In silico anti-viral assessment of phytoconstituents in a traditional (Siddha Medicine) polyherbal formulation - Targeting Mpro and pan-coronavirus post-fusion Spike protein

In vitro anti-inflammatory and in silico anti-viral assessment of phytoconstituents in polyherbal Ayurvedic formulation 'Arogyamrita Kwath'

BACKGROUND

Arogyamrita Kwath (AMK) is a polyherbal decoction comprising ten medicinal plants, viz., Albizia lebbeck, Andrographis paniculata, Tinospora cordifolia, Adhatoda vasica, Solanum xanthocarpum, Curcuma longa, Glycyrrhiza glabra, Terminalia bellirica, Withania somnifera and Trachyspermum ammi. The plants of the AMK formulation are traditionally used for the treatment of inflammation and respiratory ailments, but no scientific evidence has been reported so far for this formulation.

OBJECTIVES

To evaluate anti-inflammatory activity of AMK formulation in vitro and its fractions and to predict in silico anti-viral activity of identified potential phytoconstituents.

MATERIALS AND METHODS

The MTT cell cytotoxicity assay, nitric oxide (NO) inhibition assay and cytokines assay were carried out at concentrations 100 and 200 μg/mL. The phytoconstituents were identified by UPLC-PDA and UPLC-HRMS analyses. For pharmacoinformatics study molecular docking and molecular dynamics methods were used.

RESULTS

The study revealed that AMK significantly inhibited NO in comparison to dexamethasone (100 μg/mL) and pro-inflammatory cytokines in RAW264.7 cells. The three fractions, n-hexane, EtOAc and n-BuOH prepared from the AMK formulation were non-cytotoxic against RAW264.7 murine macrophage cells during MTT cytotoxicity assay and showed satisfactory results during cytokines assay. Ethyl acetate fraction contains active phytoconstituents in appreciable quantities. 16 phytoconstituents have been identified by UPLC-HRMS analysis in the formulation and four phytocompounds were quantified by UPLC-PDA. Molecular dynamics study helped in identifying two macromolecular targets (viral replicase and the membrane protein), which are relatively more important.

CONCLUSION

In the present study, anti-inflammatory activity of AMK was evaluated and the claimed anti-viral property was re-confirmed by molecular modelling in this work. The results clearly established that AMK showed remarkable anti-inflammatory and anti-viral activities.

In silico molecular screening of bioactive natural compounds of rosemary essential oil and extracts for pharmacological potentials against rhinoviruses

Rhinoviruses (RVs) cause upper respiratory tract infections and pneumonia in children and adults. These non-enveloped viruses contain viral coats of four capsid proteins: VP1, VP2, VP3, and VP4. The canyon on VP1 used cell surface receptor ICAM-1 as the site of attachment and for the internalization of viruses. To date, there has been no drug or vaccine available against RVs. In this study, bioactive natural compounds of rosemary (Salvia rosmarinus L.), which are known for their pharmacological potential, were considered to target the VP1 protein. A total of 30 bioactive natural compounds of rosemary were taken as ligands to target viral proteins. The PkCSM tool was used to detect their adherence to Lipinski's rule of five and the ADMET properties of the selected ligands. Further, the CB-Dock tool was used for molecular docking studies between the VP1 protein and ligands. Based on the molecular docking and ADMET profiling results, phenethyl amine (4 methoxy benzyl) was selected as the lead compound. A comparative study was performed between the lead compound and two antiviral drugs, Placonaril and Nitazoxanide, to investigate the higher potential of natural compounds over synthetic drugs. Placonaril also targets VP1 but failed in clinical trials while Nitazoxanide was examined in clinical trials against rhinoviruses. It was discovered from this study that the (4 methoxy benzyl) phenethyl amine exhibited less toxicity in comparison to other tested drugs against RVs. More research is needed to determine its potential and make it a good medication against RVs.

In Silico Approaches to Polyherbal Synergy: Protocol for a Scoping Review

BACKGROUND

According to the World Health Organization, more than 80% of the world's population relies on traditional medicine. Traditional medicine is typically based on the use of single herbal drugs or polyherbal formulations (PHFs) to manage diseases. However, the probable mode of action of these formulations is not well studied or documented. Over the past few decades, computational methods have been used to study the molecular mechanism of phytochemicals in single herbal drugs. However, the in silico methods applied to study PHFs remain unclear.

OBJECTIVE

The aim of this protocol is to develop a search strategy for a scoping review to map the in silico approaches applied in understanding the activity of PHFs used as traditional medicines worldwide.

METHODS

The scoping review will be conducted based on the methodology developed by Arksey and O'Malley and the recommendations of the Joanna Briggs Institute (JBI). A set of predetermined keywords will be used to identify the relevant studies from five databases: PubMed, Embase, Science Direct, Web of Science, and Google Scholar. Two independent reviewers will conduct the search to yield a list of relevant studies based on the inclusion and exclusion criteria. Mendeley version 1.19.8 will be used to remove duplicate citations, and title and abstract screening will be performed with Rayyan software. The JBI System for the Unified Management, Assessment, and Review of Information tool will be used for data extraction. The scoping review will be reported based on the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines.

RESULTS

Based on the core areas of the scoping review, a 3-step search strategy was developed. The initial search produced 3865 studies. After applying filters, 875 studies were short-listed for further review. Keywords were further refined to yield more relevant studies on the topic.

CONCLUSIONS

The findings are expected to determine the extent of the knowledge gap in the applications of computational methods in PHFs for any traditional medicine across the world. The study can provide answers to open research questions related to the phytochemical identification of PHFs, criteria for target identification, strategies applied for in silico studies, software used, and challenges in adopting in silico methods for understanding the mechanisms of action of PHFs. This study can thus provide a better understanding of the application and types of in silico methods for investigating PHFs.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/56646.

Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine

Traditional Chinese medicine (TCM) has been extensively employed for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is demand for discovering more SARS-CoV-2 Mpro inhibitors with diverse scaffolds to optimize anti-SARS-CoV-2 lead compounds. In this study, comprehensive in silico and in vitro assays were utilized to determine the potential inhibitors from TCM compounds against SARS-CoV-2 Mpro, which is an important therapeutic target for SARS-CoV-2. The ensemble docking analysis of 18263 TCM compounds against 15 SARS-CoV-2 Mpro conformations identified 19 TCM compounds as promising candidates. Further in vitro testing validated three compounds as inhibitors of SARS-CoV-2 Mpro and showed IC50 values of 4.64 ± 0.11, 7.56 ± 0.78, and 11.16 ± 0.26 μM, with EC50 values of 12.25 ± 1.68, 15.58 ± 0.77, and 29.32 ± 1.25 μM, respectively. Molecular dynamics (MD) simulations indicated that the three complexes remained stable over the last 100 ns of production run. An analysis of the binding mode revealed that the active compounds occupy different subsites (S1, S2, S3, and S4) of the active site of SARS-CoV-2 Mpro via specific poses through noncovalent interactions with key amino acids (e.g., HIS 41, ASN 142, GLY 143, MET 165, GLU 166, or GLN 189). Overall, this study provides evidence indicating that the three natural products obtained from TCM could be further used for anti-COVID-19 research, justifying the investigation of Chinese herbal medicinal ingredients as bioactive constituents for therapeutic targets.

The Therapeutic Potential of Natural Dietary Flavonoids against SARS-CoV-2 Infection

The exploration of non-toxic and cost-effective dietary components, such as epigallocatechin 3-gallate and myricetin, for health improvement and disease treatment has recently attracted substantial research attention. The recent COVID-19 pandemic has provided a unique opportunity for the investigation and identification of dietary components capable of treating viral infections, as well as gathering the evidence needed to address the major challenges presented by public health emergencies. Dietary components hold great potential as a starting point for further drug development for the treatment and prevention of SARS-CoV-2 infection owing to their good safety, broad-spectrum antiviral activities, and multi-organ protective capacity. Here, we review current knowledge of the characteristics-chemical composition, bioactive properties, and putative mechanisms of action-of natural bioactive dietary flavonoids with the potential for targeting SARS-CoV-2 and its variants. Notably, we present promising strategies (combination therapy, lead optimization, and drug delivery) to overcome the inherent deficiencies of natural dietary flavonoids, such as limited bioavailability and poor stability.