Computational biological activity and pharmacological properties analysis for anticancer Cyperus rotundus bioactive compounds

Nafisah, Wirdatun; Pinanti, Honesty Nurizza; Christina, Yuyun Ika; Rifa’i, Muhaimin; Djati, Muhammad Sasmito

doi:10.1063/5.0052746

Cited by 2 publications

(2 citation statements)

References 18 publications

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“…The output generated indicates two possibilities Pi (to be inactive) and Pa (to be active). If Pa>Pi, the possibility of biological activity is maximum and Pa should be greater than the cut‐off value 0.7 for stronger possibilities [41] . The molecular targets of the compounds were found using (http://www.swisstargetprediction.ch/) [42,43] and (https://prediction.charite.de/subpages/target_prediction.php) [44] servers.…”

Section: Methodsmentioning

confidence: 99%

In Silico Antiviral Drug Repurposing Against COVID‐19 Infection: Targeting the Main Protease and Human ACE2 Receptor

Rupavarshini,

Karthikeyan

2023

ChemistrySelect

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Coronavirus Disease‐2019 (COVID‐19) is a highly contagious respiratory illness caused by a novel coronavirus known as SARS‐CoV‐2. The virus exerts its pathogenic activity and infects new cells by utilizing the spike protein (S1) of the coronavirus and the Angiotensin‐converting enzyme 2 (ACE2) receptor protein found in host cells, thereby transferring the genetic material. The SARS‐CoV‐2 main protease, essential for viral replication, presents a promising therapeutic target due to its structural and sequence similarity with other beta coronaviruses, facilitating drug development from existing lead compounds. With this context, we have considered SARS‐CoV‐2 Main protease and spike protein combined with ACE2 receptor as the target protein for inhibiting the replication. In this study, we employed High‐Throughput Virtual Screening (HTVS) to screen antiviral compounds from the drug bank. Based on the docking score, two compounds were screened with respect to the selected target proteins. Subsequently, Molecular docking investigations were conducted for compound A and compound B concerning the main protease and ACE2 receptor, which yields favorable docking scores of −8.212 kcal/mol and −9.373 kcal/mol, respectively. Further molecular dynamics, DFT studies and ADMET parameters were carried out to understand the stability, reactivity, and toxicity profile of the screened compounds.

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Section: Methodsmentioning

confidence: 99%

In Silico Antiviral Drug Repurposing Against COVID‐19 Infection: Targeting the Main Protease and Human ACE2 Receptor

Rupavarshini,

Karthikeyan

2023

ChemistrySelect

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“…The compound's SMILES or mol.file was inserted to predict the biological activities, and the probability to be active (Pa) cut-off value was set for Pa > 0.5. The higher the Pa value, the more accurate the prediction results (Nafisah et al, 2021).…”

Section: Biological Activity Analysismentioning

confidence: 99%

Anti-inflammatory and antioxidant potential of Syzygium polyanthum (Wight) Walp. bioactive compounds in polycystic ovary syndrome: An in silico study

Aditya¹,

Santoso²

2022

J Pharm Pharmacogn Res

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Context: Polycystic ovary syndrome (PCOS) is significantly associated with inflammation and oxidative stress. Syzygium polyanthum is a plant rich in pharmacological properties. Aims: To evaluate the anti-inflammation and antioxidant potential of S. polyanthum bioactive compounds using in silico approach. Methods: The S. polyanthum was extracted using the ultrasound-assisted extraction (UAE) method, and the bioactive compounds were screened using Liquid Chromatography–High Resolution Mass Spectrometry (LC-HRMS) analysis. This study predicted the biological activity of S. polyanthum compounds using PASS Online server. Before docking, we analyzed the protein-protein interactions (PPIs) network of TNFα, NF-kB, SOD, and KEAP1. The molecular docking was done using Autodock Vina in PyRx software and visualized using Discovery Studio. Probability to be active (Pa) was determined. Results: The bioactive compounds found in S. polyanthum and used in this study were deoxyphomalone, NCGC00169066-01, and phloretin with retention times [min] of 0.886, 0.907, and 8.323, respectively. The predicted biological activity of compounds and controls were anti-inflammatory, immunosuppressant, TNF expression inhibitor, immunomodulatory and HIF1α expression inhibitor (Pa>0.5 for all S. polyanthum compounds and Pa<0.5 for SPD304, MG-132, and MDF). Based on PPIs network analysis, TNFα, NF-kB, SOD, and KEAP1 are associated. The molecular docking analysis showed that deoxyphomalone, NCGC00169066-01, and phloretin had inhibition potential against TNFα and NF-kB, and activation potential against SOD, due to several residues involved in the interaction of compounds-protein was the same as the interaction of inhibitor (SPD-304 and MG-132) and activator (gallic acid) control against the protein. The residues may have the same inhibition or activation mechanism as the control. However, S. polyanthum bioactive compounds may still have inhibition potential against KEAP1 through Ala548 residue that is also involved in the interaction of DMF-KEAP1. Conclusions: The bioactive compounds of S. polyanthum showed anti-inflammation and antioxidant potential, which may have a good effect in the treatment of PCOS, yet still need to be confirmed in vitro or in vivo research.

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Computational biological activity and pharmacological properties analysis for anticancer Cyperus rotundus bioactive compounds

Cited by 2 publications

References 18 publications

In Silico Antiviral Drug Repurposing Against COVID‐19 Infection: Targeting the Main Protease and Human ACE2 Receptor

In Silico Antiviral Drug Repurposing Against COVID‐19 Infection: Targeting the Main Protease and Human ACE2 Receptor

Anti-inflammatory and antioxidant potential of Syzygium polyanthum (Wight) Walp. bioactive compounds in polycystic ovary syndrome: An in silico study

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