GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro

More-Adate, Pallavi; Lokhande, Kiran Bharat; Swamy, K. Venkateswara; Nagar, Shuchi; Baheti, Akshay

doi:10.1016/j.compbiomed.2022.105679

Cited by 14 publications

(4 citation statements)

References 88 publications

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“…Their strategic positioning within the binding pocket ensures that they make crucial contacts with the ligand, anchoring and stabilizing the binding complex. Moreover these binding site residues were verified through an extensive literature survey ( Shah et al, 2019 , Taidi et al, 2022 , More-Adate et al, 2022 ).…”

Section: Methodsmentioning

confidence: 93%

In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2)

Revankar,

Bagewadi,

Shaikh

et al. 2023

Saudi Journal of Biological Sciences

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Section: Methodsmentioning

confidence: 93%

In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2)

Revankar,

Bagewadi,

Shaikh

et al. 2023

Saudi Journal of Biological Sciences

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“…Furthermore, 50,000 steps of minimization and 100 ns of unrestrained MD were performed. Then, short-range electrostatic and van der Waals interactions were computed with a distance cut-off of 1.0 nm 18 , 44 , 45 . After equilibration, coordinates were saved every 2 ps during the sampling process.…”

Section: Methodsmentioning

confidence: 99%

The novel anti-cancer feature of Brazzein through activating of hTLR5 by integration of biological evaluation: molecular docking and molecular dynamics simulation

Poursalim

Shasaltaneh

Jafarian

et al. 2022

Sci Rep

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Many of plant proteins exhibit the properties similar to the antitumor proteins although the anticancer activity of Brazzein on modulating the autophagy signaling pathway has not been determined so far. The present study aimed to develop a simplified system to enable the rational design of the activating extracellular domain of human Toll-like receptor 5 (hTLR5). To identify the anticancer effect of Brazzein, HADDOCK program and molecular dynamics (MD) simulation were applied to examine the binding of the wild type (WT) and p.A19K mutant of Brazzein to the TLR5. The expression of MAP1S and TNF-α genes was estimated based on real-time PCR. The results clearly confirmed that the WT of Brazzein activated hTLR5 in the MCF-7 cell line since the genes were more and significantly less expressed in the cells treated with the WT and p.A19K mutant than the control, respectively. The snapshots of MD simulation exhibit the consistent close interactions of hTLR5 with the two helices of Brazzein on its lateral side. The results of per residue-free energy decomposition analysis substantiate those of intermolecular contact analysis perfectly one. We propose that the WT of Brazzein can act as an antitumor drug candidate.

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“…ANPELA 1.0 has become popular and indispensable as an instructive tool in quantitative bulk proteomics for disease prediction, [1][2][3] biomarker discovery, [4][5][6] innovative drug target identification, [7,8] novel peptide exploration, [9,10] experimental scheme establishment, [11] bioinformatic algorithm comparison, and development. [12][13][14] Although bulk proteome profiling has become progressively quantitative and comprehensive, [12,15] it has historically been limited to the relatively large sample cohorts required to satisfy an in-depth measurement, which typically represents a population average and obscure significant cellular heterogeneity.…”

Section: Introductionmentioning

confidence: 99%

ANPELA: Significantly Enhanced Quantification Tool for Cytometry‐Based Single‐Cell Proteomics

et al. 2023

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ANPELA is widely used for quantifying traditional bulk proteomic data. Recently, there is a clear shift from bulk proteomics to the single-cell ones (SCP), for which powerful cytometry techniques demonstrate the fantastic capacity of capturing cellular heterogeneity that is completely overlooked by traditional bulk profiling. However, the in-depth and high-quality quantification of SCP data is still challenging and severely affected by the large numbers of quantification workflows and extreme performance dependence on the studied datasets. In other words, the proper selection of well-performing workflow(s) for any studied dataset is elusory, and it is urgently needed to have a significantly enhanced and accelerated tool to address this issue. However, no such tool is developed yet. Herein, ANPELA is therefore updated to its 2.0 version (https://idrblab.org/anpela/), which is unique in providing the most comprehensive set of quantification alternatives (>1000 workflows) among all existing tools, enabling systematic performance evaluation from multiple perspectives based on machine learning, and identifying the optimal workflow(s) using overall performance ranking together with the parallel computation. Extensive validation on different benchmark datasets and representative application scenarios suggest the great application potential of ANPELA in current SCP research for gaining more accurate and reliable biological insights.

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GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro

Cited by 14 publications

References 88 publications

In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2)

In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2)

The novel anti-cancer feature of Brazzein through activating of hTLR5 by integration of biological evaluation: molecular docking and molecular dynamics simulation

ANPELA: Significantly Enhanced Quantification Tool for Cytometry‐Based Single‐Cell Proteomics

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