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Meng Y, Liu R, Wang L, Li F, Tian Y, Lu H. Binding affinity and conformational change predictions for a series of inhibitors with RuBisCO in a carbon dioxide gas and water environment by multiple computational methods. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Yan D, Huelse JM, Kireev D, Tan Z, Chen L, Goyal S, Wang X, Frye SV, Behera M, Schneider F, Ramalingam SS, Owonikoko T, Earp HS, DeRyckere D, Graham DK. MERTK activation drives osimertinib resistance in EGFR-mutant non-small cell lung cancer. J Clin Invest 2022; 132:e150517. [PMID: 35708914 PMCID: PMC9337831 DOI: 10.1172/jci150517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Acquired resistance is inevitable in non-small cell lung cancers (NSCLCs) treated with osimertinib (OSI), and the mechanisms are not well defined. The MERTK ligand GAS6 promoted downstream oncogenic signaling in EGFR-mutated (EGFRMT) NSCLC cells treated with OSI, suggesting a role for MERTK activation in OSI resistance. Indeed, treatment with MRX-2843, a first-in-class MERTK kinase inhibitor, resensitized GAS6-treated NSCLC cells to OSI. Both GAS6 and EGF stimulated downstream PI3K/AKT and MAPK/ERK signaling in parental cells, but only GAS6 activated these pathways in OSI-resistant (OSIR) derivative cell lines. Functionally, OSIR cells were more sensitive to MRX-2843 than parental cells, suggesting acquired dependence on MERTK signaling. Furthermore, MERTK and/or its ligands were dramatically upregulated in EGFRMT tumors after treatment with OSI in both xenograft models and patient samples, consistent with induction of autocrine/paracrine MERTK activation. Moreover, treatment with MRX-2843 in combination with OSI, but not OSI alone, provided durable suppression of tumor growth in vivo, even after treatment was stopped. These data identify MERTK as a driver of bypass signaling in treatment-naive and EGFRMT-OSIR NSCLC cells and predict that MRX-2843 and OSI combination therapy will provide clinical benefit in patients with EGFRMT NSCLC.
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Affiliation(s)
- Dan Yan
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Justus M. Huelse
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zikang Tan
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Luxiao Chen
- Biostatistics and Bioinformatics Shared Resources, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Subir Goyal
- Biostatistics and Bioinformatics Shared Resources, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Madhusmita Behera
- Biostatistics and Bioinformatics Shared Resources, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Suresh S. Ramalingam
- Winship Cancer Institute, and
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Taofeek Owonikoko
- Winship Cancer Institute, and
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - H. Shelton Earp
- Department of Medicine, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Douglas K. Graham
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
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Abramyan TM, An Y, Kireev D. Off-Pocket Activity Cliffs: A Puzzling Facet of Molecular Recognition. J Chem Inf Model 2019; 60:152-161. [PMID: 31790251 DOI: 10.1021/acs.jcim.9b00731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
While accurate quantitative prediction of ligand-protein binding affinity remains an elusive goal, high-affinity ligands to therapeutic targets are being designed through heuristic optimization of ligand-protein contacts. However, herein, through large-scale data mining and analyses, we demonstrate that a ligand's binding can also be strongly affected through modifying its solvent-exposed portion that does not make contacts with the protein, thus resulting in "off-pocket activity cliffs" (OAC). We then exposed the roots of the OAC phenomenon by means of molecular dynamics (MD) simulations and MD data analyses. We expect OAC to extend our knowledge of molecular recognition and enhance the drug designer's toolkit.
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Affiliation(s)
- Tigran M Abramyan
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
| | - Yi An
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
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Han F, Liu Y, E J, Guan S, Han W, Shan Y, Wang S, Zhang H. Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study. Biopolymers 2018; 109:e23238. [PMID: 30484856 DOI: 10.1002/bip.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Analysis of simulation results suggests that the binding free energies between the substrate and WT-Cbh9A are lower than those of Y555S and W678G mutants. The pull forces and energy barrier in Y555S and W678G mutants also reduced significantly during the steered molecular dynamics (SMD) simulation compared with that of the WT-Cbh9A. And the potential mean force calculations showed that the pulling energy barrier of Y555S and W678G mutants is much lower than that of WT-Cbh9A.
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Affiliation(s)
- Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Shanshan Guan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Yaming Shan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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Berhanu WM, Hansmann UHE. Stability of amyloid oligomers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:113-41. [PMID: 25443956 DOI: 10.1016/bs.apcsb.2014.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Molecular simulations are now commonly used to complement experimental techniques in investigating amyloids and their role in human diseases. In this chapter, we will summarize techniques and approaches often used in amyloid simulations and will present recent success stories. Our examples will be focused on lessons learned from molecular dynamics simulations in aqueous environments that start from preformed aggregates. These studies explore the limitations that arise from the choice of force field, the role of mutations in the growth of amyloid aggregates, segmental polymorphism, and the importance of cross-seeding. Furthermore, they give evidence for potential toxicity mechanisms. We finally discuss the role of molecular simulations in the search for aggregation inhibitors.
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Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA.
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