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Yun SD, Scott E, Chang JY, Bahramimoghaddam H, Lynn M, Lantz C, Russell DH, Laganowsky A. Capturing RAS oligomerization on a membrane. Proc Natl Acad Sci U S A 2024; 121:e2405986121. [PMID: 39145928 DOI: 10.1073/pnas.2405986121] [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: 03/22/2024] [Accepted: 07/09/2024] [Indexed: 08/16/2024] Open
Abstract
RAS GTPases associate with the biological membrane where they function as molecular switches to regulate cell growth. Recent studies indicate that RAS proteins oligomerize on membranes, and disrupting these assemblies represents an alternative therapeutic strategy. However, conflicting reports on RAS assemblies, ranging in size from dimers to nanoclusters, have brought to the fore key questions regarding the stoichiometry and parameters that influence oligomerization. Here, we probe three isoforms of RAS [Kirsten Rat Sarcoma viral oncogene (KRAS), Harvey Rat Sarcoma viral oncogene (HRAS), and Neuroblastoma oncogene (NRAS)] directly from membranes using mass spectrometry. We show that KRAS on membranes in the inactive state (GDP-bound) is monomeric but forms dimers in the active state (GTP-bound). We demonstrate that the small molecule BI2852 can induce dimerization of KRAS, whereas the binding of effector proteins disrupts dimerization. We also show that RAS dimerization is dependent on lipid composition and reveal that oligomerization of NRAS is regulated by palmitoylation. By monitoring the intrinsic GTPase activity of RAS, we capture the emergence of a dimer containing either mixed nucleotides or GDP on membranes. We find that the interaction of RAS with the catalytic domain of Son of Sevenless (SOScat) is influenced by membrane composition. We also capture the activation and monomer to dimer conversion of KRAS by SOScat. These results not only reveal the stoichiometry of RAS assemblies on membranes but also uncover the impact of critical factors on oligomerization, encompassing regulation by nucleotides, lipids, and palmitoylation.
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Affiliation(s)
- Sangho D Yun
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | | | - Michael Lynn
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Carter Lantz
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
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2
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Haertle L, Munawar U, Hernández HNC, Arroyo-Barea A, Heckel T, Cuenca I, Martin L, Höschle C, Müller N, Vogt C, Bischler T, Del Campo PL, Han S, Buenache N, Zhou X, Bassermann F, Waldschmidt J, Steinbrunn T, Rasche L, Stühmer T, Martinez-Lopez J, Martin Kortüm K, Barrio S. Clonal competition assays identify fitness signatures in cancer progression and resistance in multiple myeloma. Hemasphere 2024; 8:e110. [PMID: 38993727 PMCID: PMC11237348 DOI: 10.1002/hem3.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 07/13/2024] Open
Abstract
Multiple myeloma (MM) is a genetically heterogeneous disease and the management of relapses is one of the biggest clinical challenges. TP53 alterations are established high-risk markers and are included in the current disease staging criteria. KRAS is the most frequently mutated gene affecting around 20% of MM patients. Applying Clonal Competition Assays (CCA) by co-culturing color-labeled genetically modified cell models, we recently showed that mono- and biallelic alterations in TP53 transmit a fitness advantage to the cells. Here, we report a similar dynamic for two mutations in KRAS (G12A and A146T), providing a biological rationale for the high frequency of KRAS and TP53 alterations at MM relapse. Resistance mutations, on the other hand, did not endow MM cells with a general fitness advantage but rather presented a disadvantage compared to the wild-type. CUL4B KO and IKZF1 A152T transmit resistance against immunomodulatory agents, PSMB5 A20T to proteasome inhibition. However, MM cells harboring such lesions only outcompete the culture in the presence of the respective drug. To better prevent the selection of clones with the potential of inducing relapse, these results argue in favor of treatment-free breaks or a switch of the drug class given as maintenance therapy. In summary, the fitness benefit of TP53 and KRAS mutations was not treatment-related, unlike patient-derived drug resistance alterations that may only induce an advantage under treatment. CCAs are suitable models for the study of clonal evolution and competitive (dis)advantages conveyed by a specific genetic lesion of interest, and their dependence on external factors such as the treatment.
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Affiliation(s)
- Larissa Haertle
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
- Department of Medicine III, Klinikum rechts der Isar Technical University of Munich Munich Germany
| | - Umair Munawar
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Hipólito N C Hernández
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Andres Arroyo-Barea
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
- Department of Biochemistry and Molecular Biology, Pharmacy School Complutense University Madrid Madrid Spain
| | - Tobias Heckel
- Core Unit Systems Medicine University of Würzburg Würzburg Germany
| | - Isabel Cuenca
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Lucia Martin
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Carlotta Höschle
- TranslaTUM, Center for Translational Cancer Research Technical University of Munich Munich Germany
| | - Nicole Müller
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Cornelia Vogt
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | | | - Paula L Del Campo
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Seungbin Han
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Natalia Buenache
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - Xiang Zhou
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Florian Bassermann
- Department of Medicine III, Klinikum rechts der Isar Technical University of Munich Munich Germany
- TranslaTUM, Center for Translational Cancer Research Technical University of Munich Munich Germany
| | - Johannes Waldschmidt
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Torsten Steinbrunn
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
- Department of Medical Oncology Dana-Farber Cancer Institute, Harvard Medical School Boston Massachusetts USA
| | - Leo Rasche
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Thorsten Stühmer
- Comprehensive Cancer Center Mainfranken University Hospital Würzburg Würzburg Germany
| | - Joaquin Martinez-Lopez
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
| | - K Martin Kortüm
- Department of Internal Medicine II University Hospital Würzburg Würzburg Germany
| | - Santiago Barrio
- Department of Hematology Hospital Universitario 12 de Octubre, Spanish National Cancer Research Center (CNIO), Complutense University Madrid Madrid Spain
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3
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Chen Y, Liu QP, Xie H, Ding J. From bench to bedside: current development and emerging trend of KRAS-targeted therapy. Acta Pharmacol Sin 2024; 45:686-703. [PMID: 38049578 PMCID: PMC10943119 DOI: 10.1038/s41401-023-01194-4] [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: 07/23/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most frequently mutated oncogene in human cancers with mutations predominantly occurring in codon 12. These mutations disrupt the normal function of KRAS by interfering with GTP hydrolysis and nucleotide exchange activity, making it prone to the GTP-bound active state, thus leading to sustained activation of downstream pathways. Despite decades of research, there has been no progress in the KRAS drug discovery until the groundbreaking discovery of covalently targeting the KRASG12C mutation in 2013, which led to revolutionary changes in KRAS-targeted therapy. So far, two small molecule inhibitors sotorasib and adagrasib targeting KRASG12C have received accelerated approval for the treatment of non-small cell lung cancer (NSCLC) harboring KRASG12C mutations. In recent years, rapid progress has been achieved in the KRAS-targeted therapy field, especially the exploration of KRASG12C covalent inhibitors in other KRASG12C-positive malignancies, novel KRAS inhibitors beyond KRASG12C mutation or pan-KRAS inhibitors, and approaches to indirectly targeting KRAS. In this review, we provide a comprehensive overview of the molecular and mutational characteristics of KRAS and summarize the development and current status of covalent inhibitors targeting the KRASG12C mutation. We also discuss emerging promising KRAS-targeted therapeutic strategies, with a focus on mutation-specific and direct pan-KRAS inhibitors and indirect KRAS inhibitors through targeting the RAS activation-associated proteins Src homology-2 domain-containing phosphatase 2 (SHP2) and son of sevenless homolog 1 (SOS1), and shed light on current challenges and opportunities for drug discovery in this field.
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Affiliation(s)
- Yi Chen
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Pei Liu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Chemical and Environment Engineering, Science and Engineering Building, The University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Hua Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
| | - Jian Ding
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Jiang Z, Li Y, Zhou X, Wen J, Zheng P, Zhu W. Research progress on small molecule inhibitors targeting KRAS G12C with acrylamide structure and the strategies for solving KRAS inhibitor resistance. Bioorg Med Chem 2024; 100:117627. [PMID: 38310752 DOI: 10.1016/j.bmc.2024.117627] [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: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
KRAS (Kirsten-RAS) is a highly mutated gene in the RAS (rat sarcoma) gene family that acts as a critical switch in intracellular signaling pathways, regulating cell proliferation, differentiation, and survival. The continuous activation of KRAS protein resulting from mutations leads to the activation of multiple downstream signaling pathways, inducing the development of malignant tumors. Despite the significant role of KRAS in tumorigenesis, targeted drugs against KRAS gene mutations have failed, and KRAS was once considered an undruggable target. The development of KRAS G12C mutant conformational modulators and the introduction of Sotorasib (R&D code: AMG510) have been a breakthrough in this field, with its remarkable clinical outcomes. Consequently, there is now a great number of KRAS G12C mutations. Patent applications for mutant GTPase KRAS G12C inhibitors, which are said to be covalently modified by cysteine codon 12, have been submitted since 2014. This review classifies KRAS G12C inhibitors based on their chemical structure and evaluates their biological properties. Additionally, it discusses the obstacles encountered in KRAS inhibitor research and the corresponding solutions.
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Affiliation(s)
- Zhiyan Jiang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi 330013, China
| | - Yan Li
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi 330013, China
| | - Xin Zhou
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi 330013, China
| | - Jie Wen
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi 330013, China
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi 330013, China.
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, 605 Fenglin Road, Nanchang, Jiangxi 330013, China.
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5
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Waybright T, Stephen AG. Nucleotide Exchange on RAS Proteins Using Hydrolysable and Non-hydrolysable Nucleotides. Methods Mol Biol 2024; 2797:35-46. [PMID: 38570451 DOI: 10.1007/978-1-0716-3822-4_4] [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] [Indexed: 04/05/2024]
Abstract
Biochemical and biophysical assays using recombinant RAS require the protein to be in either the active or inactive state. Here we describe methods to exchange the nucleotide present in the purified RAS protein with either GDPβS, GppNHp, or GTP depending on the assay requirement. In addition, we also describe the HPLC method used to validate the exchange process and provide information on the efficiency of the nucleotide exchange.
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Affiliation(s)
- Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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6
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Yun S, Scott E, Laganowsky A. Biophysical Characterization of RAS-SOS Complexes by Native Mass Spectrometry. Methods Mol Biol 2024; 2797:177-193. [PMID: 38570460 DOI: 10.1007/978-1-0716-3822-4_13] [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] [Indexed: 04/05/2024]
Abstract
RAS is regulated by specific guanine nucleotide exchange factors, such as Son of Sevenless (SOS), that activates RAS by facilitating the exchange of inactive, GDP-bound RAS with GTP. The catalytic activity of SOS is known to be allosterically modulated by an active, GTP-bound RAS. However, it remains poorly understood how oncogenic RAS mutants interact with SOS and modulate its activity. In this chapter, we describe the application of native mass spectrometry (MS) to monitor the assembly of the catalytic domain of SOS (SOScat) with RAS and cancer-associated mutants. Results from this approach have led to the discovery of different molecular assemblies and distinct conformers of SOScat engaging KRAS. It was also found that KRASG13D exhibits high affinity for SOScat and is a potent allosteric modulator of its SOScat activity. KRASG13D-GTP can allosterically increase the nucleotide exchange rate of KRAS at the active site by more than twofold compared to the wild-type protein. Furthermore, small-molecule RAS•SOS disruptors fail to dissociate KRASG13D•SOScat complexes, underscoring the need for more potent disruptors targeting oncogenic RAS mutants. Taken together, native MS will be instrumental in better understanding the interaction between oncogenic RAS mutants and SOS, which is of crucial importance for development of improved therapeutics.
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Affiliation(s)
- Sangho Yun
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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7
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Bhadhadhara K, Jani V, Koulgi S, Sonavane U, Joshi R. Studying early structural changes in SOS1 mediated KRAS activation mechanism. Curr Res Struct Biol 2023; 7:100115. [PMID: 38188543 PMCID: PMC10765296 DOI: 10.1016/j.crstbi.2023.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
KRAS activation is known to be modulated by a guanine nucleotide exchange factor (GEF), namely, Son of Sevenless1 (SOS1). SOS1 facilitates the exchange of GDP to GTP thereby leading to activation of KRAS. The binding of GDP/GTP to KRAS at the REM/allosteric site of SOS1 regulates the activation of KRAS at CDC25/catalytic site by facilitating its exchange. Different aspects of the allosteric activation of KRAS through SOS1 are still being explored. To understand the SOS1 mediated activation of KRAS, molecular dynamics simulations for a total of nine SOS1 complexes (KRAS-SOS1-KRAS) were performed. These nine systems comprised different combinations of KRAS-bound nucleotides (GTP/GDP) at REM and CDC25 sites of SOS1. Various conformational and thermodynamic parameters were analyzed for these simulation systems. MMPBSA free energy analysis revealed that binding at CDC25 site of SOS1 was significantly low for GDP-bound KRAS as compared to that of GTP-bound KRAS. It was observed that presence of either GDP/GTP bound KRAS at the REM site of SOS1 affected the activation related changes in the KRAS present at CDC25 site. The conformational changes at the catalytic site of SOS1 resulting from GDP/GTP-bound KRAS at the allosteric changes may hint at KRAS activation through different pathways (slow/fast/rare). The allosteric effect on activation of KRAS at CDC25 site may be due to conformations adopted by switch-I, switch-II, beta2 regions of KRAS at REM site. The effect of structural rearrangements occurring at allosteric KRAS may have led to increased interactions between SOS1 and KRAS at both the sites. The SOS1 residues involved in these important interactions with KRAS at the REM site were R694, S732 and K735. Whereas the ones interacting with KRAS at CDC25 site were S807, W809 and K814. This may suggest the crucial role of these residues in guiding the allosteric activation of KRAS at CDC25 site. The conformational shifts observed in the switch-I, switch-II and alpha3 regions of KRAS at CDC25 site may be attributed to be a part of allosteric activation. The binding affinities, interacting residues and conformational dynamics may provide an insight into development of inhibitors targeting the SOS1 mediated KRAS activation.
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Affiliation(s)
- Kirti Bhadhadhara
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Vinod Jani
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Shruti Koulgi
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Uddhavesh Sonavane
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Rajendra Joshi
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
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Durojaye OA, Ejaz U, Uzoeto HO, Fadahunsi AA, Opabunmi AO, Ekpo DE, Sedzro DM, Idris MO. CSC01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach. Amino Acids 2023; 55:1745-1764. [PMID: 37500789 DOI: 10.1007/s00726-023-03304-2] [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: 01/03/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
About 30% of malignant tumors include KRAS mutations, which are frequently required for the development and maintenance of malignancies. KRAS is now a top-priority cancer target as a result. After years of research, it is now understood that the oncogenic KRAS-G12C can be targeted. However, many other forms, such as the G13D mutant, are yet to be addressed. Here, we used a receptor-based pharmacophore modeling technique to generate potential inhibitors of the KRAS-G13D oncogenic mutant. Using a comprehensive virtual screening workflow model, top hits were selected, out of which CSC01 was identified as a promising inhibitor of the oncogenic KRAS mutant (G13D). The stability of CSC01 upon binding the switch II pocket was evaluated through an exhaustive molecular dynamics simulation study. The several post-simulation analyses conducted suggest that CSC01 formed a stable complex with KRAS-G13D. CSC01, through a dynamic protein-ligand interaction profiling analysis, was also shown to maintain strong interactions with the mutated aspartic acid residue throughout the simulation. Although binding free energy analysis through the umbrella sampling approach suggested that the affinity of CSC01 with the switch II pocket of KRAS-G13D is moderate, our DFT analysis showed that the stable interaction of the compound might be facilitated by the existence of favorable molecular electrostatic potentials. Furthermore, based on ADMET predictions, CSC01 demonstrated a satisfactory drug likeness and toxicity profile, making it an exemplary candidate for consideration as a potential KRAS-G13D inhibitor.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Department of Chemical Sciences, Coal City University, Emene, EnuguState, Nigeria.
| | - Umer Ejaz
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, Anhui, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Henrietta Onyinye Uzoeto
- Federal College of Dental Technology, Trans-Ekulu, Enugu State, Nigeria
- Department of Biological Sciences, Coal City University, Emene, Enugu State, Nigeria
| | - Adeola Abraham Fadahunsi
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, 04469, USA
| | - Adebayo Oluwole Opabunmi
- RNA Medical Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daniel Emmanuel Ekpo
- Institute of Biological Science and Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, 530007, China
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, 410001, Nsukka, Enugu State, Nigeria
| | - Divine Mensah Sedzro
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, 53715, WI, USA.
| | - Mukhtar Oluwaseun Idris
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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9
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Yun SD, Scott E, Moghadamchargari Z, Laganowsky A. 2'-Deoxy Guanosine Nucleotides Alter the Biochemical Properties of Ras. Biochemistry 2023; 62:2450-2460. [PMID: 37487239 PMCID: PMC11131413 DOI: 10.1021/acs.biochem.3c00258] [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] [Indexed: 07/26/2023]
Abstract
Ras proteins in the mitogen-activated protein kinase (MAPK) signaling pathway represent one of the most frequently mutated oncogenes in cancer. Ras binds guanosine nucleotides and cycles between active (GTP) and inactive (GDP) conformations to regulate the MAPK signaling pathway. Guanosine and other nucleotides exist in cells as either 2'-hydroxy or 2'-deoxy forms, and imbalances in the deoxyribonucleotide triphosphate pool have been associated with different diseases, such as diabetes, obesity, and cancer. However, the biochemical properties of Ras bound to dGNP are not well understood. Herein, we use native mass spectrometry to monitor the intrinsic GTPase activity of H-Ras and N-Ras oncogenic mutants, revealing that the rate of 2'-deoxy guanosine triphosphate (dGTP) hydrolysis differs compared to the hydroxylated form, in some cases by seven-fold. Moreover, K-Ras expressed from HEK293 cells exhibited a higher than anticipated abundance of dGNP, despite the low abundance of dGNP in cells. Additionally, the GTPase and dGTPase activity of K-RasG12C was found to be accelerated by 10.2- and 3.8-fold in the presence of small molecule covalent inhibitors, which may open opportunities for the development of Pan-Ras inhibitors. The molecular assemblies formed between H-Ras and N-Ras, including mutant forms, with the catalytic domain of SOS (SOScat) were also investigated. The results show that the different mutants of H-Ras and N-Ras not only engage SOScat differently, but these assemblies are also dependent on the form of guanosine triphosphate bound to Ras. These findings bring to the forefront a new perspective on the nucleotide-dependent biochemical properties of Ras that may have implications for the activation of the MAPK signaling pathway and Ras-driven cancers.
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Affiliation(s)
- Sangho D. Yun
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | | | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
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10
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Chao FA, Chan AH, Dharmaiah S, Schwieters CD, Tran TH, Taylor T, Ramakrishnan N, Esposito D, Nissley DV, McCormick F, Simanshu DK, Cornilescu G. Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D. Commun Biol 2023; 6:594. [PMID: 37268708 DOI: 10.1038/s42003-023-04960-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRASG13D, which suggests an exchange between two conformational states in solution. Methyl and 31P NMR spectra of active KRASG13D in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major Pγ atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRASG13D and KRASG13D-RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRASG13D, showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.
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Affiliation(s)
- Fa-An Chao
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, 20892-5624, Bethesda, MD, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
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11
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Zhou Z, Zhou G, Zhou C, Fan Z, Cui R, Li Y, Li R, Gu Y, Li H, Ge Z, Cai X, Jiang B, Wang D, Zheng M, Xu T, Zhang S. Discovery of a Potent, Cooperative, and Selective SOS1 PROTAC ZZ151 with In Vivo Antitumor Efficacy in KRAS-Mutant Cancers. J Med Chem 2023; 66:4197-4214. [PMID: 36897932 DOI: 10.1021/acs.jmedchem.3c00075] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The linker moiety of a proteolysis-targeting chimera (PROTAC) molecule plays a critical role in modulating the degradation activity, target selectivity, and physico-chemical properties. However, the basics and underlying mechanisms of chemical modifications of the linker structure causing dramatic changes in the PROTAC degradation activity warrant further investigation. Herein, we report the design and characterization of a highly potent and selective SOS1 PROTAC ZZ151. After systematically modifying the linker length and composition, we observed that subtle modification of just one atom of the linker moiety of ZZ151 resulted in remarkable changes in the formation of the ternary complex and thus dramatically affected the degradation activities. ZZ151 quickly, specifically, and effectively induced SOS1 degradation; displayed potent antiproliferation activities against a broad panel of KRAS mutant-driven cancer cells; and showed superior anticancer activities in the KRASG12D- and G12V-mutant xenografts in mice. ZZ151 is a promising lead for developing new chemotherapies targeting KRAS mutants.
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Affiliation(s)
- Zehui Zhou
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Guizhen Zhou
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chuan Zhou
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zisheng Fan
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Rongrong Cui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yupeng Li
- Masonic Cancer Center & Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rui Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yuejiao Gu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Huajie Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zhiming Ge
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiaojia Cai
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Bing Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Dan Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Tianfeng Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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12
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [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: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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13
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Yang H, Zhou X, Fu D, Le C, Wang J, Zhou Q, Liu X, Yuan Y, Ding K, Xiao Q. Targeting RAS mutants in malignancies: successes, failures, and reasons for hope. Cancer Commun (Lond) 2023; 43:42-74. [PMID: 36316602 PMCID: PMC9859734 DOI: 10.1002/cac2.12377] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/15/2022] [Accepted: 10/13/2022] [Indexed: 01/22/2023] Open
Abstract
RAS genes are the most frequently mutated oncogenes and play critical roles in the development and progression of malignancies. The mutation, isoform (KRAS, HRAS, and NRAS), position, and type of substitution vary depending on the tissue types. Despite decades of developing RAS-targeted therapies, only small subsets of these inhibitors are clinically effective, such as the allele-specific inhibitors against KRASG12C . Targeting the remaining RAS mutants would require further experimental elucidation of RAS signal transduction, RAS-altered metabolism, and the associated immune microenvironment. This study reviews the mechanisms and efficacy of novel targeted therapies for different RAS mutants, including KRAS allele-specific inhibitors, combination therapies, immunotherapies, and metabolism-associated therapies.
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Affiliation(s)
- Hang Yang
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Xinyi Zhou
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Dongliang Fu
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Chenqin Le
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
| | - Jiafeng Wang
- Department of Pharmacology and Department of Gastroenterology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058P. R. China
| | - Quan Zhou
- Department of Cell BiologySchool of Basic Medical SciencesZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Xiangrui Liu
- Department of Pharmacology and Department of Gastroenterology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Ying Yuan
- Department of Medical Oncologythe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310058P. R. China
| | - Kefeng Ding
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
| | - Qian Xiao
- Department of Colorectal Surgery and OncologyKey Laboratory of Cancer Prevention and InterventionMinistry of EducationThe Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310009P. R. China
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14
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Rosen JC, Sacher A, Tsao MS. Direct GDP-KRAS G12C inhibitors and mechanisms of resistance: the tip of the iceberg. Ther Adv Med Oncol 2023; 15:17588359231160141. [PMID: 36950276 PMCID: PMC10026147 DOI: 10.1177/17588359231160141] [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: 10/08/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog mutations are observed in 25% of lung adenocarcinoma and 40% of these are G12C mutations. Historically, no approved targeted agents were available for patients with any KRAS mutation, and response rates to standard-of-care therapies were suboptimal. Newly developed inhibitors directed toward KRASG12C have been successful in clinical trials with overall response rates ranging between 32% and 46%, and two FDA approvals were granted in May 2021 and December 2022 as second-line or later monotherapies. However, rapid tumor resistance complicates their use as a monotherapy. With the rapid development of this novel class of inhibitors, it is important to discern the different types of tumor resistance that may arise and how each can differently contribute to tumor growth and survival. G12C inhibitor resistance is under investigation and combinations of therapies with G12C inhibitors have been proposed. Much of this insight is gleaned from preclinical investigations, as our knowledge of clinical resistance is in its infancy. In this review, we summarize the preclinical development of KRASG12C inhibitors, their clinical evaluations, different types of resistance mechanisms to these compounds, and ways of overcoming them. Finally, we underscore the importance of basic and translational investigations of these molecules in a landscape where their clinical evaluations garner the most attention, and we set the stage for what is to come.
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Affiliation(s)
- Joshua C. Rosen
- Princess Margaret Hospital Cancer Centre,
University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and
Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto,
ON, Canada
| | - Adrian Sacher
- Princess Margaret Hospital Cancer Centre,
University Health Network, Toronto, ON, Canada
- Division of Medical Oncology, Department of
Medicine, Princess Margaret Cancer Centre, Temerty Faculty of Medicine,
University of Toronto, Toronto, ON, Canada
- Department of Immunology, Temerty Faculty of
Medicine, University of Toronto, Toronto, ON, Canada
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15
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Zhu C, Guan X, Zhang X, Luan X, Song Z, Cheng X, Zhang W, Qin JJ. Targeting KRAS mutant cancers: from druggable therapy to drug resistance. Mol Cancer 2022; 21:159. [PMID: 35922812 PMCID: PMC9351107 DOI: 10.1186/s12943-022-01629-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) is the most frequently mutated oncogene, occurring in a variety of tumor types. Targeting KRAS mutations with drugs is challenging because KRAS is considered undruggable due to the lack of classic drug binding sites. Over the past 40 years, great efforts have been made to explore routes for indirect targeting of KRAS mutant cancers, including KRAS expression, processing, upstream regulators, or downstream effectors. With the advent of KRAS (G12C) inhibitors, KRAS mutations are now druggable. Despite such inhibitors showing remarkable clinical responses, resistance to monotherapy of KRAS inhibitors is eventually developed. Significant progress has been made in understanding the mechanisms of drug resistance to KRAS-mutant inhibitors. Here we review the most recent advances in therapeutic approaches and resistance mechanisms targeting KRAS mutations and discuss opportunities for combination therapy.
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Affiliation(s)
- Chunxiao Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Xiaoqing Guan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,Key Laboratory of Prevention, Diagnosis, and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
| | - Xinuo Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.,College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research and Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhengbo Song
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xiangdong Cheng
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China. .,Key Laboratory of Prevention, Diagnosis, and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China.
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research and Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China. .,School of Pharmacy, Second Military Medical University, Shanghai, 200433, China.
| | - Jiang-Jiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China. .,School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China. .,Key Laboratory of Prevention, Diagnosis, and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China.
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16
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He X, Du K, Wang Y, Fan J, Li M, Ni D, Lu S, Bian X, Liu Y. Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Front Mol Biosci 2022; 9:860962. [PMID: 35463958 PMCID: PMC9023742 DOI: 10.3389/fmolb.2022.860962] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
The Ras-specific guanine nucleotide exchange factors Son of Sevenless (SOS) regulates Ras activation by converting inactive GDP-bound to active GTP-bound states. The catalytic activity of Ras is further allosterically regulated by GTP−Ras bound to a distal site through a positive feedback loop. To address the mechanism underlying the long-range allosteric activation of the catalytic K-Ras4B by an additional allosteric GTP–Ras through SOS, we employed molecular dynamics simulation of the K-Ras4BG13D•SOScat complex with and without an allosteric GTP-bound K-Ras4BG13D. We found that the binding of an allosteric GTP−K-Ras4BG13D enhanced the affinity between the catalytic K-Ras4BG13D and SOScat, forming a more stable conformational state. The peeling away of the switch I from the nucleotide binding site facilitated the dissociation of GDP, thereby contributing to the increased nucleotide exchange rate. The community networks further showed stronger edge connection upon allosteric GTP−K-Ras4BG13D binding, which represented an increased interaction between catalytic K-Ras4BG13D and SOScat. Moreover, GTP−K-Ras4BG13D binding transmitted allosteric signaling pathways though the Cdc25 domain of SOS that enhanced the allosteric regulatory from the K-Ras4BG13D allosteric site to the catalytic site. This study may provide an in-depth mechanism for abnormal activation and allosteric regulation of K-Ras4BG13D.
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Affiliation(s)
- Xuan He
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kui Du
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
| | - Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Xiaolan Bian, ; Yaqin Liu,
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17
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Johnson C, Burkhart DL, Haigis KM. Classification of KRAS-Activating Mutations and the Implications for Therapeutic Intervention. Cancer Discov 2022; 12:913-923. [PMID: 35373279 PMCID: PMC8988514 DOI: 10.1158/2159-8290.cd-22-0035] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
Abstract
Members of the family of RAS proto-oncogenes, discovered just over 40 years ago, were among the first cancer-initiating genes to be discovered. Of the three RAS family members, KRAS is the most frequently mutated in human cancers. Despite intensive biological and biochemical study of RAS proteins over the past four decades, we are only now starting to devise therapeutic strategies to target their oncogenic properties. Here, we highlight the distinct biochemical properties of common and rare KRAS alleles, enabling their classification into functional subtypes. We also discuss the implications of this functional classification for potential therapeutic avenues targeting mutant subtypes. SIGNIFICANCE Efforts in the recent past to inhibit KRAS oncogenicity have focused on kinases that function in downstream signal transduction cascades, although preclinical successes have not translated to patients with KRAS-mutant cancer. Recently, clinically effective covalent inhibitors of KRASG12C have been developed, establishing two principles that form a foundation for future efforts. First, KRAS is druggable. Second, each mutant form of KRAS is likely to have properties that make it uniquely druggable.
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Affiliation(s)
- Christian Johnson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Deborah L Burkhart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
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18
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Khan I, Koide A, Zuberi M, Ketavarapu G, Denbaum E, Teng KW, Rhett JM, Spencer-Smith R, Hobbs GA, Camp ER, Koide S, O'Bryan JP. Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants. Cell Rep 2022; 38:110322. [PMID: 35139380 PMCID: PMC8936000 DOI: 10.1016/j.celrep.2022.110322] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/12/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
RAS guanosine triphosphatases (GTPases) are mutated in nearly 20% of human tumors, making them an attractive therapeutic target. Following our discovery that nucleotide-free RAS (apo RAS) regulates cell signaling, we selectively target this state as an approach to inhibit RAS function. Here, we describe the R15 monobody that exclusively binds the apo state of all three RAS isoforms in vitro, regardless of the mutation status, and captures RAS in the apo state in cells. R15 inhibits the signaling and transforming activity of a subset of RAS mutants with elevated intrinsic nucleotide exchange rates (i.e., fast exchange mutants). Intracellular expression of R15 reduces the tumor-forming capacity of cancer cell lines driven by select RAS mutants and KRAS(G12D)-mutant patient-derived xenografts (PDXs). Thus, our approach establishes an opportunity to selectively inhibit a subset of RAS mutants by targeting the apo state with drug-like molecules. Khan et al. develop a high-affinity monobody to nucleotide-free RAS that, when expressed intracellularly, inhibits oncogenic RAS-mediated signaling and tumorigenesis. This study reveals the feasibility of targeting the nucleotide-free state to inhibit tumors driven by oncogenic RAS mutants that possess elevated nucleotide exchange activity.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA; Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gayatri Ketavarapu
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Eric Denbaum
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Russell Spencer-Smith
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - G Aaron Hobbs
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ernest Ramsay Camp
- Department of Surgery, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA; Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA.
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