1
|
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 PMCID: PMC11348296 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.
Collapse
Affiliation(s)
- Sangho D. Yun
- Department of Chemistry, Texas A&M University, College Station, TX77843
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX77843
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University, College Station, TX77843
| | | | - Michael Lynn
- Department of Chemistry, Texas A&M University, College Station, TX77843
| | - Carter Lantz
- Department of Chemistry, Texas A&M University, College Station, TX77843
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX77843
| |
Collapse
|
2
|
Chetta M, Basile A, Tarsitano M, Rivieccio M, Oro M, Capitanio N, Bukvic N, Priolo M, Rosati A. The Target Therapy Hyperbole: "KRAS (p.G12C)"-The Simplification of a Complex Biological Problem. Cancers (Basel) 2024; 16:2389. [PMID: 39001451 PMCID: PMC11240669 DOI: 10.3390/cancers16132389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) gene variations are linked to the development of numerous cancers, including non-small cell lung cancer (NSCLC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). The lack of typical drug-binding sites has long hampered the discovery of therapeutic drugs targeting KRAS. Since "CodeBreaK 100" demonstrated Sotorasib's early safety and efficacy and led to its approval, especially in the treatment of non-small cell lung cancer (NSCLC), the subsequent identification of specific inhibitors for the p.G12C mutation has offered hope. However, the CodeBreaK 200 study found no significant difference in overall survival (OS) between patients treated with Docetaxel and Sotorasib (AMG 510), adding another degree of complexity to this ongoing challenge. The current study compares the three-dimensional structures of the two major KRAS isoforms, KRAS4A and KRAS4B. It also investigates the probable structural changes caused by the three major mutations (p.G12C, p.G12D, and p.G12V) within Sotorasib's pocket domain. The computational analysis demonstrates that the wild-type and mutant isoforms have distinct aggregation propensities, resulting in the creation of alternate oligomeric configurations. This study highlights the increased complexity of the biological issue of using KRAS as a therapeutic target. The present study stresses the need for a better understanding of the structural dynamics of KRAS and its mutations to design more effective therapeutic approaches. It also emphasizes the potential of computational approaches to shed light on the complicated molecular pathways that drive KRAS-mediated oncogenesis. This study adds to the ongoing efforts to address the therapeutic hurdles presented by KRAS in cancer treatment.
Collapse
Affiliation(s)
- Massimiliano Chetta
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Anna Basile
- StressBioLab, Department of Medicine, Surgery and Dentistry “Schola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (A.B.); (A.R.)
| | - Marina Tarsitano
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Maria Rivieccio
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Maria Oro
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy;
| | - Nenad Bukvic
- Medical Genetics Section, University Hospital Consortium Corporation Polyclinics of Bari, 70124 Bari, Italy;
| | - Manuela Priolo
- U.O.C. Medical and Laboratory Genetics, A.O.R.N., Cardarelli, 80131 Naples, Italy; (M.T.); (M.R.); (M.O.); (M.P.)
| | - Alessandra Rosati
- StressBioLab, Department of Medicine, Surgery and Dentistry “Schola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (A.B.); (A.R.)
| |
Collapse
|
3
|
Majrashi TA, Sabt A, Almahli H, El Hassab MA, Noamaan MA, Elkaeed EB, Hamissa MF, Maslamani AN, Shaldam MA, Eldehna WM. DFT and molecular simulation validation of the binding activity of PDEδ inhibitors for repression of oncogenic k-Ras. PLoS One 2024; 19:e0300035. [PMID: 38457483 PMCID: PMC10923412 DOI: 10.1371/journal.pone.0300035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
The development of effective drugs targeting the K-Ras oncogene product is a significant focus in anticancer drug development. Despite the lack of successful Ras signaling inhibitors, recent research has identified PDEδ, a KRAS transporter, as a potential target for inhibiting the oncogenic KRAS signaling pathway. This study aims to investigate the interactions between eight K-Ras inhibitors (deltarazine, deltaflexin 1 and 2, and its analogues) and PDEδ to understand their binding modes. The research will utilize computational techniques such as density functional theory (DFT) and molecular electrostatic surface potential (MESP), molecular docking, binding site analyses, molecular dynamic (MD) simulations, electronic structure computations, and predictions of the binding free energy. Molecular dynamic simulations (MD) will be used to predict the binding conformations and pharmacophoric features in the active site of PDEδ for the examined structures. The binding free energies determined using the MMPB(GB)SA method will be compared with the observed potency values of the tested compounds. This computational approach aims to enhance understanding of the PDEδ selective mechanism, which could contribute to the development of novel selective inhibitors for K-Ras signaling.
Collapse
Affiliation(s)
- Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mahmoud A. El Hassab
- Faculty of Pharmacy, Department of Medicinal Chemistry, King Salman International University (KSIU), South Sinai, Egypt
| | - Mahmoud A. Noamaan
- Faculty of Science, Mathematics Department, Cairo University, Giza, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Riyadh, Saudi Arabia
| | - Mohamed Farouk Hamissa
- Medicinal and Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Giza, Egypt
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | | | - Moataz A. Shaldam
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Wagdy M. Eldehna
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
| |
Collapse
|
4
|
Wang Y, Zhang J, Li K, Xia S, Gou S. Multitargeting HDAC Inhibitors Containing a RAS/RAF Protein Interfering Unit. J Med Chem 2024; 67:2066-2082. [PMID: 38261411 DOI: 10.1021/acs.jmedchem.3c01941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
In this work, a series of multitargeting histone deacetylase (HDAC) inhibitors capable of regulating the signal transduction between RAS protein and downstream effectors were obtained by introducing a zinc-ion-binding group into the framework of rigosertib via different linkers. Among them, two representative compounds, XSJ-7 and XSJ-10, not only showed stronger antiproliferative activity against many types of cancer cells including solid tumor cells but also presented more potent inhibition on different subtypes of HDAC than suberoylanilide hydroxamic acid (SAHA). Significantly, XSJ-10 presented moderate pharmacokinetic behaviors and showed stronger antitumor activity than oxaliplatin, SAHA, and rigosertib in the HT-29 xenograft mouse models without significant systemic toxicity. Research on the anticancer mechanism of XSJ-10 revealed that it can effectively induce the apoptosis of cancer cells and suppress the tumor by strongly inhibiting the RAS-RAF-MEK-ERK signaling pathway and the acetylation level of HDAC3.
Collapse
Affiliation(s)
- Yuanjiang Wang
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China
| | - Jianluo Zhang
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Kun Li
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Shengjin Xia
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Shaohua Gou
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China
| |
Collapse
|
5
|
Ye X. Quantitative Membrane Proteomics for Discovery of Actionable Drug Targets at the Surface of RAS-Driven Human Cancer Cells. Methods Mol Biol 2024; 2823:27-46. [PMID: 39052212 DOI: 10.1007/978-1-0716-3922-1_3] [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: 07/27/2024]
Abstract
With the advent of promising lung cancer immunotherapies targeting proteins at the cell surface of RAS-driven human cancers, the mass spectrometry (MS)-based surfaceomics remains a feasible strategy for therapeutic target discovery. This chapter describes a protocol for discovery of druggable protein targets at the surface of RAS-driven human cancer cells. This method relies on bottom-up MS-based quantitative surfaceomics that employs in parallel, targeted hydrazide-based cell-surface glycoproteomics and global shotgun membrane proteomics to enable unbiased quantitative profiling of thousands of cell surface membrane proteins. A large-scale molecular map of the KRASG12V surface was attained, resulting in confident detection and quantitation of more than 500 cell surface membrane proteins that were found to be unique or upregulated at the surface of cells harboring the KRASG12V mutant. A multistep bioinformatic progression revealed a subset of unique and/or significantly upregulated proteins as priority drug targets selected for orthogonal cross-validation using immunofluorescence, structured illumination microscopy, and western blotting. Among cross-validated targets, CUB domain containing protein 1 (CDCP1) and basigin (BSG-CD147) were selected as leading targets due to their involvement in cell adhesion and migration, consistent with the KRASG12V malignant phenotype as revealed by scanning electron microscopy and phenotypic cancer cell assays. Follow-up studies confirmed CDCP1 as an actionable therapeutic target, resulting in development of recombinant antibodies capable of killing KRAS-transformed cancer cells in preclinical setting. The present MS-based surfaceomics workflow represents a powerful drug target discovery platform that enables development of innovative immunotherapeutics (e.g., antibody drug conjugate against CDCP1) for attacking oncogenic RAS-driven cancers at the cell surface.
Collapse
Affiliation(s)
- Xiaoying Ye
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| |
Collapse
|
6
|
Kaczmarczyk JA, Whiteley GR, Blonder J. Detection and Quantitation of Endogenous Membrane-Bound RAS Proteins and KRAS Mutants in Cancer Cell Lines Using 1D-SDS-PAGE LC-MS 2. Methods Mol Biol 2024; 2823:269-289. [PMID: 39052226 DOI: 10.1007/978-1-0716-3922-1_17] [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: 07/27/2024]
Abstract
In healthy cells, membrane-anchored wild-type RAS proteins (i.e., HRAS, KRAS4A, KRAS4B, and NRAS) regulate critical cellular processes (e.g., proliferation, differentiation, survival). When mutated, RAS proteins are principal oncogenic drivers in approximately 30% of all human cancers. Among them, KRAS mutants are found in nearly 80% of all patients diagnosed with RAS-driven malignancies and are regarded as high-priority anti-cancer drug targets. Due to the lack of highly qualified/specific RAS isoform and mutant RAS monoclonal antibodies, there is a vital need for an effective antibody-free approach capable of identifying and quantifying membrane-bound RAS proteins in isoform- and mutation-specific manner. Here, we describe the development of a simple antibody-free protocol that relies on ultracentrifugation to isolate the membrane fraction coupled with single-dimensional (1D) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to fractionate and enrich membrane-bound endogenous RAS isoforms. Next, bottom-up proteomics that utilizes in-gel digestion followed by reversed-phase high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS2) is used for detection and relative quantitation of all wild-type RAS proteins (i.e., HRAS, KRAS4A, KRAS4B, and NRAS) and corresponding RAS mutants (e.g., G12D, G13D, G12S, G12V). Notably, this simple 1D-SDS-PAGE-HPLC-MS2-based protocol can be automated and widely applied to multiple cancer cell lines to investigate concentration changes in membrane-bound endogenous RAS proteins and corresponding mutants in the context of drug discovery.
Collapse
Affiliation(s)
- Jan A Kaczmarczyk
- Meso Scale Diagnostics, Rockville, MD, USA.
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Gordon R Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Josip Blonder
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| |
Collapse
|
7
|
Shree S, McLean MA, Stephen AG, Sligar SG. Revealing KRas4b topology on the membrane surface. Biochem Biophys Res Commun 2023; 678:122-127. [PMID: 37633182 PMCID: PMC10528110 DOI: 10.1016/j.bbrc.2023.08.035] [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: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
KRas4b is a membrane-bound regulatory protein belonging to the family of small GTPases that function as a molecular switch, facilitating signal transduction from activated membrane receptors to intracellular pathways controlling cell growth and proliferation. Oncogenic mutations locking KRas4b in the active GTP state are responsible for nearly 85% of all Ras-driven cancers. Understanding the membrane-bound state of KRas4b is crucial for designing new therapeutic approaches targeting oncogenic KRas-driven signaling pathways. Extensive research demonstrates the significant involvement of the membrane bilayer in Ras-effector interactions, with anionic lipids playing a critical role in determining protein conformations The preferred topology of KRas4b for interacting with signaling partners has been a long-time question. Computational studies suggest a membrane-proximal conformation, while other biophysical methods like neutron reflectivity propose a membrane-distal conformation. To address these gaps, we employed FRET measurements to investigate the conformation of KRas4b. Using fully post-translationally modified KRas4b, we designed a Nanodisc based FRET assay to study KRas4b-membrane interactions. We suggest an extended conformation of KRas4b relative to the membrane surface. Measurement of FRET donor - acceptor distances reveal that a negatively charged membrane surface weakly favors closer association with the membrane surface. Our findings provide insights into the role of anionic lipids in determining the dynamic conformations of KRas4b and shed light on the predominant conformation of its topology on lipid headgroups.
Collapse
Affiliation(s)
- Shweta Shree
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Mark A McLean
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, United States
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
| |
Collapse
|
8
|
Morstein J, Shrestha R, Van QN, López CA, Arora N, Tonelli M, Liang H, Chen D, Zhou Y, Hancock JF, Stephen AG, Turbyville TJ, Shokat KM. Direct Modulators of K-Ras-Membrane Interactions. ACS Chem Biol 2023; 18:2082-2093. [PMID: 37579045 PMCID: PMC10510109 DOI: 10.1021/acschembio.3c00413] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Protein-membrane interactions (PMIs) are ubiquitous in cellular signaling. Initial steps of signal transduction cascades often rely on transient and dynamic interactions with the inner plasma membrane leaflet to populate and regulate signaling hotspots. Methods to target and modulate these interactions could yield attractive tool compounds and drug candidates. Here, we demonstrate that the conjugation of a medium-chain lipid tail to the covalent K-Ras(G12C) binder MRTX849 at a solvent-exposed site enables such direct modulation of PMIs. The conjugated lipid tail interacts with the tethered membrane and changes the relative membrane orientation and conformation of K-Ras(G12C), as shown by molecular dynamics (MD) simulation-supported NMR studies. In cells, this PMI modulation restricts the lateral mobility of K-Ras(G12C) and disrupts nanoclusters. The described strategy could be broadly applicable to selectively modulate transient PMIs.
Collapse
Affiliation(s)
- Johannes Morstein
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Rebika Shrestha
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N. Van
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - César A. López
- Theoretical
Biology and Biophysics Group, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Neha Arora
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Marco Tonelli
- National
Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Hong Liang
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - De Chen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Yong Zhou
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - John F. Hancock
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Andrew G. Stephen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J. Turbyville
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| |
Collapse
|
9
|
Pagba CV, Gupta AK, Gorfe AA. Small-Molecule Inhibition of KRAS through Conformational Selection. ACS OMEGA 2023; 8:31419-31426. [PMID: 37663463 PMCID: PMC10468774 DOI: 10.1021/acsomega.3c04013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023]
Abstract
Mutations in KRAS account for about 20% of human cancers. Despite the major progress in recent years toward the development of KRAS inhibitors, including the discovery of covalent inhibitors of the G12C KRAS variant for the treatment of non-small-cell lung cancer, much work remains to be done to discover broad-acting inhibitors to treat many other KRAS-driven cancers. In a previous report, we showed that a 308.4 Da small-molecule ligand [(2R)-2-(N'-(1H-indole-3-carbonyl)hydrazino)-2-phenyl-acetamide] binds to KRAS with low micro-molar affinity [Chem. Biol. Drug Des.2019; 94(2):1441-1456]. Binding of this ligand, which we call ACA22, to the p1 pocket of KRAS and its interactions with residues at beta-strand 1 and the switch loops have been supported by data from nuclear magnetic resonance spectroscopy and microscale thermophoresis experiments. However, the inhibitory potential of the compound was not demonstrated. Here, we show that ACA22 inhibits KRAS-mediated signal transduction in cells expressing wild type (WT) and G12D mutant KRAS and reduces levels of guanosine triphosphate-loaded WT KRAS more effectively than G12D KRAS. We ruled out the direct effect on nucleotide exchange or effector binding as possible mechanisms of inhibition using a variety of biophysical assays. Combining these observations with binding data that show comparable affinities of the compound for the active and inactive forms of the mutant but not the WT, we propose conformational selection as a possible mechanism of action of ACA22.
Collapse
Affiliation(s)
- Cynthia V Pagba
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Amit K Gupta
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| |
Collapse
|
10
|
Glycolysis regulates KRAS plasma membrane localization and function through defined glycosphingolipids. Nat Commun 2023; 14:465. [PMID: 36709325 PMCID: PMC9884228 DOI: 10.1038/s41467-023-36128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
Oncogenic KRAS expression generates a metabolic dependency on aerobic glycolysis, known as the Warburg effect. We report an effect of increased glycolytic flux that feeds into glycosphingolipid biosynthesis and is directly linked to KRAS oncogenic function. High resolution imaging and genetic approaches show that a defined subset of outer leaflet glycosphingolipids, including GM3 and SM4, is required to maintain KRAS plasma membrane localization, with GM3 engaging in cross-bilayer coupling to maintain inner leaflet phosphatidylserine content. Thus, glycolysis is critical for KRAS plasma membrane localization and nanoscale spatial organization. Reciprocally oncogenic KRAS selectively upregulates cellular content of these same glycosphingolipids, whose depletion in turn abrogates KRAS oncogenesis in pancreatic cancer models. Our findings expand the role of the Warburg effect beyond ATP generation and biomass building to high-level regulation of KRAS function. The positive feedforward loop between oncogenic KRAS signaling and glycosphingolipid synthesis represents a vulnerability with therapeutic potential.
Collapse
|
11
|
Oncogenic KRAS is dependent upon an EFR3A-PI4KA signaling axis for potent tumorigenic activity. Nat Commun 2021; 12:5248. [PMID: 34504076 PMCID: PMC8429657 DOI: 10.1038/s41467-021-25523-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/10/2021] [Indexed: 11/15/2022] Open
Abstract
The HRAS, NRAS, and KRAS genes are collectively mutated in a fifth of all human cancers. These mutations render RAS GTP-bound and active, constitutively binding effector proteins to promote signaling conducive to tumorigenic growth. To further elucidate how RAS oncoproteins signal, we mined RAS interactomes for potential vulnerabilities. Here we identify EFR3A, an adapter protein for the phosphatidylinositol kinase PI4KA, to preferentially bind oncogenic KRAS. Disrupting EFR3A or PI4KA reduces phosphatidylinositol-4-phosphate, phosphatidylserine, and KRAS levels at the plasma membrane, as well as oncogenic signaling and tumorigenesis, phenotypes rescued by tethering PI4KA to the plasma membrane. Finally, we show that a selective PI4KA inhibitor augments the antineoplastic activity of the KRASG12C inhibitor sotorasib, suggesting a clinical path to exploit this pathway. In sum, we have discovered a distinct KRAS signaling axis with actionable therapeutic potential for the treatment of KRAS-mutant cancers. The lipid composition of the plasma membrane defines the localisation of KRAS and its oncogenic function. Here the authors show that EFR3A binds to active KRAS to recruit PI4KA and alters the lipid composition of the plasma membrane to promote KRAS oncogenic signalling and tumorigenesis.
Collapse
|
12
|
Nussinov R, Zhang M, Maloney R, Jang H. Ras isoform-specific expression, chromatin accessibility, and signaling. Biophys Rev 2021; 13:489-505. [PMID: 34466166 PMCID: PMC8355297 DOI: 10.1007/s12551-021-00817-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The anchorage of Ras isoforms in the membrane and their nanocluster formations have been studied extensively, including their detailed interactions, sizes, preferred membrane environments, chemistry, and geometry. However, the staggering challenge of their epigenetics and chromatin accessibility in distinct cell states and types, which we propose is a major factor determining their specific expression, still awaits unraveling. Ras isoforms are distinguished by their C-terminal hypervariable region (HVR) which acts in intracellular transport, regulation, and membrane anchorage. Here, we review some isoform-specific activities at the plasma membrane from a structural dynamic standpoint. Inspired by physics and chemistry, we recognize that understanding functional specificity requires insight into how biomolecules can organize themselves in different cellular environments. Within this framework, we suggest that isoform-specific expression may largely be controlled by the chromatin density and physical compaction, which allow (or curb) access to "chromatinized DNA." Genes are preferentially expressed in tissues: proteins expressed in pancreatic cells may not be equally expressed in lung cells. It is the rule-not an exception, and it can be at least partly understood in terms of chromatin organization and accessibility state. Genes are expressed when they can be sufficiently exposed to the transcription machinery, and they are less so when they are persistently buried in dense chromatin. Notably, chromatin accessibility can similarly determine expression of drug resistance genes.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism National Cancer Institute, 1050 Boyles St, Frederick, MD 21702 USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University, 69978 Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism National Cancer Institute, 1050 Boyles St, Frederick, MD 21702 USA
| | - Ryan Maloney
- Computational Structural Biology Section Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism National Cancer Institute, 1050 Boyles St, Frederick, MD 21702 USA
| | - Hyunbum Jang
- Computational Structural Biology Section Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism National Cancer Institute, 1050 Boyles St, Frederick, MD 21702 USA
| |
Collapse
|
13
|
Liot S, El Kholti N, Balas J, Genestier L, Verrier B, Valcourt U, Lambert E. Development of thymic tumor in [LSL:Kras G12D; Pdx1-CRE] mice, an adverse effect associated with accelerated pancreatic carcinogenesis. Sci Rep 2021; 11:15075. [PMID: 34302028 PMCID: PMC8302691 DOI: 10.1038/s41598-021-94566-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022] Open
Abstract
Pancreatic Ductal AdenoCarcinoma (PDAC) represents about 90% of pancreatic cancers. It is one of the most aggressive cancer, with a 5-year survival rate below 10% due to late diagnosis and poor therapeutic efficiency. This bad prognosis thus encourages intense research in order to better understand PDAC pathogenesis and molecular basis leading to the development of innovative therapeutic strategies. This research frequently involves the KC (LSL:KrasG12D;Pdx1-CRE) genetically engineered mouse model, which leads to pancreatic cancer predisposition. However, as frequently encountered in animal models, the KC mouse model also exhibits biases. Herein, we report a new adverse effect of KrasG12D mutation in KC mouse model. In our hands, 10% of KC mice developed clinical signs reaching pre-defined end-points between 100- and 150-days post-parturition, and associated with large thymic mass development. Histological and genetic analyses of this massive thymus enabled us (1) to characterize it as a highly proliferative thymic lymphoma and (2) to detect the unexpected recombination of the Lox-STOP-Lox cassette upstream KrasG12D allele and subsequent KRASG12D protein expression in all cells composing thymic masses. Finally, we highlighted that development of such thymic tumor was associated with accelerated pancreatic carcinogenesis, immune compartment disorganization, and in some cases, lung malignancies.
Collapse
Affiliation(s)
- Sophie Liot
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Naïma El Kholti
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Jonathan Balas
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Laurent Genestier
- UR LIB « Lymphoma Immuno-Biology", Université Claude Bernard Lyon I, Lyon, France
| | - Bernard Verrier
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Ulrich Valcourt
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France
| | - Elise Lambert
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Claude Bernard Lyon 1, Institut de Biologie et Chimie Des Protéines, 7, passage du Vercors, 69367, Lyon Cedex 07, France.
| |
Collapse
|
14
|
Brandt AC, Koehn OJ, Williams CL. SmgGDS: An Emerging Master Regulator of Prenylation and Trafficking by Small GTPases in the Ras and Rho Families. Front Mol Biosci 2021; 8:685135. [PMID: 34222337 PMCID: PMC8242357 DOI: 10.3389/fmolb.2021.685135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Newly synthesized small GTPases in the Ras and Rho families are prenylated by cytosolic prenyltransferases and then escorted by chaperones to membranes, the nucleus, and other sites where the GTPases participate in a variety of signaling cascades. Understanding how prenylation and trafficking are regulated will help define new therapeutic strategies for cancer and other disorders involving abnormal signaling by these small GTPases. A growing body of evidence indicates that splice variants of SmgGDS (gene name RAP1GDS1) are major regulators of the prenylation, post-prenylation processing, and trafficking of Ras and Rho family members. SmgGDS-607 binds pre-prenylated small GTPases, while SmgGDS-558 binds prenylated small GTPases. This review discusses the history of SmgGDS research and explains our current understanding of how SmgGDS splice variants regulate the prenylation and trafficking of small GTPases. We discuss recent evidence that mutant forms of RabL3 and Rab22a control the release of small GTPases from SmgGDS, and review the inhibitory actions of DiRas1, which competitively blocks the binding of other small GTPases to SmgGDS. We conclude with a discussion of current strategies for therapeutic targeting of SmgGDS in cancer involving splice-switching oligonucleotides and peptide inhibitors.
Collapse
Affiliation(s)
- Anthony C Brandt
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Olivia J Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Carol L Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| |
Collapse
|
15
|
Van QN, Prakash P, Shrestha R, Balius TE, Turbyville TJ, Stephen AG. RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention. Biomolecules 2021; 11:377. [PMID: 33802474 PMCID: PMC8000715 DOI: 10.3390/biom11030377] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/18/2023] Open
Abstract
RAS proteins are mutated in approximately 20% of all cancers and are generally associated with poor clinical outcomes. RAS proteins are localized to the plasma membrane and function as molecular switches, turned on by partners that receive extracellular mitogenic signals. In the on-state, they activate intracellular signal transduction cascades. Membrane-bound RAS molecules segregate into multimers, known as nanoclusters. These nanoclusters, held together through weak protein-protein and protein-lipid associations, are highly dynamic and respond to cellular input signals and fluctuations in the local lipid environment. Disruption of RAS nanoclusters results in downregulation of RAS-mediated mitogenic signaling. In this review, we discuss the propensity of RAS proteins to display clustering behavior and the interfaces that are associated with these assemblies. Strategies to therapeutically disrupt nanocluster formation or the stabilization of signaling incompetent RAS complexes are discussed.
Collapse
Affiliation(s)
| | | | | | | | | | - Andrew G. Stephen
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, National Cancer Institute RAS Initiative, Inc., Frederick, MD 21702, USA; (Q.N.V.); (P.P.); (R.S.); (T.E.B.); (T.J.T.)
| |
Collapse
|
16
|
Ji B, Skup M. Roles of palmitoylation in structural long-term synaptic plasticity. Mol Brain 2021; 14:8. [PMID: 33430908 PMCID: PMC7802216 DOI: 10.1186/s13041-020-00717-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
Long-term potentiation (LTP) and long-term depression (LTD) are important cellular mechanisms underlying learning and memory processes. N-Methyl-d-aspartate receptor (NMDAR)-dependent LTP and LTD play especially crucial roles in these functions, and their expression depends on changes in the number and single channel conductance of the major ionotropic glutamate receptor α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) located on the postsynaptic membrane. Structural changes in dendritic spines comprise the morphological platform and support for molecular changes in the execution of synaptic plasticity and memory storage. At the molecular level, spine morphology is directly determined by actin cytoskeleton organization within the spine and indirectly stabilized and consolidated by scaffold proteins at the spine head. Palmitoylation, as a uniquely reversible lipid modification with the ability to regulate protein membrane localization and trafficking, plays significant roles in the structural and functional regulation of LTP and LTD. Altered structural plasticity of dendritic spines is also considered a hallmark of neurodevelopmental disorders, while genetic evidence strongly links abnormal brain function to impaired palmitoylation. Numerous studies have indicated that palmitoylation contributes to morphological spine modifications. In this review, we have gathered data showing that the regulatory proteins that modulate the actin network and scaffold proteins related to AMPAR-mediated neurotransmission also undergo palmitoylation and play roles in modifying spine architecture during structural plasticity.
Collapse
Affiliation(s)
- Benjun Ji
- Nencki Institute of Experimental Biology, 02-093, Warsaw, Poland.
| | - Małgorzata Skup
- Nencki Institute of Experimental Biology, 02-093, Warsaw, Poland.
| |
Collapse
|