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Article

In Silico Identification of Natural Product-Based Inhibitors Targeting IL-1β/IL-1R Protein–Protein Interface

by
Ting-ting Liu
1,
Yan-kun Chen
1,
Muhammad Adil
2,3,
Mazen Almehmadi
4,*,
Fahad M. Alshabrmi
5,
Mamdouh Allahyani
4,
Ahad Amer Alsaiari
4,
Pei Liu
1,
Muhammad Raheel Khan
6,7 and
Qinghua Peng
1,*
1
School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha 410200, China
2
Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi 46000, Pakistan
3
Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland
4
Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
5
Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
6
Centre of Polymer and Carbon Materials, Polish Academy of Sciences, ul. Sklodowskiej-Curie 34, 41-819 Zabrze, Poland
7
Department of Chemical Sciences, Joint Doctoral School, Silesian University of Technology, 44-100 Gliwice, Poland
*
Authors to whom correspondence should be addressed.
Molecules 2023, 28(13), 4885; https://doi.org/10.3390/molecules28134885
Submission received: 8 May 2023 / Revised: 9 June 2023 / Accepted: 19 June 2023 / Published: 21 June 2023
(This article belongs to the Special Issue Bioactivities and In Silico Study of Phytochemicals)
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Abstract

IL-1β mediates inflammation and regulates immune responses, cell proliferation, and differentiation. Dysregulation of IL-1β is linked to inflammatory and autoimmune diseases. Elevated IL-1β levels are found in patients with severe COVID-19, indicating its excessive production may worsen the disease. Also, dry eye disease patients show high IL-1β levels in tears and conjunctival epithelium. Therefore, IL-1β signaling is a potential therapeutic targeting for COVID-19 and aforementioned diseases. No small-molecule IL-1β inhibitor is clinically approved despite efforts. Developing such inhibitors is highly desirable. Herein, a docking-based strategy was used to screen the TCM (Traditional Chinese Medicine) database to identify possible IL-1β inhibitors with desirable pharmacological characteristics by targeting the IL-1β/IL-1R interface. Primarily, the docking-based screening was performed by selecting the crucial residues of IL-1β interface to retrieve the potential compounds. Afterwards, the compounds were shortlisted on the basis of binding scores and significant interactions with the crucial residues of IL-1β. Further, to gain insights into the dynamic behavior of the protein–ligand interactions, MD simulations were performed. The analysis suggests that four selected compounds were stabilized in an IL-1β pocket, possibly blocking the formation of an IL-1β/IL-1R complex. This indicates their potential to interfere with the immune response, making them potential therapeutic agents to investigate further.
Keywords: IL-1β; virtual screening; molecular docking; MD simulation; natural products IL-1β; virtual screening; molecular docking; MD simulation; natural products

Share and Cite

MDPI and ACS Style

Liu, T.-t.; Chen, Y.-k.; Adil, M.; Almehmadi, M.; Alshabrmi, F.M.; Allahyani, M.; Alsaiari, A.A.; Liu, P.; Khan, M.R.; Peng, Q. In Silico Identification of Natural Product-Based Inhibitors Targeting IL-1β/IL-1R Protein–Protein Interface. Molecules 2023, 28, 4885. https://doi.org/10.3390/molecules28134885

AMA Style

Liu T-t, Chen Y-k, Adil M, Almehmadi M, Alshabrmi FM, Allahyani M, Alsaiari AA, Liu P, Khan MR, Peng Q. In Silico Identification of Natural Product-Based Inhibitors Targeting IL-1β/IL-1R Protein–Protein Interface. Molecules. 2023; 28(13):4885. https://doi.org/10.3390/molecules28134885

Chicago/Turabian Style

Liu, Ting-ting, Yan-kun Chen, Muhammad Adil, Mazen Almehmadi, Fahad M. Alshabrmi, Mamdouh Allahyani, Ahad Amer Alsaiari, Pei Liu, Muhammad Raheel Khan, and Qinghua Peng. 2023. "In Silico Identification of Natural Product-Based Inhibitors Targeting IL-1β/IL-1R Protein–Protein Interface" Molecules 28, no. 13: 4885. https://doi.org/10.3390/molecules28134885

APA Style

Liu, T.-t., Chen, Y.-k., Adil, M., Almehmadi, M., Alshabrmi, F. M., Allahyani, M., Alsaiari, A. A., Liu, P., Khan, M. R., & Peng, Q. (2023). In Silico Identification of Natural Product-Based Inhibitors Targeting IL-1β/IL-1R Protein–Protein Interface. Molecules, 28(13), 4885. https://doi.org/10.3390/molecules28134885

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