Ligand-based virtual screening and molecular docking of two cytotoxic compounds isolated from Papaver lacerum

Bayazeid, Omer; Bedir, Erdal; Yalçın, Funda Nuray

doi:10.1016/j.phytol.2019.01.007

Cited by 7 publications

(5 citation statements)

References 20 publications

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“…The docking experiments were performed 100 times for each compound, and the 30 lowest energy conformations (poses) were recorded in order of increasing potential energy of the conformation in kcal/mol. For specific binding analysis, the best conformation for each compound was visualized and evaluated for analyses of binding modes between atoms or moieties of the ligands and specific residues of the target proteins [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of potential immunomodulators from Pulsatilla decoction that act on therapeutic targets for ulcerative colitis based on pharmacological activity, absorbed ingredients, and in-silico molecular docking

et al. 2022

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Background Pulsatilla decoction (Bai-Tou-Weng-Tang, BTWT) is a classic formula prescription of a traditional Chinese medicine that is used to treat ulcerative colitis (UC). However, its active components and underlying mechanism of action remain unclear. In the present study, we aimed to identify potential immunomodulators from BTWT that act at therapeutic targets for UC. Methods The protective effects of BTWT granules were examined in mice with colitis induced by dextran sulfate sodium. The absorbed components of BTWT were identified using LC-MS, and selected protein targets of these components in UC were investigated using molecular docking. Results Oral administration of BTWT granules significantly alleviated disease severity and colon shortening, and inhibited the inflammatory response in mice with chronic colitis. In these mice, 11 compounds from the BTWT granules were detected in the serum and/or colon. The molecular docking study demonstrated that compounds from Radix pulsatillae, such as anemoside A3, interacted with STAT3 and S1PR1; compounds from Rhizoma coptidis and/or Cortex phellodendri, such as palmatine, interacted with JAK3, PD-1, and PD-L1; and components of Cortex fraxini such as aesculin interacted with S1PR1, JAK3, STAT3 and PD-L1. Further in-vitro experiments showing that the compounds inhibited TNF-α and IL-6 production and STAT3 activation in RAW 264.7 cells suggested that these compounds have immunomodulatory activities. Conclusion We revealed for the first time that 11 absorbed ingredients from BTWT were immunomodulators against therapeutic targets for UC. These findings suggest that the identified compounds are the active components of BTWT, and the identified protein targets underlie the mechanism of action of BTWT against UC.

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Section: Methodsmentioning

confidence: 99%

Identification of potential immunomodulators from Pulsatilla decoction that act on therapeutic targets for ulcerative colitis based on pharmacological activity, absorbed ingredients, and in-silico molecular docking

et al. 2022

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“…Protein minimization was performed with the side chains kept rigid and the ligand flexible. The selected site was isolated and minimized followed by protonating the protein [ 19 ]. The natural product library (Catalog No.L1400) which is a collection of unique collection of 2370 natural products was used for docking.…”

Section: Methodsmentioning

confidence: 99%

Phenylethanoid glycosides as a possible COVID-19 protease inhibitor: a virtual screening approach

2021

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“…Protein minimization was performed with the side chains kept rigid and the ligand exible. The selected site was isolated and minimized followed by protonating the protein [19]. The natural product library (Catalog No.L1400) which is a collection of unique collection of 2370 natural products was used for docking.…”

Section: Methodsmentioning

confidence: 99%

“…The coronavirus disease (COVID- 19) was declared a global pandemic by the World Health Organization (WHO) in March 2020. Of notice, the virus can infect humans and animal causing a wide range of diseases.…”

Section: Introductionmentioning

confidence: 99%

Phenylethanoid glycosides as a possible COVID-19 protease inhibitor: a virtual screening approach

Bernardi

Ghaani

Bayazeid

2021

Preprint

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From the beginning of pandemic more than 100 million people have been infected with a death rate higher than 2%. Indeed, the current exit strategy involving the spreading of vaccines must be combined with progress in effective treatments development. This scenario is sadly supported by the vaccine’s immune activation time and the inequalities in the global immunization schedule. Bringing the crises under control means providing the world population with accessible and impactful new therapeutics. We screened a natural product library that contains a unique collection of 2370 natural products into the binding site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). According to the docking score and to the interaction at the active site, three phenylethanoid glycosides (forsythiaside A, isoacteoside and verbascoside) were selected. In order to provide better insight into the atomistic interaction and test the impact of the three selected compounds at the binding site, we resorted to a half microsecond-long molecular dynamics simulation. As a result, we are showing that forsythiaside A is the most stable molecule and it is likely to possess the highest inhibitory effect against SARS-CoV-2 Mpro. Phenylethanoid glycosides also have been reported to have both protease and kinase activity. This kinase inhibitory activity is very beneficial in fighting viruses inside the body as kinases are required for viral entry, metabolism, and/or reproduction. The dual activity (kinase/protease) of phenylethanoid glycosides makes them very promising anit-COVID-19 agents.

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Ligand-based virtual screening and molecular docking of two cytotoxic compounds isolated from Papaver lacerum

Cited by 7 publications

References 20 publications

Identification of potential immunomodulators from Pulsatilla decoction that act on therapeutic targets for ulcerative colitis based on pharmacological activity, absorbed ingredients, and in-silico molecular docking

Identification of potential immunomodulators from Pulsatilla decoction that act on therapeutic targets for ulcerative colitis based on pharmacological activity, absorbed ingredients, and in-silico molecular docking

Phenylethanoid glycosides as a possible COVID-19 protease inhibitor: a virtual screening approach

Phenylethanoid glycosides as a possible COVID-19 protease inhibitor: a virtual screening approach

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