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

Mandal, Sumit Kumar; Rehman, MD Muzaffar-Ur; Katyal, Ashish; Rajvanshi, Kanishk; Kannan, Manoj; Garg, Mohit; Murugesan, Sankaranarayanan; Deepa, P.R.

doi:10.1016/j.jtcme.2023.07.004

Cited by 4 publications

(2 citation statements)

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“…However, the in silico strategies used to study PHFs are not well understood. Several methods appear to be used to conduct in silico studies on PHFs [ 21 , 22 ]. This scoping review can thus help to identify the most effective in silico methods in this context and can further help to guide the design of future in silico studies on various types of PHFs used in traditional medicine.…”

Section: Discussionmentioning

confidence: 99%

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

Chandhiruthil Sathyan,

Yadav,

Gupta

et al. 2024

JMIR Res Protoc

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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

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Section: Discussionmentioning

confidence: 99%

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

Chandhiruthil Sathyan,

Yadav,

Gupta

et al. 2024

JMIR Res Protoc

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“…PF-07321332, named Nirmatrelvir, recently received approval for usage in conjunction with ritonavir . Remarkably, chemical ingredients originating from natural products, such as Traditional Chinese medicines (TCMs), Siddha Medicine, and Ayurvedic herbal formulations, have drawn increasing attention in the treatment of COVID-19 or inhibiting the target activities of SARS-CoV-2. − By targeting SARS-CoV-2 Mpro, a considerable number of compounds derived from TCMs were identified. For example, baicalin and baicalein from Shuanghuanglian were characterized as valuable noncovalent inhibitors of SARS-CoV-2 Mpro .…”

Section: Introductionmentioning

confidence: 99%

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

Jin,

Zhang,

et al. 2024

J. Chem. Inf. Model.

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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 IC 50 values of 4.

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

Singh,

Mittal,

Mittal

et al. 2024

Sci Rep

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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.

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

Cited by 4 publications

References 50 publications

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

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

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

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

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