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Li K, Cai J, Jiang Z, Meng Q, Meng Z, Xiao H, Chen G, Qiao C, Luo L, Yu J, Li X, Wei Y, Li H, Liu C, Shen B, Wang J, Feng J. Unveiling novel insights into human IL-6 - IL-6R interaction sites through 3D computer-guided docking and systematic site mutagenesis. Sci Rep 2024; 14:18293. [PMID: 39112658 PMCID: PMC11306327 DOI: 10.1038/s41598-024-69429-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
The cytokine interleukin-6 (IL-6) plays a crucial role in autoimmune and inflammatory diseases. Understanding the precise mechanism of IL-6 interaction at the amino acid level is essential to develop IL-6-inhibiting compounds. In this study, we employed computer-guided drug design tools to predict the key residues that are involved in the interaction between IL-6 and its receptor IL-6R. Subsequently, we generated IL-6 mutants and evaluated their binding affinity to IL-6R and the IL-6R - gp130 complex, as well as monitoring their biological activities. Our findings revealed that the R167A mutant exhibited increased affinity for IL-6R, leading to enhanced binding to IL-6R - gp130 complex and subsequently elevated intracellular phosphorylation of STAT3 in effector cells. On the other hand, although E171A reduced its affinity for IL-6R, it displayed stronger binding to the IL-6R - gp130 complex, thereby enhancing its biological activity. Furthermore, we identified the importance of R178 and R181 for the precise recognition of IL-6 by IL-6R. Mutants R181A/V failed to bind to IL-6R, while maintaining an affinity for the IL-6 - gp130 complex. Additionally, deletion of the D helix resulted in complete loss of IL-6 binding affinity for IL-6R. Overall, this study provides valuable insights into the binding mechanism of IL-6 and establishes a solid foundation for future design of novel IL-6 inhibitors.
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Affiliation(s)
- Kaitong Li
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Junyu Cai
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Zhiyang Jiang
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Qingbin Meng
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Zhao Meng
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - He Xiao
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Guojiang Chen
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Chunxia Qiao
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Longlong Luo
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jijun Yu
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xinying Li
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yinxiang Wei
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Hui Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Chenghua Liu
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Beifen Shen
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jing Wang
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Jiannan Feng
- Laboratory for Genetic Engineering of Antibodies and Functional Proteins, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
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Shamkh IM, Elkazzaz M, Radwan ES, Najeeb J, Rehman MT, AlAjmi MF, Shahwan M, Sufyan M, Alaqeel NK, Ibrahim IA, Jabbar B, Khan MS, Karpiński TM, Haikal A, Aljowaie RM, Almutairi SM, Ahmed A. AI-driven Discovery of Celecoxib and Dexamethasone for Exploring their Mode of Action as Human Interleukin (IL-6) Inhibitors to Treat COVID-19-induced Cytokine Storm in Humans. Curr Pharm Des 2023; 29:2752-2762. [PMID: 37921134 DOI: 10.2174/0113816128260449231017091824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/31/2023] [Accepted: 08/25/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND In the case of COVID-19 patients, it has been observed that the immune system of the infected person exhibits an extreme inflammatory response known as cytokine release syndrome (CRS) where the inflammatory cytokines are swiftly produced in quite large amounts in response to infective stimuli. Numerous case studies of COVID-19 patients with severe symptoms have documented the presence of higher plasma concentrations of human interleukin-6 (IL-6), which suggests that IL-6 is a crucial factor in the pathophysiology of the disease. In order to prevent CRS in COVID-19 patients, the drugs that can exhibit binding interactions with IL-6 and block the signaling pathways to decrease the IL-6 activity may be repurposed. METHODS This research work focused on molecular docking-based screening of the drugs celecoxib (CXB) and dexamethasone (DME) to explore their potential to interact with the binding sites of IL-6 protein and reduce the hyper-activation of IL-6 in the infected personnel. RESULTS Both of the drugs were observed to bind with the IL-6 (IL-6 receptor alpha chain) and IL-6Rα receptor with the respective affinities of -7.3 kcal/mol and -6.3 kcal/mol, respectively, for CXB and DME. Moreover, various types of binding interactions of the drugs with the target proteins were also observed in the docking studies. The dynamic behaviors of IL-6/IL-6Rα in complex with the drugs were also explored through molecular dynamics simulation analysis. The results indicated significant stabilities of the acquired drug-protein complexes up to 100 ns. CONCLUSION The findings of this study have suggested the potential of the drugs studied to be utilized as antagonists for countering CRS in COVID-19 ailment. This study presents the studied drugs as promising candidates both for the clinical and pre-clinical treatment of COVID-19.
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Affiliation(s)
- Israa M Shamkh
- Chemo and Bioinformatics Lab, Bio Search Research Institution BSRI, Giza 12613, Egypt
| | - Mahmoud Elkazzaz
- Department of Chemistry and Biochemistry, Faculty of Science, Damietta University, Damietta 7952567, Egypt
| | - Enas S Radwan
- Faculty of Science, Zarqa University, Zarqa 13132, Jordan
| | - Jawayria Najeeb
- Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nouf Khalifa Alaqeel
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Ibrahim A Ibrahim
- Botany and Microbiology Department (Biotechnology Program), Faculty of Science, Damietta University, Damietta, Egypt
| | - Basit Jabbar
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mohammad Shahbaz Khan
- Children's National Hospital, George Washington University, Washington, DC 20010, USA
| | - Tomasz M Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, Poznań 61-712, Poland
| | - Abdullah Haikal
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Reem M Aljowaie
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Amr Ahmed
- Director of Tuberculosis Ghubera Mobile Team, Public Health Department, First Health Cluster, Ministry of Health, Riyadh 966-11, Saudi Arabia
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Bhavaniramya S, Sibiya A, Alothaim AS, Al Othaim A, Ramar V, Veluchamy A, Manikandan P, Vaseeharan B. Evaluating the structural and immune mechanism of Interleukin-6 for the investigation of goat milk peptides as potential treatments for COVID-19. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:101924. [PMID: 35233153 PMCID: PMC8875951 DOI: 10.1016/j.jksus.2022.101924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
The function of Immune control, haematopoiesis, and inflammation all depend on the cytokine Interleukin 6 (IL-6), and higher expression of IL-6 is seen in COVID-19 and other diseases. The immune protein IL-6 activation is dependent on binding interactions with IL-6Rα, mIL-6R, and sIL-6R for its cellular function. Termination of these reaction could benefit for controlling the over-expression in COVID-19 patients and that may arise as inhibitors for controlling COVID-19. Traditionally, the goat milk has been prescribed as medicine in ayurvedic practice and through this work, we have explored the benefits of peptides from goat milk as IL-6 inhibitors, and it have the potential of inhibiting the over expression of IL-6 and control the COVID-19 disease. Computational experiments have shown that goat peptides had strong interactions with IL-6, with higher scoring profiles and energy efficiency ranging from −6.00 kcal/mol to −9.00 kcal/mol in docking score and −39.00 kcal/mol in binding energy. Especially the YLGYLEQLLR, VLVLDTDYK and AMKPWIQPK peptides from goat milk holds better scoring and shows strong interactions were identified as the most potential IL-6 inhibitor candidates in this study. Peptides from Goat proteins, which are capable of binding to the IL-6 receptor with strong binding conformations, have no negative effects on other immune system proteins.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Ayoub Al Othaim
- Department of Medical Laboratories, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli 620024, India
| | - Alaguraj Veluchamy
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Palanisamy Manikandan
- Department of Medical Laboratories, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia
- Greenlink Analytical and Research Laboratory, India Private Limited, Coimbatore 641 014, India
| | - Baskaralingam Vaseeharan
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen S, Coates L, Cooper C, Demerdash O, Daidone I, Eblen J, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller D, Kovalevsky A, Larkin J, Lawrence T, LeGrand S, Liu SH, Mitchell J, Park G, Parks J, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith J, Smith M, Soto C, Tsaris A, Thavappiragasam M, Tillack A, Vermaas J, Vuong V, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J Chem Inf Model 2020; 60:5832-5852. [PMID: 33326239 PMCID: PMC7754786 DOI: 10.1021/acs.jcim.0c01010] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
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Affiliation(s)
- A. Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - R. Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M. Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - J. Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - D. Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - S. Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - K. G. Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - S.Y. Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - L. Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C.J. Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - O. Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - I. Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, I-67010 L’Aquila, Italy
| | - J.D. Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - S. Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536, USA
| | - S. Forli
- Scripps Research, La Jolla, CA, 92037, USA
| | - J. Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - J. C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - J. Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121, USA
| | - O. Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - D.W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - A. Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Larkin
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - T.J. Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - S.-H. Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - J.C. Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - G. Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - J.M. Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - A. Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - L. Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - D. Poole
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - L. Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439, USA
| | - D. Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - A. Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - Y. Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - J.C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - M.D. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - C. Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - J.V. Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - V.Q. Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - J. Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - S. Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - M. Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201, USA
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