the GC-MS, antimicrobial and synergistic potential of T. serpyllum essential oil (TEO). Chemical characterization of TEO showed the presence of thymol (15.79%), Phenol, 2-(1,1-dimethylethyl) (11.55%), o-Cymene (10.96%) as major phytocompounds. Antimicrobial activity of TEO in terms zone of inhibition (ZOI) varied from 13.66 ± 0.58 mm to 33.66 ± 1.52 mm, while, thymol (10%, v/v) showed ZOI ranged from 15.5 ± 0.5 mm to 26.33 ± 2.08 mm against tested bacterial and fungal species. MIC of TEO was 0.039% to 0.078% against tested bacterial and fungal species, whereas, thymol showed 1.25% to 2.5% MIC against tested bacterial and fungal species. Different combinations of TEO (2MIC to ½MIC) and thymol (2MIC to ½MIC) with antibacterial and antifungal antibiotics (2MIC to ½MIC) were found to increase the efficacy of antibiotics by 4-130 folds against bacterial and fungal pathogens. Molecular docking showed the good binding of thymol with both bacterial and fungal targets. Whereas MD simulation showed the stability of thymol complexed with target proteins over 100 ns time scale. Thymol also fulfills the Lipinski rule and showed characteristics similar to that of drugs. Therefore, it can be concluded from the present study that TEO and its major phytocompound, thymol can act as a bioactivity enhancer of antibacterial and antifungal antibiotics and could be used as a potential candidate to fight against antimicrobial drug resistance.Communicated by Ramaswamy H. Sarma.

Phytoconstituents of traditional Himalayan Herbs as potential inhibitors of Human Papillomavirus (HPV-18) for cervical cancer treatment: An In silico Approach

Human papillomavirus (HPV) induced cervical cancer is becoming a major cause of mortality in women. The present research aimed to identify the natural inhibitors of HPV-18 E1 protein (1R9W) from Himalayan herbs with lesser toxicity and higher potency. In this study, one hundred nineteen phytoconstituents of twenty important traditional medicinal plants of Northwest Himalayas were selected for molecular docking with the target protein 1R9W of HPV-18 E1 Molecular docking was performed by AutoDock vina software. ADME/T screening of the bioactive phytoconstituents was done by SwissADME, admetSAR, and Protox II. A couple of best protein-ligand complexes were selected for 100 ns MD simulation. Molecular docking results revealed that among all the selected phytoconstituents only thirty-five phytoconstituents showed the binding affinity similar or more than the standard anti-cancer drugs viz. imiquimod (-6.1 kJ/mol) and podofilox (-6.9 kJ/mol). Among all the selected thirty-five phytoconstituents, eriodictyol-7-glucuronide, stigmasterol, clicoemodin and thalirugidine showed the best interactions with a docking score of -9.1, -8.7, -8.4, and -8.4 kJ/mol. Based on the ADME screening, only two phytoconstituents namely stigmasterol and clicoemodin selected as the best inhibitor of HPV protein. MD simulation study also revealed that stigmasterol and clicoemodin were stable inside the binding pocket of 1R9W, Stigmasterol and clicoemodin can be used as a potential investigational drug to cure HPV infections.

Methylxanthines as Potential Inhibitor of SARS-CoV-2: an In Silico Approach

The aim of the present study was to test the binding affinity of methylxanthines (caffeine/theine, methylxanthine, theobromine, theophylline and xanthine) to three potential target proteins namely Spike protein (6LZG), main protease (6LU7) and nucleocapsid protein N-terminal RNA binding domain (6M3M) of SARS-CoV-2. Proteins and ligand were generated using AutoDock 1.5.6 software. Binding affinity of methylxanthines with SARS-CoV-2 target proteins was determined using Autodock Vina. MD simulation of the best interacting complexes was performed using GROMACS 2018.3 (in duplicate) and Desmond program version 2.0 (academic version) (in triplicate) to study the stabile interaction of protein-ligand complexes. Among the selected methylxanthines, theophylline showed the best binding affinity with all the three targets of SARS-CoV-2 (6LZG - 5.7 kcal mol^-1, 6LU7 - 6.5 kcal mol^-1, 6M3M - 5.8 kcal mol^-1). MD simulation results of 100 ns (in triplicate) showed that theophylline is stable in the binding pockets of all the selected SARS-CoV-2 proteins. Moreover, methylxanthines are safer and less toxic as shown by high LD₅₀ value with Protox II software as compared to drug chloroquine. This research supports the use of methylxanthines as a SARS-CoV-2 inhibitor. It also lays the groundwork for future studies and could aid in the development of a treatment for SARS-CoV-2 and related viral infections.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40495-021-00276-3.

In silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly

Currently, there is no specific treatment to cure COVID-19. Many medicinal plants have antiviral, antioxidant, antibacterial, antifungal, anticancer, wound healing etc. Therefore, the aim of the current study was to screen for potent inhibitors of N-terminal domain (NTD) of nucleocapsid phosphoprotein of SARS-CoV-2. The structure of NTD of RNA binding domain of nucleocapsid phosphoprotein of SARS coronavirus 2 was retrieved from the Protein Data Bank (PDB 6VYO) and the structures of 100 different phytocompounds were retrieved from Pubchem. The receptor protein and ligands were prepared using Schrodinger's Protein Preparation Wizard. Molecular docking was done by using the Schrodinger's maestro 12.0 software. Drug likeness and toxicity of active phytocompounds was predicted by using Swiss adme, admetSAR and protox II online servers. Molecular dynamic simulation of the best three protein- ligand complexes (alizarin, aloe-emodin and anthrarufin) was performed to study the interaction stability. We have identified three potential active sites (named as A, B, C) on receptor protein for efficient binding of the phytocompounds. We found that, among 100 phytocompounds, emodin, aloe-emodin, anthrarufin, alizarine, and dantron of Rheum emodi showed good binding affinity at all the three active sites of RNA binding domain of nucleocapsid phosphoprotein of COVID-19.The binding energies of emodin, aloe-emodin, anthrarufin, alizarine, and dantron were -8.299, -8.508, -8.456, -8.441, and -8.322 Kcal mol^-1 respectively (site A), -7.714, -6.433, -6.354, -6.598, and -6.99 Kcal mol^-1 respectively (site B), and -8.299, 8.508, 8.538, 8.841, and 8.322 Kcal mol^-1 respectively (site C). All the active phytocompounds follows the drug likeness properties, non-carcinogenic, and non-toxic. Theses phytocompounds (alone or in combination) could be developed into effective therapy against COVID-19. From MD simulation data, we found that all three complexes of 6VYO with alizarin, aloe-emodin and anthrarufin were stable up to 50 ns. These phytocompounds can be tested further for in vitro or in vivo and used as a potential drug to cure SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.

In silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly

Currently, there is no specific treatment to cure COVID-19. Many medicinal plants have antiviral, antioxidant, antibacterial, antifungal, anticancer, wound healing etc. Therefore, the aim of the current study was to screen for potent inhibitors of N-terminal domain (NTD) of nucleocapsid phosphoprotein of SARS-CoV-2. The structure of NTD of RNA binding domain of nucleocapsid phosphoprotein of SARS coronavirus 2 was retrieved from the Protein Data Bank (PDB 6VYO) and the structures of 100 different phytocompounds were retrieved from Pubchem. The receptor protein and ligands were prepared using Schrodinger's Protein Preparation Wizard. Molecular docking was done by using the Schrodinger's maestro 12.0 software. Drug likeness and toxicity of active phytocompounds was predicted by using Swiss adme, admetSAR and protox II online servers. Molecular dynamic simulation of the best three protein- ligand complexes (alizarin, aloe-emodin and anthrarufin) was performed to study the interaction stability. We have identified three potential active sites (named as A, B, C) on receptor protein for efficient binding of the phytocompounds. We found that, among 100 phytocompounds, emodin, aloe-emodin, anthrarufin, alizarine, and dantron of Rheum emodi showed good binding affinity at all the three active sites of RNA binding domain of nucleocapsid phosphoprotein of COVID-19.The binding energies of emodin, aloe-emodin, anthrarufin, alizarine, and dantron were -8.299, -8.508, -8.456, -8.441, and -8.322 Kcal mol^-1 respectively (site A), -7.714, -6.433, -6.354, -6.598, and -6.99 Kcal mol^-1 respectively (site B), and -8.299, 8.508, 8.538, 8.841, and 8.322 Kcal mol^-1 respectively (site C). All the active phytocompounds follows the drug likeness properties, non-carcinogenic, and non-toxic. Theses phytocompounds (alone or in combination) could be developed into effective therapy against COVID-19. From MD simulation data, we found that all three complexes of 6VYO with alizarin, aloe-emodin and anthrarufin were stable up to 50 ns. These phytocompounds can be tested further for in vitro or in vivo and used as a potential drug to cure SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.

Phytocompounds from Himalayan Medicinal Plants as Potential Drugs to Treat Multidrug-Resistant Salmonella typhimurium: An In Silico Approach

Medicinal plants can be used as natural therapeutics to treat diseases in humans. Enteric bacteria possess efflux pumps to remove bile salts from cells to avoid potential membrane damage. Resistance to bile and antibiotics is associated with the survival of Salmonella enterica subspecies enterica serovar Typhimurium (S. typhimurium) within a host. The present study aimed to investigate the binding affinity of major phytocompounds derived from 35 medicinal plants of the North Western Himalayas with the RamR protein (PDB ID 6IE9) of S. typhimurium. Proteins and ligands were prepared using AutoDock software 1.5.6. Molecular docking was performed using AutoDock Vina and MD simulation was performed at 100 ns. Drug likeness and toxicity predictions of hit phytocompounds were evaluated using molinspiration and ProTox II online servers. Moreover, docking, drug likeness, and toxicity results revealed that among all the selected phytocompounds, beta-sitosterol exhibited the most efficacious binding affinity with RamR protein (PDB ID 6IE9) and was nontoxic in nature. MD simulation data revealed that beta-sitosterol in complex with 6IE9 can be used as an antimicrobial. Furthermore, beta-sitosterol is stable in the binding pocket of the target protein; hence, it can be further explored as a drug to inhibit resistance-nodulation-division efflux pumps.

Phytocompounds of Rheum emodi, Thymus serpyllum, and Artemisia annua Inhibit Spike Protein of SARS-CoV-2 Binding to ACE2 Receptor: In Silico Approach

COVID-19, the disease caused by SARS-CoV-2, has been declared as a global pandemic. Traditional medicinal plants have long history to treat viral infections. Our in silico approach suggested that unique phytocompounds such as emodin, thymol and carvacrol, and artemisinin could physically bind SARS-CoV-2 spike glycoproteins (6VXX and 6VYB), SARS-CoV-2 B.1.351 South Africa variant of Spike glycoprotein (7NXA), and even with ACE2 and prevent the SARS-CoV-2 binding to the host ACE2, TMPRSS2 and neutrapilin-1 receptors. Since Chloroquine has been looked as potential therapy against COVID-19, we also compared the binding of chloroquine and artemisinin for its interaction with spike proteins (6VXX, 6VYB) and its variant 7NXA, respectively. Molecular docking study of phytocompounds and SARS-CoV-2 spike protein was performed by using AutoDock/Vina software. Molecular dynamics (MD) simulation was performed for 50ns. Among all the phytocompounds, molecular docking studies revealed lowest binding energy of artemisinin with 6VXX and 6VYB, with E_total -10.5 KJ mol^-1 and -10.3 KJ mol^-1 respectively. Emodin showed the best binding affinity with 6VYB with E_total -8.8 KJ mol^-1and SARS-CoV-2 B.1.351 variant (7NXA) with binding energy of -6.4KJ mol^-1. Emodin showed best interactions with TMPRSS 2 and ACE2 with E_total of -7.1 and -7.3 KJ mol^-1 respectively, whereas artemisinin interacts with TMPRSS 2 and ACE2 with E_total of -6.9 and -7.4 KJ mol^-1 respectively. All the phytocompounds were non-toxic and non-carcinogenic. MD simulation showed that artemisinin has more stable interaction with 6VYB as compared to 6VXX, and hence proposed as potential phytochemical to prevent SARS-CoV-2 interaction with ACE-2 receptor.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40495-021-00259-4.

Molecular docking studies of phytocompounds of Rheum emodi Wall with proteins responsible for antibiotic resistance in bacterial and fungal pathogens: in silico approach to enhance the bio-availability of antibiotics

Rheum emodi Wall. (Himalayan rhubarb) has many pharmacological activities such as antioxidant, antimicrobial, antiviral, anticancer and wound healing. The present study was aimed to understand if major phytocompounds of Rheum emodi could bind proteins responsible for antibiotic resistance in bacterial and fungal pathogens and enhance the potency of antibiotics. The major phytocompounds of R. emodi (emodin, rhein-13c6 and chrysophenol dimethy ether) were retrieved from the Pubchem and target proteins were retrieved from RCSB protein data bank. The docking study was performed by using AutoDock vina software and Molinspiration, swiss ADME servers were used for the determination of Lipinski rule of 5, drug-likeness prediction respectively, whereas, admetSAR and Protox-II tools were used for toxicity prediction. To study the docking accuracy of protein-ligand complexes, MD simulation for 100 ns was done by using Desmond program version 2.0 (Academic version). Among all the selected phytocompounds, emodin showed the best binding affinity against bacterial (Penicillin binding protein 3, 3VSL and fungal target (cytochrome P450 14 alpha-sterol demethylase 1EA1) with binding energy -8.2 and -8.0 Kcal mol^-1 respectively. Similarly, rhein-13C6 showed the best binding affinity against fungal target (n-myristoyl transferase 1IYL) with binding energy -8.0 Kcal mol^-1 which is higher than antibacterial and antifungal antibiotics. All the selected phytocompounds also fulfill Lipinski rule, non-carcinogenic and non-cytotoxic in nature. These compounds also showed high LD₅₀ value showing non-toxicity of these phytocompounds. MD simulation studies of phytocompounds (emodin and rhein-13C6) define the stability of protein-ligand complexes with in 100 ns time scale.Communicated by Freddie R. Salsbury.