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Suzuki M, Uchibori K, Oh-Hara T, Nomura Y, Suzuki R, Takemoto A, Araki M, Matsumoto S, Sagae Y, Kukimoto-Niino M, Kawase Y, Shirouzu M, Okuno Y, Nishio M, Fujita N, Katayama R. A macrocyclic kinase inhibitor overcomes triple resistant mutations in EGFR-positive lung cancer. NPJ Precis Oncol 2024; 8:46. [PMID: 38396251 PMCID: PMC10891166 DOI: 10.1038/s41698-024-00542-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Brigatinib-based therapy was effective against osimertinib-resistant EGFR C797S mutants and is undergoing clinical studies. However, tumor relapse suggests additional resistance mutations might emerge. Here, we first demonstrated the binding mode of brigatinib to the EGFR-T790M/C797S mutant by crystal structure analysis and predicted brigatinib-resistant mutations through a cell-based assay including N-ethyl-N-nitrosourea (ENU) mutagenesis. We found that clinically reported L718 and G796 compound mutations appeared, consistent with their proximity to the binding site of brigatinib, and brigatinib-resistant quadruple mutants such as EGFR-activating mutation/T790M/C797S/L718M were resistant to all the clinically available EGFR-TKIs. BI-4020, a fourth-generation EGFR inhibitor with a macrocyclic structure, overcomes the quadruple and major EGFR-activating mutants but not the minor mutants, such as L747P or S768I. Molecular dynamics simulation revealed the binding mode and affinity between BI-4020 and EGFR mutants. This study identified potential therapeutic strategies using the new-generation macrocyclic EGFR inhibitor to overcome the emerging ultimate resistance mutants.
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Affiliation(s)
- Mai Suzuki
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
- Department of Medical Genome Science, Graduate School of Frontier Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Ken Uchibori
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomoko Oh-Hara
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Yumi Nomura
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Ryusei Suzuki
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Ai Takemoto
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, Japan
| | - Shigeyuki Matsumoto
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, Japan
| | - Yukari Sagae
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, Japan
| | - Mutsuko Kukimoto-Niino
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-Ku, Kyoto, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naoya Fujita
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.
- Department of Medical Genome Science, Graduate School of Frontier Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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Ahlstrom LS, Vorontsov II, Shi J, Miyashita O. Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations. PLoS One 2017; 12:e0170337. [PMID: 28107510 PMCID: PMC5249168 DOI: 10.1371/journal.pone.0170337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.
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Affiliation(s)
- Logan S. Ahlstrom
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ivan I. Vorontsov
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Jun Shi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Osamu Miyashita
- RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo, Japan
- * E-mail:
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