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Yin G, Lv G, Zhang J, Jiang H, Lai T, Yang Y, Ren Y, Wang J, Yi C, Chen H, Huang Y, Xiao C. Early-stage structure-based drug discovery for small GTPases by NMR spectroscopy. Pharmacol Ther 2022; 236:108110. [PMID: 35007659 DOI: 10.1016/j.pharmthera.2022.108110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Small GTPase or Ras superfamily, including Ras, Rho, Rab, Ran and Arf, are fundamental in regulating a wide range of cellular processes such as growth, differentiation, migration and apoptosis. They share structural and functional similarities for binding guanine nucleotides and hydrolyzing GTP. Dysregulations of Ras proteins are involved in the pathophysiology of multiple human diseases, however there is still a stringent need for effective treatments targeting these proteins. For decades, small GTPases were recognized as 'undruggable' targets due to their complex regulatory mechanisms and lack of deep pockets for ligand binding. NMR has been critical in deciphering the structural and dynamic properties of the switch regions that are underpinning molecular switch functions of small GTPases, which pave the way for developing new effective inhibitors. The recent progress of drug or lead molecule development made for small GTPases profoundly delineated how modern NMR techniques reshape the field of drug discovery. In this review, we will summarize the progress of structural and dynamic studies of small GTPases, the NMR techniques developed for structure-based drug screening and their applications in early-stage drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guohua Lv
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Jerry Zhang
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Tianqi Lai
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Yushan Yang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Yong Ren
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Chenju Yi
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China; Research Institute of Xi'an Jiaotong University, Zhejiang, Hangzhou, Zhejiang Province 311215, PR China
| | - Yun Huang
- Howard Hughes Medical Institute, Chevy Chase 20815, MD, USA; Department of Physiology & Biophysics, Weill Cornell Medicine, New York 10065, NY, USA.
| | - Chaoni Xiao
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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Cao S, Chung S, Kim S, Li Z, Manor D, Buck M. K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function. J Biol Chem 2019; 294:7068-7084. [PMID: 30792310 DOI: 10.1074/jbc.ra118.004021] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Ras genes potently drive human cancers, with mutated proto-oncogene GTPase KRAS4B (K-Ras4B) being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the "holy grail" of present-day cancer therapy, and recent discoveries of small-molecule KRas4B inhibitors were made thanks to a deeper understanding of the structure and dynamics of this GTPase. Because interactions with biological membranes are key for Ras function, Ras-lipid interactions have become a major focus, especially because such interactions evidently involve both the Ras C terminus for lipid anchoring and its G-protein domain. Here, using NMR spectroscopy and molecular dynamics simulations complemented by biophysical- and cell-biology assays, we investigated the interaction between K-Ras4B with the signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2). We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2 and identified the specific residues in these structural elements employed in these interactions, likely occurring in two K-Ras4B orientation states relative to the membrane. Importantly, we found that some of these residues known to be oncogenic when mutated (D47K, D92N, K104M, and D126N) are critical for K-Ras-mediated transformation of fibroblast cells, but do not substantially affect basal and assisted nucleotide hydrolysis and exchange. Moreover, the K104M substitution abolished localization of K-Ras to the plasma membrane. The findings suggest that specific G-domain residues can critically regulate Ras function by mediating interactions with membrane-associated PIP2 lipids; these insights that may inform the future design of therapeutic reagents targeting Ras activity.
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Affiliation(s)
- Shufen Cao
- From the Departments of Physiology and Biophysics
| | | | | | - Zhenlu Li
- From the Departments of Physiology and Biophysics
| | - Danny Manor
- Nutrition, .,Pharmacology, and.,the Case Comprehensive Cancer Center and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, .,the Case Comprehensive Cancer Center and.,Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106 and.,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
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