1
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Girard E, Lopes P, Spoerner M, Dhaussy AC, Prangé T, Kalbitzer HR, Colloc'h N. High Pressure Promotes Binding of the Allosteric Inhibitor Zn 2+-Cyclen in Crystals of Activated H-Ras. Chemistry 2024; 30:e202400304. [PMID: 38647362 DOI: 10.1002/chem.202400304] [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: 01/24/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
In this work, we experimentally investigate the potency of high pressure to drive a protein toward an excited state where an inhibitor targeted for this state can bind. Ras proteins are small GTPases cycling between active GTP-bound and inactive GDP-bound states. Various states of GTP-bound Ras in active conformation coexist in solution, amongst them, state 2 which binds to effectors, and state 1, weakly populated at ambient conditions, which has a low affinity for effectors. Zn2+-cyclen is an allosteric inhibitor of Ras protein, designed to bind specifically to the state 1. In H-Ras(wt).Mg2+.GppNHp crystals soaked with Zn2+-cyclen, no binding could be observed, as expected in the state 2 conformation which is the dominant state at ambient pressure. Interestingly, Zn2+-cyclen binding is observed at 500 MPa pressure, close to the nucleotide, in Ras protein that is driven by pressure to a state 1 conformer. The unknown binding mode of Zn2+-cyclen to H-Ras can thus be fully characterized in atomic details. As a more general conjunction from our study, high pressure x-ray crystallography turns out to be a powerful method to induce transitions allowing drug binding in proteins that are in low-populated conformations at ambient conditions, enabling the design of specific inhibitors.
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Affiliation(s)
- Eric Girard
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Pedro Lopes
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Spoerner
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | | | - Thierry Prangé
- CiTCoM, CNRS, Faculté de Pharmacie, Université de Paris-Cité, Paris, France
| | - Hans Robert Kalbitzer
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Nathalie Colloc'h
- ISTCT UMR6030, Centre Cyceron, CNRS - Université de Caen Normandie - Normandie Université, Caen, France
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2
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Pagba CV, Gupta AK, Dilsha K, Sadrpour P, Jakubec J, Prakash P, van der Hoeven D, Cho KJ, Gilbertson S, Gorfe AA. Biophysical and Biochemical Characterization of Structurally Diverse Small Molecule Hits for KRAS Inhibition. Chembiochem 2024; 25:e202300827. [PMID: 38349283 DOI: 10.1002/cbic.202300827] [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: 12/12/2023] [Revised: 02/12/2024] [Indexed: 03/08/2024]
Abstract
We describe six compounds as early hits for the development of direct inhibitors of KRAS, an important anticancer drug target. We show that these compounds bind to KRAS with affinities in the low micromolar range and exert different effects on its interactions with binding partners. Some of the compounds exhibit selective binding to the activated form of KRAS and inhibit signal transduction through both the MAPK or the phosphatidylinositide 3-kinase PI3K-protein kinase B (AKT) pathway in cells expressing mutant KRAS. Most inhibit intrinsic and/or SOS-mediated KRAS activation while others inhibit RAS-effector interaction. We propose these compounds as starting points for the development of non-covalent allosteric KRAS inhibitors.
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Affiliation(s)
- Cynthia V Pagba
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Amit K Gupta
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Kasuni Dilsha
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Parisa Sadrpour
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Jacob Jakubec
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St., Houston, Texas, 77030, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - Scott Gilbertson
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, TX 77204, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
- Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, 6431 Fannin St., Houston, Texas, 77030, USA
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3
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Yu Z, Wang Z, Cui X, Cao Z, Zhang W, Sun K, Hu G. Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics. Molecules 2024; 29:645. [PMID: 38338389 PMCID: PMC10856033 DOI: 10.3390/molecules29030645] [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: 11/27/2023] [Revised: 01/01/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The HRAS protein is considered a critical target for drug development in cancers. It is vital for effective drug development to understand the effects of mutations on the binding of GTP and GDP to HRAS. We conducted Gaussian accelerated molecular dynamics (GaMD) simulations and free energy landscape (FEL) calculations to investigate the impacts of two mutations (A59E and K117R) on GTP and GDP binding and the conformational states of the switch domain. Our findings demonstrate that these mutations not only modify the flexibility of the switch domains, but also affect the correlated motions of these domains. Furthermore, the mutations significantly disrupt the dynamic behavior of the switch domains, leading to a conformational change in HRAS. Additionally, these mutations significantly impact the switch domain's interactions, including their hydrogen bonding with ligands and electrostatic interactions with magnesium ions. Since the switch domains are crucial for the binding of HRAS to effectors, any alterations in their interactions or conformational states will undoubtedly disrupt the activity of HRAS. This research provides valuable information for the design of drugs targeting HRAS.
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Affiliation(s)
- Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
| | - Zhen Wang
- Pingyin People’s Hospital, Jinan 250400, China; (Z.W.); (X.C.)
| | - Xiuzhen Cui
- Pingyin People’s Hospital, Jinan 250400, China; (Z.W.); (X.C.)
| | - Zanxia Cao
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
| | - Wanyunfei Zhang
- School of Science, Xi’an Polytechnic University, Xi’an 710048, China; (W.Z.); (K.S.)
| | - Kunxiao Sun
- School of Science, Xi’an Polytechnic University, Xi’an 710048, China; (W.Z.); (K.S.)
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
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4
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Eliminating oncogenic RAS: back to the future at the drawing board. Biochem Soc Trans 2023; 51:447-456. [PMID: 36688434 PMCID: PMC9987992 DOI: 10.1042/bst20221343] [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: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/24/2023]
Abstract
RAS drug development has made enormous strides in the past ten years, with the first direct KRAS inhibitor being approved in 2021. However, despite the clinical success of covalent KRAS-G12C inhibitors, we are immediately confronted with resistances as commonly found with targeted drugs. Previously believed to be undruggable due to its lack of obvious druggable pockets, a couple of new approaches to hit this much feared oncogene have now been carved out. We here concisely review these approaches to directly target four druggable sites of RAS from various angles. Our analysis focuses on the lessons learnt during the development of allele-specific covalent and non-covalent RAS inhibitors, the potential of macromolecular binders to facilitate the discovery and validation of targetable sites on RAS and finally an outlook on a future that may engage more small molecule binders to become drugs. We foresee that the latter could happen mainly in two ways: First, non-covalent small molecule inhibitors may be derived from the development of covalent binders. Second, reversible small molecule binders could be utilized for novel targeting modalities, such as degraders of RAS. Provided that degraders eliminate RAS by recruiting differentially expressed E3-ligases, this approach could enable unprecedented tissue- or developmental stage-specific destruction of RAS with potential advantages for on-target toxicity. We conclude that novel creative ideas continue to be important to exterminate RAS in cancer and other RAS pathway-driven diseases, such as RASopathies.
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5
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Shu L, Wang D, Saba NF, Chen ZG. A Historic Perspective and Overview of H-Ras Structure, Oncogenicity, and Targeting. Mol Cancer Ther 2021; 19:999-1007. [PMID: 32241873 DOI: 10.1158/1535-7163.mct-19-0660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/02/2019] [Accepted: 01/14/2020] [Indexed: 12/24/2022]
Abstract
H-Ras is a unique isoform of the Ras GTPase family, one of the most prominently mutated oncogene families across the cancer landscape. Relative to other isoforms, though, mutations of H-Ras account for the smallest proportion of mutant Ras cancers. Yet, in recent years, there have been renewed efforts to study this isoform, especially as certain H-Ras-driven cancers, like those of the head and neck, have become more prominent. Important advances have therefore been made not only in the understanding of H-Ras structural biology but also in approaches designed to inhibit and impair its signaling activity. In this review, we outline historic and present initiatives to elucidate the mechanisms of H-Ras-dependent tumorigenesis as well as highlight ongoing developments in the quest to target this critical oncogene.
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Affiliation(s)
- Lihua Shu
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Dongsheng Wang
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia
| | - Nabil F Saba
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.
| | - Zhuo G Chen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia.
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6
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Chen J, Wang W, Pang L, Zhu W. Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics. Phys Chem Chem Phys 2021; 22:21238-21250. [PMID: 32930679 DOI: 10.1039/d0cp03766d] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Uncovering molecular basis with regard to the conformational change of two switches I and II in the GppNHp (GNP)-bound H-Ras is highly significant for the understanding of Ras signaling. For this purpose, accelerated molecular dynamics (aMD) simulations and principal component (PC) analysis are integrated to probe the effect of mutations G12V, T35S and Q61K on conformational transformation between two switches of the GNP-bound H-Ras. The RMSF and cross-correlation analyses suggest that three mutations exert a vital effect on the flexibility and internal dynamics of two switches in the GNP-bound H-Ras. The results stemming from PC analysis indicate that two switches in the GNP-bound WT H-Ras tend to form a closed state in most conformations, while those in the GNP-bound mutated H-Ras display transformation between different states. This conclusion is further supported by free energy landscapes constructed by using the distances of residues 12 away from 35 and 35 away from 61 as reaction coordinates and different experimental studies. Interaction scanning is performed on aMD trajectories and the information shows that conformational transformations of two switches I and II induced by mutations extremely affect the GNP-residue interactions. Meanwhile, the scanning results also signify that residues G15, A18, F28, K117, A146 and K147 form stable contacts with GNP, while residues D30, E31, Y32, D33, P34 and E62 in two switches I and II produce unstable contacts with GNP. This study not only reveals dynamic behavior changes of two switches in H-Ras induced by mutations, but also unveils general principles and mechanisms with regard to functional conformational changes of H-Ras.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| | - Weiliang Zhu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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7
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Chen X, Gao H, Long D. Millisecond Allosteric Dynamics of Activated Ras Reproduced with a Slowly Hydrolyzable GTP Analogue. Chembiochem 2020; 22:1079-1083. [PMID: 33140496 DOI: 10.1002/cbic.202000698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/01/2020] [Indexed: 12/29/2022]
Abstract
The millisecond timescale dynamics of activated Ras transiently sample a low-populated conformational state that has distinct surface property from the major state and represents a promising target for binding of small-molecule compounds. To avoid the complications of hydrolysis, dynamics and other properties of active Ras have so far been routinely investigated by using non-hydrolyzable GTP analogues, which, however, were previously reported to alter both the kinetics and distribution of the conformational exchange. In this study, we quantitatively measured and validated the internal dynamics of Ras complexed with a slowly hydrolyzable GTP analogue, GTPγS, which increases the lifetime of active Ras by 23 times relative to that of native GTP. It was found that GTPγS, in addition to its better mimicking of the exchange kinetics than the commonly used non-hydrolyzable analogues GppNHp and GppCH2 p, can rigorously reproduce the natural dynamics network in active Ras, thus indicating its fitness for use in the development of allosteric inhibitors.
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Affiliation(s)
- Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, and School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, P. R. China
| | - Hexuan Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, and School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, P. R. China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, and School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, P. R. China.,Department of Chemistry, University of Science and Technology of China Hefei, Anhui 230026, P. R. China
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8
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Marshall CB, KleinJan F, Gebregiworgis T, Lee KY, Fang Z, Eves BJ, Liu NF, Gasmi-Seabrook GMC, Enomoto M, Ikura M. NMR in integrated biophysical drug discovery for RAS: past, present, and future. JOURNAL OF BIOMOLECULAR NMR 2020; 74:531-554. [PMID: 32804298 DOI: 10.1007/s10858-020-00338-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Mutations in RAS oncogenes occur in ~ 30% of human cancers, with KRAS being the most frequently altered isoform. RAS proteins comprise a conserved GTPase domain and a C-terminal lipid-modified tail that is unique to each isoform. The GTPase domain is a 'switch' that regulates multiple signaling cascades that drive cell growth and proliferation when activated by binding GTP, and the signal is terminated by GTP hydrolysis. Oncogenic RAS mutations disrupt the GTPase cycle, leading to accumulation of the activated GTP-bound state and promoting proliferation. RAS is a key target in oncology, however it lacks classic druggable pockets and has been extremely challenging to target. RAS signaling has thus been targeted indirectly, by harnessing key downstream effectors as well as upstream regulators, or disrupting the proper membrane localization required for signaling, by inhibiting either lipid modification or 'carrier' proteins. As a small (20 kDa) protein with multiple conformers in dynamic equilibrium, RAS is an excellent candidate for NMR-driven characterization and screening for direct inhibitors. Several molecules have been discovered that bind RAS and stabilize shallow pockets through conformational selection, and recent compounds have achieved substantial improvements in affinity. NMR-derived insight into targeting the RAS-membrane interface has revealed a new strategy to enhance the potency of small molecules, while another approach has been development of peptidyl inhibitors that bind through large interfaces rather than deep pockets. Remarkable progress has been made with mutation-specific covalent inhibitors that target the thiol of a G12C mutant, and these are now in clinical trials. Here we review the history of RAS inhibitor development and highlight the utility of NMR and integrated biophysical approaches in RAS drug discovery.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ben J Eves
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ningdi F Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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Gasper R, Wittinghofer F. The Ras switch in structural and historical perspective. Biol Chem 2020; 401:143-163. [PMID: 31600136 DOI: 10.1515/hsz-2019-0330] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022]
Abstract
Since its discovery as an oncogene more than 40 years ago, Ras has been and still is in the focus of many academic and pharmaceutical labs around the world. A huge amount of work has accumulated on its biology. However, many questions about the role of the different Ras isoforms in health and disease still exist and a full understanding will require more intensive work in the future. Here we try to survey some of the structural findings in a historical perspective and how it has influenced our understanding of structure-function and mechanistic relationships of Ras and its interactions. The structures show that Ras is a stable molecular machine that uses the dynamics of its switch regions for the interaction with all regulators and effectors. This conformational flexibility has been used to create small molecule drug candidates against this important oncoprotein.
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Affiliation(s)
- Raphael Gasper
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
| | - Fred Wittinghofer
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany
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10
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Liu D, Chen X, Long D. NMR-Derived Conformational Ensemble of State 1 of Activated Ras Reveals Insights into a Druggable Pocket. J Phys Chem Lett 2020; 11:3642-3646. [PMID: 32302142 DOI: 10.1021/acs.jpclett.0c00858] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The lack of apparent pockets in the ground conformation of Ras has long challenged the rational design of inhibitors against this oncogenic protein. The sparsely populated, transiently formed state 1 of activated Ras, on the other hand, shows appreciable surface roughness and is increasingly recognized as a potential target for drug discovery. State 1, however, is extremely flexible, and a static structure cannot fully unveil its conformational space that can be exploited for drug design. Here, we present a conformational ensemble of state 1 that was derived using chemical shift-based modeling. The ensemble reveals the intrinsic plasticity of a druggable pocket in state 1 and demonstrates the mechanism of conformational selection for inhibitor recognition. The large set of structural templates in the ensemble, providing a comprehensive description of thermally accessible pocket conformations, is expected to significantly aid the rational design of anti-Ras drugs.
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Affiliation(s)
- Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, China
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11
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Pálfy G, Vida I, Perczel A. 1H, 15N backbone assignment and comparative analysis of the wild type and G12C, G12D, G12V mutants of K-Ras bound to GDP at physiological pH. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:1-7. [PMID: 31468366 PMCID: PMC7069925 DOI: 10.1007/s12104-019-09909-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/02/2019] [Indexed: 05/14/2023]
Abstract
K-Ras protein is a membrane-bound small GTPase acting as a molecular switch. It plays a key role in many signal transduction pathways regulating cell proliferation, differentiation, survival, etc. It alternates between its GTP-bound active and the GDP-bound inactive conformers regulated by guanine nucleotide exchange factors and GTPase activating proteins. Its most frequent oncogenic mutants are G12C, G12D, and G12V that have impaired GTPase activity, thus induce malignant tumors. Here we report the resonance assignment of the backbone 1H and 15N nuclei of K-Ras wildtype, G12C, G12D and G12V proteins' catalytic G domain (1-169 residues) in GDP-bound state, and 13C of backbone and side chains of G12C mutant at physiological pH 7.4. Triple resonance data were used to get secondary structure information and backbone dynamics of G12C, the best-known drug target among K-Ras mutants. Simultaneous investigation of G12C, G12D and G12V mutants, along with the wild type form at the very same conditions allowed us to perform a comprehensive analysis based on the combined chemical shifts to reveal the effect of mutation at G12 position on structure. Intriguingly, the G12C and G12V mutants found to be structurally very similar at the three most important regions of K-Ras (P-loop, Switch-I, Switch-II), while the G12D mutant significantly differs at P-loop and Switch-II from the wildtype as well as G12C and G12V mutants. However, in Switch-I it hardly deviates from the wildtype protein.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, 1/a. Pázmány Péter stny, Budapest, H-1117, Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, 1/a. Pázmány Péter stny, Budapest, H-1117, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, 1/a. Pázmány Péter stny, Budapest, H-1117, Hungary.
- MTA-ELTE Protein Modeling Research Group, Institute of Chemistry, Eötvös Loránd University, 1/a. Pázmány Péter stny, Budapest, H-1117, Hungary.
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12
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Dynamic Protein Allosteric Regulation and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:25-43. [DOI: 10.1007/978-981-13-8719-7_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Chen X, Yao H, Wang H, Mao Y, Liu D, Long D. Extending the Lifetime of Native GTP‐Bound Ras for Site‐Resolved NMR Measurements: Quantifying the Allosteric Dynamics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Haijie Yao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Hui Wang
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Yunyun Mao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life SciencesUniversity of Science and Technology of China 443 Huangshan Street Hefei Anhui 230027 China
- Department of ChemistryUniversity of Science and Technology of China Hefei Anhui China
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14
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Chen X, Yao H, Wang H, Mao Y, Liu D, Long D. Extending the Lifetime of Native GTP-Bound Ras for Site-Resolved NMR Measurements: Quantifying the Allosteric Dynamics. Angew Chem Int Ed Engl 2019; 58:2730-2733. [PMID: 30681242 DOI: 10.1002/anie.201812902] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Indexed: 12/18/2022]
Abstract
Characterization of native GTP-bound Ras is important for an appreciation of its cellular signaling and for the design of inhibitors, which however has been depressed by its intrinsic instability. Herein, an effective approach for extending the lifetime of Ras⋅GTP samples by exploiting the active role of Son of Sevenless (Sos) is demonstrated that sustains the activated state of Ras. This approach, combined with a postprocessing method that suppresses residual Ras⋅GDP signals, is applied to the site-resolved NMR measurement of the allosteric dynamics of Ras⋅GTP. The observed network of concerted motions well covers the recently identified allosteric inhibitor-binding pockets, but the motions are more confined than those of Ras⋅GppNHp, advocating the use of native GTP for development of allosteric inhibitors. The Sos-based approach is anticipated to generally facilitate experiments on active Ras when native GTP is preferred.
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Affiliation(s)
- Xiaomin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Haijie Yao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Hui Wang
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Yunyun Mao
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China
| | - Dong Long
- Hefei National Laboratory for Physical Sciences at the Microscale & School of Life Sciences, University of Science and Technology of China, 443 Huangshan Street, Hefei, Anhui, 230027, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, China
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Abdelkarim H, Hitchinson B, Banerjee A, Gaponenko V. Advances in NMR Methods to Identify Allosteric Sites and Allosteric Ligands. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:171-186. [PMID: 31707704 DOI: 10.1007/978-981-13-8719-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
NMR allows assessment of protein structure in solution. Unlike conventional X-ray crystallography that provides snapshots of protein conformations, all conformational states are simultaneously accessible to analysis by NMR. This is a significant advantage for discovery and characterization of allosteric effects. These effects are observed when binding at one site of the protein affects another distinct site through conformational transitions. Allosteric regulation of proteins has been observed in multiple physiological processes in health and disease, providing an opportunity for the development of allosteric inhibitors. These compounds do not directly interact with the orthosteric site of the protein but influence its structure and function. In this book chapter, we provide an overview on how NMR methods are utilized to identify allosteric sites and to discover novel inhibitors, highlighting examples from the field. We also describe how NMR has contributed to understanding of allosteric mechanisms and propose that it is likely to play an important role in clarification and further development of key concepts of allostery.
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Affiliation(s)
- Hazem Abdelkarim
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ben Hitchinson
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
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