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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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Harmalkar DS, Sivaraman A, Nada H, Lee J, Kang H, Choi Y, Lee K. Natural products as IL-6 inhibitors for inflammatory diseases: Synthetic and SAR perspective. Med Res Rev 2024; 44:1683-1726. [PMID: 38305581 DOI: 10.1002/med.22022] [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: 03/28/2022] [Revised: 09/07/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
Interleukin-6 (IL-6), a pleiotropic cytokine, plays a pivotal role in the pathophysiology of various diseases including diabetes, atherosclerosis, Alzheimer's disease, multiple myeloma, rheumatoid arthritis, and prostate cancer. The signaling pathways associated with IL-6 offer promising targets for therapeutic interventions in inflammatory diseases and IL-6-dependent tumors. Although certain anti-IL-6 monoclonal antibodies are currently employed clinically, their usage is hampered by drawbacks such as high cost and potential immunogenicity, limiting their application. Thus, the imperative arises to develop novel small non-peptide molecules acting as IL-6 inhibitors. Various natural products derived from diverse sources have been investigated for their potential to inhibit IL-6 activity. Nevertheless, these natural products remain inadequately explored in terms of their structure-activity relationships. In response, our review aims to provide syntheses and structure activity perspective of natural IL-6 inhibitors. The comprehensive amalgamation of information presented in this review holds the potential to serve as a foundation for forthcoming research endeavors by medicinal chemists, facilitating the design of innovative IL-6 inhibitors to address the complexities of inflammatory diseases.
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Affiliation(s)
- Dipesh S Harmalkar
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
- Department of Chemistry, Government College of Arts, Science & Commerce, Sanquelim, Goa, India
| | - Aneesh Sivaraman
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Hossam Nada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
| | - Joohan Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
| | - Hyeseul Kang
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
| | - Yongseok Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
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Mori C, Nagatoishi S, Matsunaga R, Kuroda D, Nakakido M, Tsumoto K. Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex. Biochem Biophys Res Commun 2023; 682:174-179. [PMID: 37820452 DOI: 10.1016/j.bbrc.2023.10.010] [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: 09/19/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
Interleukin-11 (IL-11) is a member of the interleukin-6 (IL-6) family of cytokines. IL-11 is a regulator of multiple events in hematopoiesis, and IL-11-mediated signaling is implicated in inflammatory disease, cancer, and fibrosis. All IL-6 family cytokines signal through the signal-transducing receptor, glycoprotein 130 (gp130), but these cytokines have distinct as well as overlapping biological functions. To understand IL-11 signaling at the molecular level, we performed a comprehensive interaction analysis of the IL-11 signaling complex, comparing it with the IL-6 complex, one of the best-characterized cytokine complexes. Our thermodynamic analysis revealed a clear difference between IL-11 and IL-6. Surface plasmon resonance analysis showed that the interaction between IL-11 and IL-11 receptor α (IL-11Rα) is entropy driven, whereas that between IL-6 and IL-6 receptor α (IL-6Rα) is enthalpy driven. Our analysis using isothermal titration calorimetry revealed that the binding of gp130 to the IL-11/IL-11Rα complex results in entropy loss, but that the interaction of gp130 with the IL-6/IL-6Rα complex results in entropy gain. Our hydrogen-deuterium exchange mass spectrometry experiments suggested that the D2 domain of gp130 was not involved in IL-6-like interactions in the IL-11/IL-11Rα complex. It has been reported that IL-6 interaction with gp130 in the signaling complex was characterized through the hydrophobic interface located in its D2 domain of gp130. Our findings suggest that unique interactions of the IL-11 signaling complex with gp130 are responsible for the distinct biological activities of IL-11 compared to IL-6.
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Affiliation(s)
- Chinatsu Mori
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Ryo Matsunaga
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Makoto Nakakido
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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Grubbe WS, Byléhn F, Alvarado W, de Pablo JJ, Mendoza JL. Molecular analysis of the type III interferon complex and its applications in protein engineering. Biophys J 2023; 122:4254-4263. [PMID: 37794680 PMCID: PMC10645568 DOI: 10.1016/j.bpj.2023.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Type III interferons (IFNλs) are cytokines with critical roles in the immune system and are attractive therapeutic candidates due to their tissue-specific activity. Despite entering several clinical trials, results have demonstrated limited efficacy and potency, partially attributed to low-affinity protein-protein interactions (PPIs) responsible for receptor complex formation. Subsequently, structural studies of the native IFNλ signaling complexes remain inaccessible. While protein engineering can overcome affinity limitations, tools to investigate low-affinity systems like these remain limited. To provide insights into previous efforts to strengthen the PPIs within this complex, we perform a molecular analysis of the extracellular ternary complexes of IFNλ3 using both computational and experimental approaches. We first use molecular simulations and modeling to quantify differences in PPIs and residue strain fluctuations, generate detailed free energy landscapes, and reveal structural differences between an engineered, high-affinity complex, and a model of the wild-type, low-affinity complex. This analysis illuminates distinct behaviors of these ligands, yielding mechanistic insights into IFNλ complex formation. We then apply these computational techniques in protein engineering and design by utilizing simulation data to identify hotspots of interaction to rationally engineer the native cytokine-receptor complex for increased stability. These simulations are then validated by experimental techniques, showing that a single mutation at a computationally predicted site of interaction between the two receptors increases PPIs and improves complex formation for all IFNλs. This study highlights the power of molecular dynamics simulations for protein engineering and design as applied to the IFNλ family but also presents a potential tool for analysis and engineering of other systems with low-affinity PPIs.
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Affiliation(s)
- William S Grubbe
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Fabian Byléhn
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Walter Alvarado
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Argonne National Laboratory, Lemont, Illinois
| | - Juan L Mendoza
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois.
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Gupta M, Ha K, Agarwal R, Quarles LD, Smith JC. Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor. Proteins 2020; 89:163-173. [PMID: 32881084 DOI: 10.1002/prot.26002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/26/2020] [Accepted: 08/25/2020] [Indexed: 11/07/2022]
Abstract
Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. Here, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.
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Affiliation(s)
- Madhulika Gupta
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
| | - Khanh Ha
- Tickle College of Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
| | - Leigh Darryl Quarles
- Division of Nephrology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
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Sousa RP, Laurent AD, Quéméner A, Mortier E, Questel JYL. Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations. Molecules 2019; 24:molecules24183261. [PMID: 31500206 PMCID: PMC6767322 DOI: 10.3390/molecules24183261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022] Open
Abstract
Interleukin 15 (IL-15), a four-helix bundle cytokine, is involved in a plethora of different cellular functions and, particularly, plays a key role in the development and activation of immune responses. IL-15 forms receptor complexes by binding with IL-2Rβ- and common γ (γc)-signaling subunits, which are shared with other members of the cytokines family (IL-2 for IL-2Rβ- and all other γc- cytokines for γc). The specificity of IL-15 is brought by the non-signaling α-subunit, IL-15Rα. Here we present the results of molecular dynamics simulations carried out on four relevant forms of IL-15: its monomer, IL-15 interacting individually with IL-15Rα (IL-15/IL-15Rα), with IL-2Rβ/γc subunits (IL-15/IL-2Rβ/γc) or with its three receptors simultaneously (IL-15/IL-15Rα/IL-2Rβ/γc). Through the analyses of the various trajectories, new insights on the structural features of the interfaces are highlighted, according to the considered form. The comparison of the results with the experimental data, available from X-ray crystallography, allows, in particular, the rationalization of the importance of IL-15 key residues (e.g., Asp8, Lys10, Glu64). Furthermore, the pivotal role of water molecules in the stabilization of the various protein-protein interfaces and their H-bonds networks are underlined for each of the considered complexes.
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Affiliation(s)
- Rui P Sousa
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
- CRCINA, CNRS, Inserm, Université d'Angers, Université de Nantes, F-44200 Nantes, France.
- Immunotherapy, Graft, Oncology (IGO) LabEx, Nantes, France.
| | - Adèle D Laurent
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Agnès Quéméner
- CRCINA, CNRS, Inserm, Université d'Angers, Université de Nantes, F-44200 Nantes, France.
- Immunotherapy, Graft, Oncology (IGO) LabEx, Nantes, France.
| | - Erwan Mortier
- CRCINA, CNRS, Inserm, Université d'Angers, Université de Nantes, F-44200 Nantes, France.
- Immunotherapy, Graft, Oncology (IGO) LabEx, Nantes, France.
- IMPACT Platform, SFR Santé, CNRS, Inserm, Université de Nantes, Nantes, F-44000, France.
| | - Jean-Yves Le Questel
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
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Alred EJ, Lodangco I, Gallaher J, Hansmann UH. Mutations Alter RNA-Mediated Conversion of Human Prions. ACS OMEGA 2018; 3:3936-3944. [PMID: 29732450 PMCID: PMC5928492 DOI: 10.1021/acsomega.7b02007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Prion diseases are connected with self-replication and self-propagation of misfolded proteins. The rate-limiting factor is the formation of the initial seed. We have recently studied the early stages in the conversion between functional PrPC and the infectious scrapie PrPSC form, triggered by the binding of RNA. Here, we study how this process is modulated by the prion sequence. We focus on residues 129 and 178, which are connected to the hereditary neurodegenerative disease fatal familial insomnia.
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