1
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Lu L, Sun N, Wang Y. Development and therapeutic potential of allosteric retinoic acid receptor-related orphan receptor γt (RORγt) inverse agonists for autoimmune diseases. Eur J Med Chem 2023; 258:115574. [PMID: 37336069 DOI: 10.1016/j.ejmech.2023.115574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
The transcription factor retinoic acid receptor-related orphan receptor γt (RORγt) is an attractive drug target for some autoimmune diseases owing to its roles in the differentiation of human T helper 17 (Th17) cells which produce pro-inflammatory cytokine interleukin (IL)-17. RORγt agonists and inverse agonists are classically targeted to the hydrophobic and highly conserved orthosteric binding pocket of RORγt ligand binding domain (LBD). Although successful, this approach also brings some challenges, including off-target effects due to lack of selectivity over other nuclear receptors (NRs). Allosteric regulation of RORγt by synthetic small molecules has recently emerged as novel research interests for its interesting modes of action (MOA), satisfying bioactivity profile and improved selectivity. In this review, we delineated the discovery and identification of the allosteric pocket of RORγt. Subsequently, we focused on examples of small molecules that allosterically inhibit RORγt, with a central attention on structural-activity-relationship (SAR) information, biological activity, pharmacokinetic (PK) property, and the ligand binding mode of these compounds. We also discussed the potential role of RORγt allosteric inverse agonists as small molecule therapeutics for autoimmune diseases.
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Affiliation(s)
- Lixue Lu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Nannan Sun
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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2
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Fouda A, Negi S, Zaremba O, Gaidar RS, Moroz YS, Rusanov E, Paraskevas S, Tchervenkov J. Discovery, Synthesis, and In Vitro Characterization of 2,3 Derivatives of 4,5,6,7-Tetrahydro-Benzothiophene as Potent Modulators of Retinoic Acid Receptor-Related Orphan Receptor γt. J Med Chem 2023; 66:7355-7373. [PMID: 37172324 PMCID: PMC10259452 DOI: 10.1021/acs.jmedchem.3c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Indexed: 05/14/2023]
Abstract
Retinoic acid receptor-related orphan receptor γt (RORγt) is a nuclear receptor that is expressed in a variety of tissues and is a potential drug target for the treatment of inflammatory and auto-immune diseases, metabolic diseases, and resistant cancer types. We herein report the discovery of 2,3 derivatives of 4,5,6,7-tetrahydro-benzothiophene modulators of RORγt. We also report the solubility in acidic/neutral pH, mouse/human/dog/rat microsomal stability, Caco-2, and MDR1-MDCKII permeabilities of a set of these derivatives. For this group of modulators, inverse agonism by steric clashes and push-pull mechanisms induce greater instability to protein conformation compared to agonist lock hydration. Independent of the two mechanisms, we observed a basal modulatory activity of the tested 2,3 derivatives of 4,5,6,7-tetrahydro-benzothiophene toward RORγt due to the interactions with the Cys320-Glu326 and Arg364-Phe377 hydrophilic regions. The drug discovery approach reported in the current study can be employed to discover modulators of nuclear receptors and other globular protein targets.
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Affiliation(s)
- Ahmed Fouda
- Department
of Experimental Surgery, McGill University, Montréal, Québec H3G 1A4, Canada
- Research
Institute of the McGill University Health Centre, Montréal, Québec H3H 2R9, Canada
| | - Sarita Negi
- Research
Institute of the McGill University Health Centre, Montréal, Québec H3H 2R9, Canada
| | | | | | - Yurii S. Moroz
- Chemspace
LLC, Kyïv 02094, Ukraine
- Taras
Shevchenko National University of Kyïv, Kyïv 01601, Ukraine
| | - Eduard Rusanov
- Institute
of Organic Chemistry, National Academy of
Sciences of Ukraine, Kyïv 02094, Ukraine
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Zürich CH-8093, Switzerland
| | - Steven Paraskevas
- Department
of Experimental Surgery, McGill University, Montréal, Québec H3G 1A4, Canada
- Research
Institute of the McGill University Health Centre, Montréal, Québec H3H 2R9, Canada
- Department
of Surgery, McGill University, Montréal, Québec H3G 1A4, Canada
- McGill
University Health Centre, Montréal, Québec H4A 3J1, Canada
| | - Jean Tchervenkov
- Department
of Experimental Surgery, McGill University, Montréal, Québec H3G 1A4, Canada
- Research
Institute of the McGill University Health Centre, Montréal, Québec H3H 2R9, Canada
- Department
of Surgery, McGill University, Montréal, Québec H3G 1A4, Canada
- McGill
University Health Centre, Montréal, Québec H4A 3J1, Canada
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3
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Jokinen EM, Niemeläinen M, Kurkinen ST, Lehtonen JV, Lätti S, Postila PA, Pentikäinen OT, Niinivehmas SP. Virtual Screening Strategy to Identify Retinoic Acid-Related Orphan Receptor γt Modulators. Molecules 2023; 28:molecules28083420. [PMID: 37110655 PMCID: PMC10145393 DOI: 10.3390/molecules28083420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Molecular docking is a key method used in virtual screening (VS) campaigns to identify small-molecule ligands for drug discovery targets. While docking provides a tangible way to understand and predict the protein-ligand complex formation, the docking algorithms are often unable to separate active ligands from inactive molecules in practical VS usage. Here, a novel docking and shape-focused pharmacophore VS protocol is demonstrated for facilitating effective hit discovery using retinoic acid receptor-related orphan receptor gamma t (RORγt) as a case study. RORγt is a prospective target for treating inflammatory diseases such as psoriasis and multiple sclerosis. First, a commercial molecular database was flexibly docked. Second, the alternative docking poses were rescored against the shape/electrostatic potential of negative image-based (NIB) models that mirror the target's binding cavity. The compositions of the NIB models were optimized via iterative trimming and benchmarking using a greedy search-driven algorithm or brute force NIB optimization. Third, a pharmacophore point-based filtering was performed to focus the hit identification on the known RORγt activity hotspots. Fourth, free energy binding affinity evaluation was performed on the remaining molecules. Finally, twenty-eight compounds were selected for in vitro testing and eight compounds were determined to be low μM range RORγt inhibitors, thereby showing that the introduced VS protocol generated an effective hit rate of ~29%.
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Affiliation(s)
- Elmeri M Jokinen
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20014 Turku, Finland
| | - Miika Niemeläinen
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
| | - Sami T Kurkinen
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20014 Turku, Finland
| | - Jukka V Lehtonen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20500 Turku, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, FI-20500 Turku, Finland
| | - Sakari Lätti
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20014 Turku, Finland
| | - Pekka A Postila
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20014 Turku, Finland
| | - Olli T Pentikäinen
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20014 Turku, Finland
| | - Sanna P Niinivehmas
- MedChem.fi, Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20014 Turku, Finland
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4
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Fiorillo B, Roselli R, Finamore C, Biagioli M, di Giorgio C, Bordoni M, Conflitti P, Marchianò S, Bellini R, Rapacciuolo P, Cassiano C, Limongelli V, Sepe V, Catalanotti B, Fiorucci S, Zampella A. Discovery of a Novel Class of Dual GPBAR1 Agonists-RORγt Inverse Agonists for the Treatment of IL-17-Mediated Disorders. ACS OMEGA 2023; 8:5983-5994. [PMID: 36816679 PMCID: PMC9933477 DOI: 10.1021/acsomega.2c07907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Retinoic acid receptor-related orphan receptor γ-t (RORγt) and GPBAR1, a transmembrane G-protein-coupled receptor for bile acids, are attractive drug targets to develop clinically relevant small modulators as potent therapeutics for autoimmune diseases. Herein, we designed, synthesized, and evaluated several new bile acid-derived ligands with potent dual activity. Furthermore, we performed molecular docking and MD calculations of the best dual modulators in the two targets to identify the binding modes as well as to better understand the molecular basis of the inverse agonism of RORγt by bile acid derivatives. Among these compounds, 7 was identified as a GPBAR1 agonist (EC50 5.9 μM) and RORγt inverse agonist (IC50 0.107 μM), with excellent pharmacokinetic properties. Finally, the most promising ligand displayed robust anti-inflammatory activity in vitro and in vivo in a mouse model of 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis.
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Affiliation(s)
- Bianca Fiorillo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Rosalinda Roselli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Claudia Finamore
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Michele Biagioli
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Cristina di Giorgio
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | | | - Paolo Conflitti
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Silvia Marchianò
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Rachele Bellini
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Pasquale Rapacciuolo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Valentina Sepe
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Bruno Catalanotti
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
| | - Stefano Fiorucci
- Department of Medicine and Surgery, University of Perugia, Piazza L. Severi, 1-06132 Perugia, Italy
| | - Angela Zampella
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, I-80131 Naples, Italy
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5
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Zhang J, Chen B, Zhang C, Sun N, Huang X, Wang W, Fu W. Modes of action insights from the crystallographic structures of retinoic acid receptor-related orphan receptor-γt (RORγt). Eur J Med Chem 2023; 247:115039. [PMID: 36566711 DOI: 10.1016/j.ejmech.2022.115039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
RORγt plays an important role in mediating IL-17 production and some tumor cells. It has four functional domains, of which the ligand-binding domain (LBD) is responsible for binding agonists to recruit co-activators or inverse agonists to prevent co-activator recruiting the agonists. Thus, potent ligands targeting the LBD of this protein could provide novel treatments for cancer and autoimmune diseases. In this perspective, we summarized and discussed various modes of action (MOA) of RORγt-ligand binding structures. The ligands can bind with RORγt at either orthosteric site or the allosteric site, and the binding modes at these two sites are different for agonists and inverse agonist. At the orthosteric site, the binding of agonist is to stabilize the H479-Y502-F506 triplet interaction network of RORγt. The binding of inverse agonist features as these four apparent ways: (1) blocking the entrance of the agonist pocket in RORγt; (2) directly breaking the H479-Y502 pair interactions; (3) destabilizing the triplet H479-Y502-F506 interaction network through perturbing the conformation of the side chain in M358 at the bottom of the binding pocket; (4) and destabilizing the triplet H479-Y502-F506 through changing the conformation of the side chain of residue W317 side chain. At the allosteric site of RORγt, the binding of inverse agonist was found recently to inhibit the activation of protein by interacting directly with H12, which results in unfolding of helix 11' and orientation of H12 to directly block cofactor peptide binding. This overview of recent advances in the RORγt structures is expected to provide a guidance of designing more potent drugs to treat RORγt-related diseases.
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Affiliation(s)
- Junjie Zhang
- School of Pharmacy & Minhang Hospital, Fudan University, Shanghai, 201301, PR China
| | - Baiyu Chen
- School of Pharmacy & Minhang Hospital, Fudan University, Shanghai, 201301, PR China
| | - Chao Zhang
- School of Pharmacy & Minhang Hospital, Fudan University, Shanghai, 201301, PR China
| | - Nannan Sun
- School of Pharmacy & Minhang Hospital, Fudan University, Shanghai, 201301, PR China
| | - Xiaoqin Huang
- Center for Research Computing, Office of Information Technology, Center for Theoretical Biological Physics, Rice University, Houston, TX, 77030, USA
| | - Wuqing Wang
- School of Pharmacy & Minhang Hospital, Fudan University, Shanghai, 201301, PR China
| | - Wei Fu
- School of Pharmacy & Minhang Hospital, Fudan University, Shanghai, 201301, PR China.
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6
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Yu MC, Yang F, Ding XY, Sun NN, Jiang ZY, Huang YF, Yan YR, Zhu C, Xie Q, Chen ZF, Guo SQ, Jiang HL, Chen KX, Luo C, Luo XM, Chen SJ, Wang YH. Crystallography-guided discovery of carbazole-based retinoic acid-related orphan receptor gamma-t (RORγt) modulators: insights into different protein behaviors with "short" and "long" inverse agonists. Acta Pharmacol Sin 2021; 42:1524-1534. [PMID: 33239687 PMCID: PMC8379218 DOI: 10.1038/s41401-020-00552-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
A series of 6-substituted carbazole-based retinoic acid-related orphan receptor gamma-t (RORγt) modulators were discovered through 6-position modification guided by insights from the crystallographic profiles of the "short" inverse agonist 6. With the increase in the size of the 6-position substituents, the "short" inverse agonist 6 first reversed its function to agonists and then to "long" inverse agonists. The cocrystal structures of RORγt complexed with the representative "short" inverse agonist 6 (PDB: 6LOB), the agonist 7d (PDB: 6LOA) and the "long" inverse agonist 7h (PDB: 6LO9) were revealed by X-ray analysis. However, minor differences were found in the binding modes of "short" inverse agonist 6 and "long" inverse agonist 7h. To further reveal the molecular mechanisms of different RORγt inverse agonists, we performed molecular dynamics simulations and found that "short" or "long" inverse agonists led to different behaviors of helixes H11, H11', and H12 of RORγt. The "short" inverse agonist 6 destabilizes H11' and dislocates H12, while the "long" inverse agonist 7h separates H11 and unwinds H12. The results indicate that the two types of inverse agonists may behave differently in downstream signaling, which may help identify novel inverse agonists with different regulatory mechanisms.
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Affiliation(s)
- Ming-Cheng Yu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Feng Yang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Yu Ding
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Nan-Nan Sun
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zheng-Yuan Jiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Ya-Fei Huang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yu-Rong Yan
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Chen Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Fudan Zhangjiang Institute, Shanghai, 201203, China
| | - Zhi-Feng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Si-Qi Guo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hua-Liang Jiang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Kai-Xian Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Cheng Luo
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Xiao-Min Luo
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Shi-Jie Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Yong-Hui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, 201203, China.
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7
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Gautam V, Nimmanpipug P, Zain SM, Rahman NA, Lee VS. Molecular Dynamics Simulations in Designing DARPins as Phosphorylation-Specific Protein Binders of ERK2. Molecules 2021; 26:molecules26154540. [PMID: 34361694 PMCID: PMC8347146 DOI: 10.3390/molecules26154540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) play key roles in promoting cell survival and proliferation through the phosphorylation of various substrates. Remarkable antitumour activity is found in many inhibitors that act upstream of the ERK pathway. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. Here, we report a class of repeat proteins-designed ankyrin repeat protein (DARPin) macromolecules targeting ERK2 as inhibitors. The structural basis of ERK2-DARPin interactions based on molecular dynamics (MD) simulations was studied. The information was then used to predict stabilizing mutations employing a web-based algorithm, MAESTRO. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations. Two mutations, Ala → Asp and Ser → Leu, were found to perform better than the original sequence (DARPin E40) based on the associated energy and key residues involved in protein-protein interaction. MD simulations and analysis of the data obtained on these mutations supported our predictions.
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Affiliation(s)
- Vertika Gautam
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (V.G.); (S.M.Z.); (N.A.R.)
| | - Piyarat Nimmanpipug
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Center of Excellence for Innovation in Analytical Science and Technology (I-ANALY-S-T), Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sharifuddin Md Zain
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (V.G.); (S.M.Z.); (N.A.R.)
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (V.G.); (S.M.Z.); (N.A.R.)
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (V.G.); (S.M.Z.); (N.A.R.)
- Center of Excellence for Innovation in Analytical Science and Technology (I-ANALY-S-T), Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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8
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Xia Y, Yu M, Zhao Y, Xia L, Huang Y, Sun N, Song M, Guo H, Zhang Y, Zhu D, Xie Q, Wang Y. Discovery of tetrahydroquinolines and benzomorpholines as novel potent RORγt agonists. Eur J Med Chem 2020; 211:113013. [PMID: 33272782 DOI: 10.1016/j.ejmech.2020.113013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/24/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023]
Abstract
The retinoic acid receptor-related orphan receptor γt (RORγt) is an important nuclear receptor that regulates the differentiation of Th17 cells and production of interleukin 17(IL-17). RORγt agonists increase basal activity of RORγt and could provide a potential approach to cancer immunotherapy. Herein, hit compound 1 was identified as a weak RORγt agonist during in-house library screening. Changes in LHS core of 1 led to the identification of tetrahydroquinoline compound 6 as a partial RORγt agonist (max. act. = 39.3%). Detailed structure-activity relationship on substituent of the LHS core, amide linker and RHS arylsulfonyl moiety was explored and a novel series of tetrahydroquinolines and benzomorpholines was discovered as potent RORγt agonists. Tetrahydroquinoline compound 8g (EC50 = 8.9 ± 0.4 nM, max. act. = 104.5%) and benzomorpholine compound 9g (EC50 = 7.5 ± 0.6 nM, max. act. = 105.8%) were representative compounds with high RORγt agonistic activity in dual FRET assay, and they showed good activity in cell-based Gal4 reporter gene assay and Th17 cell differentiation assay (104.5% activation at 300 nM of 8g; 59.4% activation at 300 nM of 9g). The binding modes of 8g and 9g as well as the two RORγt inverse agonists accidentally discovered were also discussed.
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Affiliation(s)
- Yuehan Xia
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Mingcheng Yu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Yunpeng Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Li Xia
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Yafei Huang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Nannan Sun
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China; Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, Shanghai, 201203, China
| | - Meiqi Song
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Huimin Guo
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Yunyi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Di Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China
| | - Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China; Fudan Zhangjiang Institute, Shanghai, 201203, China.
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 ZhanghengRoad, Pudong, Shanghai, 201203, China.
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9
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Huang M, Bolin S, Miller H, Ng HL. RORγ Structural Plasticity and Druggability. Int J Mol Sci 2020; 21:ijms21155329. [PMID: 32727079 PMCID: PMC7432406 DOI: 10.3390/ijms21155329] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/08/2020] [Accepted: 07/15/2020] [Indexed: 12/19/2022] Open
Abstract
Retinoic acid receptor-related orphan receptor γ (RORγ) is a transcription factor regulating the expression of the pro-inflammatory cytokine IL-17 in human T helper 17 (Th17) cells. Activating RORγ can induce multiple IL-17-mediated autoimmune diseases but may also be useful for anticancer therapy. Its deep immunological functions make RORɣ an attractive drug target. Over 100 crystal structures have been published describing atomic interactions between RORɣ and agonists and inverse agonists. In this review, we focus on the role of dynamic properties and plasticity of the RORɣ orthosteric and allosteric binding sites by examining structural information from crystal structures and simulated models. We discuss the possible influences of allosteric ligands on the orthosteric binding site. We find that high structural plasticity favors the druggability of RORɣ, especially for allosteric ligands.
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Affiliation(s)
- Mian Huang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA; (M.H.); (H.M.)
| | - Shelby Bolin
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA;
| | - Hannah Miller
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA; (M.H.); (H.M.)
| | - Ho Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA; (M.H.); (H.M.)
- Correspondence:
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10
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Leijten-van de Gevel IA, Brunsveld L. Delineation of the molecular determinants of the unique allosteric binding site of the orphan nuclear receptor RORγt. J Biol Chem 2020; 295:9183-9191. [PMID: 32439807 PMCID: PMC7335795 DOI: 10.1074/jbc.ra120.013581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Nuclear receptors (NRs) are high-interest targets in drug discovery because of their involvement in numerous biological processes and diseases. Classically, NRs are targeted via their hydrophobic, orthosteric pocket. Although successful, this approach comes with challenges, including off-target effects due to lack of selectivity. Allosteric modulation of NR activity constitutes a promising pharmacological strategy. The retinoic acid receptor-related orphan receptor-γt (RORγt) is a constitutively active NR that positively regulates the expression of interleukin-17 in T helper 17 cells. Inhibiting this process is an emerging strategy for managing autoimmune diseases. Recently, an allosteric binding pocket in the C-terminal region of the ligand-binding domain (LBD) of RORγt was discovered that is amenable to small-molecule drug discovery. Compounds binding this pocket induce a reorientation of helix 12, thereby preventing coactivator recruitment. Therefore, inverse agonists binding this site with high affinity are actively being pursued. To elucidate the pocket formation mechanism, verify the uniqueness of this pocket, and substantiate the relevance of targeting this site, here we identified the key characteristics of the RORγt allosteric region. We evaluated the effects of substitutions in the LBD on coactivator, orthosteric, and allosteric ligand binding. We found that two molecular elements unique to RORγt, the length of helix 11' and a Gln-487 residue, are crucial for the formation of the allosteric pocket. The unique combination of elements present in RORγt suggests a high potential for subtype-selective targeting of this NR to more effectively treat patients with autoimmune diseases.
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Affiliation(s)
- Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands.
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11
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Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations. Comput Struct Biotechnol J 2020; 18:1676-1685. [PMID: 32670507 PMCID: PMC7338990 DOI: 10.1016/j.csbj.2020.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 11/22/2022] Open
Abstract
To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carried out for certain characteristic structures obtained from the MD simulations to reveal important interactions between the amino acid residues of RORγt, and to distinguish the different effects in the binding of an agonist and an inverse agonist on the structure of RORγt. The results elucidate that the hydrogen bond between His479 of helix11 (H11) and Tyr502 of helix12 (H12) is important to keep the H12 conformation in the agonist-bound RORγt. In contrast, in the inverse-agonist-bound RORγt, the side chain of His479 rotates, significantly weakening the interaction between His479 and Tyr502, leading to a conformational change in H12. Therefore, the present molecular simulations clearly indicate that the conformational change in the side chain of His479 in the inverse-agonist-bound RORγt is the main reason for the H12 destabilization induced by the binding of the inverse agonist. Such a conformational change does not occur on the binding of the agonist in RORγt, owing to the strong hydrogen bond between His479 and Tyr502.
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12
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Discovery of novel N-sulfonamide-tetrahydroquinolines as potent retinoic acid receptor-related orphan receptor γt inverse agonists for the treatment of autoimmune diseases. Eur J Med Chem 2020; 187:111984. [DOI: 10.1016/j.ejmech.2019.111984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 11/19/2022]
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13
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Strutzenberg TS, Garcia-Ordonez RD, Novick SJ, Park H, Chang MR, Doebellin C, He Y, Patouret R, Kamenecka TM, Griffin PR. HDX-MS reveals structural determinants for RORγ hyperactivation by synthetic agonists. eLife 2019; 8:47172. [PMID: 31172947 PMCID: PMC6579513 DOI: 10.7554/elife.47172] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/01/2019] [Indexed: 01/03/2023] Open
Abstract
Members of the nuclear receptor (NR) superfamily regulate both physiological and pathophysiological processes ranging from development and metabolism to inflammation and cancer. Synthetic small molecules targeting NRs are often deployed as therapeutics to correct aberrant NR signaling or as chemical probes to explore the role of the receptor in physiology. Nearly half of NRs do not have specific cognate ligands (termed orphan NRs) and it’s unclear if they possess ligand dependent activities. Here we demonstrate that ligand-dependent action of the orphan RORγ can be defined by selectively disrupting putative endogenous—but not synthetic—ligand binding. Furthermore, the characterization of a library of RORγ modulators reveals that structural dynamics of the receptor assessed by HDX-MS correlate with activity in biochemical and cell-based assays. These findings, corroborated with X-ray co-crystallography and site-directed mutagenesis, collectively reveal the structural determinants of RORγ activation, which is critical for designing RORγ agonists for cancer immunotherapy.
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Affiliation(s)
- Timothy S Strutzenberg
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - HaJeung Park
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Mi Ra Chang
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Christelle Doebellin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Yuanjun He
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Rémi Patouret
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States
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14
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Agrahari AK, Krishna Priya M, Praveen Kumar M, Tayubi IA, Siva R, Prabhu Christopher B, George Priya Doss C, Zayed H. Understanding the structure-function relationship of HPRT1 missense mutations in association with Lesch-Nyhan disease and HPRT1-related gout by in silico mutational analysis. Comput Biol Med 2019; 107:161-171. [PMID: 30831305 DOI: 10.1016/j.compbiomed.2019.02.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
The nucleotide salvage pathway is used to recycle degraded nucleotides (purines and pyrimidines); one of the enzymes that helps to recycle purines is hypoxanthine guanine phosphoribosyl transferase 1 (HGPRT1). Therefore, defects in this enzyme lead to the accumulation of DNA and nucleotide lesions and hence replication errors and genetic disorders. Missense mutations in hypoxanthine phosphoribosyl transferase 1 (HPRT1) are associated with deficiencies such as Lesch-Nyhan disease and chronic gout, which have manifestations such as arthritis, neurodegeneration, and cognitive disorders. In the present study, we collected 88 non-synonymous single nucleotide polymorphisms (nsSNPs) from the UniProt, dbSNP, ExAC, and ClinVar databases. We used a series of sequence-based and structure-based in silico tools to prioritize and characterize the most pathogenic and stabilizing or destabilizing nsSNPs. Moreover, to obtain the structural impact of the pathogenic mutations, we mapped the mutations to the crystal structure of the HPRT protein. We further subjected these mutant proteins to a 50 ns molecular dynamics simulation (MDS). The MDS trajectory showed that all mutant proteins altered the structural conformation and dynamic behavior of the HPRT protein and corroborated its association with LND and gout. This study provides essential information regarding the use of HPRT protein mutants as potential targets for therapeutic development.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - M Krishna Priya
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - Medapalli Praveen Kumar
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, 21911, Saudi Arabia
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | | | - C George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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15
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Yukawa T, Nara Y, Kono M, Sato A, Oda T, Takagi T, Sato T, Banno Y, Taya N, Imada T, Shiokawa Z, Negoro N, Kawamoto T, Koyama R, Uchiyama N, Skene R, Hoffman I, Chen CH, Sang B, Snell G, Katsuyama R, Yamamoto S, Shirai J. Design, Synthesis, and Biological Evaluation of Retinoic Acid-Related Orphan Receptor γt (RORγt) Agonist Structure-Based Functionality Switching Approach from In House RORγt Inverse Agonist to RORγt Agonist. J Med Chem 2019; 62:1167-1179. [DOI: 10.1021/acs.jmedchem.8b01181] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomoya Yukawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Mitsunori Kono
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ayumu Sato
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tsuneo Oda
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Terufumi Takagi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takayuki Sato
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoshihiro Banno
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Naohiro Taya
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takashi Imada
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Zenyu Shiokawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Nobuyuki Negoro
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tetsuji Kawamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ryokichi Koyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Noriko Uchiyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Robert Skene
- Takeda California, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Isaac Hoffman
- Takeda California, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Chien-Hung Chen
- Takeda California, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - BiChing Sang
- Takeda California, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Gyorgy Snell
- Takeda California, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Ryosuke Katsuyama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Yamamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Junya Shirai
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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