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Hossain MA. Targeting the RAS upstream and downstream signaling pathway for cancer treatment. Eur J Pharmacol 2024; 979:176727. [PMID: 38866361 DOI: 10.1016/j.ejphar.2024.176727] [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: 03/08/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Cancer often involves the overactivation of RAS/RAF/MEK/ERK (MAPK) and PI3K-Akt-mTOR pathways due to mutations in genes like RAS, RAF, PTEN, and PIK3CA. Various strategies are employed to address the overactivation of these pathways, among which targeted therapy emerges as a promising approach. Directly targeting specific proteins, leads to encouraging results in cancer treatment. For instance, RTK inhibitors such as imatinib and afatinib selectively target these receptors, hindering ligand binding and reducing signaling initiation. These inhibitors have shown potent efficacy against Non-Small Cell Lung Cancer. Other inhibitors, like lonafarnib targeting Farnesyltransferase and GGTI 2418 targeting geranylgeranyl Transferase, disrupt post-translational modifications of proteins. Additionally, inhibition of proteins like SOS, SH2 domain, and Ras demonstrate promising anti-tumor activity both in vivo and in vitro. Targeting downstream components with RAF inhibitors such as vemurafenib, dabrafenib, and sorafenib, along with MEK inhibitors like trametinib and binimetinib, has shown promising outcomes in treating cancers with BRAF-V600E mutations, including myeloma, colorectal, and thyroid cancers. Furthermore, inhibitors of PI3K (e.g., apitolisib, copanlisib), AKT (e.g., ipatasertib, perifosine), and mTOR (e.g., sirolimus, temsirolimus) exhibit promising efficacy against various cancers such as Invasive Breast Cancer, Lymphoma, Neoplasms, and Hematological malignancies. This review offers an overview of small molecule inhibitors targeting specific proteins within the RAS upstream and downstream signaling pathways in cancer.
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Affiliation(s)
- Md Arafat Hossain
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
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2
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Weidner P, Saar D, Söhn M, Schroeder T, Yu Y, Zöllner FG, Ponelies N, Zhou X, Zwicky A, Rohrbacher FN, Pattabiraman VR, Tanriver M, Bauer A, Ahmed H, Ametamey SM, Riffel P, Seger R, Bode JW, Wade RC, Ebert MPA, Kragelund BB, Burgermeister E. Myotubularin-related-protein-7 inhibits mutant (G12V) K-RAS by direct interaction. Cancer Lett 2024; 588:216783. [PMID: 38462034 DOI: 10.1016/j.canlet.2024.216783] [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: 12/04/2023] [Revised: 02/19/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024]
Abstract
Inhibition of K-RAS effectors like B-RAF or MEK1/2 is accompanied by treatment resistance in cancer patients via re-activation of PI3K and Wnt signaling. We hypothesized that myotubularin-related-protein-7 (MTMR7), which inhibits PI3K and ERK1/2 signaling downstream of RAS, directly targets RAS and thereby prevents resistance. Using cell and structural biology combined with animal studies, we show that MTMR7 binds and inhibits RAS at cellular membranes. Overexpression of MTMR7 reduced RAS GTPase activities and protein levels, ERK1/2 phosphorylation, c-FOS transcription and cancer cell proliferation in vitro. We located the RAS-inhibitory activity of MTMR7 to its charged coiled coil (CC) region and demonstrate direct interaction with the gastrointestinal cancer-relevant K-RASG12V mutant, favouring its GDP-bound state. In mouse models of gastric and intestinal cancer, a cell-permeable MTMR7-CC mimicry peptide decreased tumour growth, Ki67 proliferation index and ERK1/2 nuclear positivity. Thus, MTMR7 mimicry peptide(s) could provide a novel strategy for targeting mutant K-RAS in cancers.
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Affiliation(s)
- Philip Weidner
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Saar
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michaela Söhn
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Torsten Schroeder
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yanxiong Yu
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Frank G Zöllner
- Computer Assisted Clinical Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Intelligent Systems in Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Cooperative Core Facility Animal Scanner ZI, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Norbert Ponelies
- Orthopaedics & Trauma Surgery, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiaobo Zhou
- Department of Medicine I, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - André Zwicky
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Bioscience of ETH, Zurich, Switzerland
| | - Florian N Rohrbacher
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Bioscience of ETH, Zurich, Switzerland
| | - Vijaya R Pattabiraman
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Bioscience of ETH, Zurich, Switzerland
| | - Matthias Tanriver
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Bioscience of ETH, Zurich, Switzerland
| | - Alexander Bauer
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hazem Ahmed
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences of ETH, Zurich, Switzerland
| | - Simon M Ametamey
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences of ETH, Zurich, Switzerland
| | - Philipp Riffel
- Clinic of Radiology and Nuclear Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rony Seger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jeffrey W Bode
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Bioscience of ETH, Zurich, Switzerland
| | - Rebecca C Wade
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; Heidelberg University, Zentrum für Molekulare Biologie (ZMBH), DKFZ-ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany
| | - Matthias P A Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; DKFZ-Hector Institute at the University Medical Center, Mannheim, Germany
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
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3
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Parise A, Magistrato A. Assessing the mechanism of fast-cycling cancer-associated mutations of Rac1 small Rho GTPase. Protein Sci 2024; 33:e4939. [PMID: 38501467 PMCID: PMC10949326 DOI: 10.1002/pro.4939] [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: 09/07/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 03/20/2024]
Abstract
Rho-GTPases proteins function as molecular switches alternating from an active to an inactive state upon Guanosine triphosphate (GTP) binding and hydrolysis to Guanosine diphosphate (GDP). Among them, Rac subfamily regulates cell dynamics, being overexpressed in distinct cancer types. Notably, these proteins are object of frequent cancer-associated mutations at Pro29 (P29S, P29L, and P29Q). To assess the impact of these mutations on Rac1 structure and function, we performed extensive all-atom molecular dynamics simulations on wild-type (wt) and oncogenic isoforms of this protein in GDP- and GTP-bound states. Our results unprecedentedly elucidate that P29Q/S-induced structural and dynamical perturbations of Rac1 core domain weaken the binding of the catalytic site Mg2+ ion, and reduce the GDP residence time within protein, enhancing the GDP/GTP exchange rate and Rac1 activity. This broadens our knowledge of the role of cancer-associated mutations on small GTPases mechanism supplying valuable information for future drug discovery efforts targeting specific Rac1 isoforms.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle ricerche (CNR)‐IOM c/o International School for Advanced Studies (SISSA/ISAS)TriesteItaly
| | - Alessandra Magistrato
- Consiglio Nazionale delle ricerche (CNR)‐IOM c/o International School for Advanced Studies (SISSA/ISAS)TriesteItaly
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4
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Haspel N, Jang H, Nussinov R. Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. J Chem Inf Model 2024; 64:862-873. [PMID: 38215280 DOI: 10.1021/acs.jcim.3c01412] [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: 01/14/2024]
Abstract
The Ras homologue family member A (RhoA) is a member of the Rho family, a subgroup of the Ras superfamily. RhoA interacts with the 115 kDa guanine nucleotide exchange factor (p115-RhoGEF), which assists in activation and binding with downstream effectors. Here, we use molecular dynamics (MD) simulations and essential dynamics analysis of the inactive RhoA-GDP and active RhoA-GTP, when bound to p115-RhoGEF to decipher the mechanism of RhoA activation at the structural level. We observe that inactive RhoA-GDP maintains its position near the catalytic site on the Dbl homology (DH) domain of p115-RhoGEF through the interaction of its Switch I region with the DH domain. We further show that the active RhoA-GTP is engaged in more interactions with the p115-RhoGEF membrane-bound Pleckstrin homology (PH) domain as compared to RhoA-GDP. We hypothesize that the role of the interactions between the active RhoA-GTP and the PH domain is to help release it from the DH domain upon activation. Our results support this premise, and our simulations uncover the beginning of this process and provide structural details. They also point to allosteric communication pathways that take part in RhoA activation to promote and strengthen the interaction between the active RhoA-GTP and the PH domain. Allosteric regulation also occurs among other members of the Rho superfamily. Collectively, we suggest that in the activation process, the role of the RhoA-GTP interaction with the PH domain is to release RhoA-GTP from the DH domain after activation, making it available to downstream effectors.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, University of Massachusetts Boston, Boston, Massachusetts 02125, United States
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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5
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de Jesus VHF, Mathias-Machado MC, de Farias JPF, Aruquipa MPS, Jácome AA, Peixoto RD. Targeting KRAS in Pancreatic Ductal Adenocarcinoma: The Long Road to Cure. Cancers (Basel) 2023; 15:5015. [PMID: 37894382 PMCID: PMC10605759 DOI: 10.3390/cancers15205015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains an important cause of cancer-related mortality, and it is expected to play an even bigger part in cancer burden in the years to come. Despite concerted efforts from scientists and physicians, patients have experienced little improvement in survival over the past decades, possibly because of the non-specific nature of the tested treatment modalities. Recently, the discovery of potentially targetable molecular alterations has paved the way for the personalized treatment of PDAC. Indeed, the central piece in the molecular framework of PDAC is starting to be unveiled. KRAS mutations are seen in 90% of PDACs, and multiple studies have demonstrated their pivotal role in pancreatic carcinogenesis. Recent investigations have shed light on the differences in prognosis as well as therapeutic implications of the different KRAS mutations and disentangled the relationship between KRAS and effectors of downstream and parallel signaling pathways. Additionally, the recognition of other mechanisms involving KRAS-mediated pathogenesis, such as KRAS dosing and allelic imbalance, has contributed to broadening the current knowledge regarding this molecular alteration. Finally, KRAS G12C inhibitors have been recently tested in patients with pancreatic cancer with relative success, and inhibitors of KRAS harboring other mutations are under clinical development. These drugs currently represent a true hope for a meaningful leap forward in this dreadful disease.
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Affiliation(s)
| | | | | | | | - Alexandre A. Jácome
- Department of Gastrointestinal Medical Oncology, Oncoclínicas, Belo Horizonte 30360-680, Brazil
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Lim TKH, Skoulidis F, Kerr KM, Ahn MJ, Kapp JR, Soares FA, Yatabe Y. KRAS G12C in advanced NSCLC: Prevalence, co-mutations, and testing. Lung Cancer 2023; 184:107293. [PMID: 37683526 DOI: 10.1016/j.lungcan.2023.107293] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/15/2023] [Accepted: 07/05/2023] [Indexed: 09/10/2023]
Abstract
KRAS is the most commonly mutated oncogene in advanced, non-squamous, non-small cell lung cancer (NSCLC) in Western countries. Of the various KRAS mutants, KRAS G12C is the most common variant (~40%), representing 10-13% of advanced non-squamous NSCLC. Recent regulatory approvals of the KRASG12C-selective inhibitors sotorasib and adagrasib for patients with advanced or metastatic NSCLC harboring KRASG12C have transformed KRAS into a druggable target. In this review, we explore the evolving role of KRAS from a prognostic to a predictive biomarker in advanced NSCLC, discussing KRAS G12C biology, real-world prevalence, clinical relevance of co-mutations, and approaches to molecular testing. Real-world evidence demonstrates significant geographic differences in KRAS G12C prevalence (8.9-19.5% in the US, 9.3-18.4% in Europe, 6.9-9.0% in Latin America, and 1.4-4.3% in Asia) in advanced NSCLC. Additionally, the body of clinical data pertaining to KRAS G12C co-mutations such as STK11, KEAP1, and TP53 is increasing. In real-world evidence, KRAS G12C-mutant NSCLC was associated with STK11, KEAP1, and TP53 co-mutations in 10.3-28.0%, 6.3-23.0%, and 17.8-50.0% of patients, respectively. Whilst sotorasib and adagrasib are currently approved for use in the second-line setting and beyond for patients with advanced/metastatic NSCLC, testing and reporting of the KRAS G12C variant should be included in routine biomarker testing prior to first-line therapy. KRAS G12C test results should be clearly documented in patients' health records for actionability at progression. Where available, next-generation sequencing is recommended to facilitate simultaneous testing of potentially actionable biomarkers in a single run to conserve tissue. Results from molecular testing should inform clinical decisions in treating patients with KRAS G12C-mutated advanced NSCLC.
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Affiliation(s)
| | - Ferdinandos Skoulidis
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith M Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen, UK
| | - Myung-Ju Ahn
- Department of Medicine, Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | - Fernando A Soares
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil; Faculty of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center, Tokyo, Japan.
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7
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Xie X, Yu T, Li X, Zhang N, Foster LJ, Peng C, Huang W, He G. Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials. Signal Transduct Target Ther 2023; 8:335. [PMID: 37669923 PMCID: PMC10480221 DOI: 10.1038/s41392-023-01589-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tingting Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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8
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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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9
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Narayan B, Kiel C, Buchete NV. Classification of GTP-dependent K-Ras4B active and inactive conformational states. J Chem Phys 2023; 158:091104. [PMID: 36889947 DOI: 10.1063/5.0139181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Classifying reliably active and inactive molecular conformations of wildtype (WT) and mutated oncogenic proteins is a key, ongoing challenge in molecular cancer studies. Here, we probe the GTP-bound K-Ras4B conformational dynamics using long-time atomistic molecular dynamics (MD) simulations. We extract and analyze the detailed underlying free energy landscape of WT K-Ras4B. We use two key reaction coordinates, labeled d1 and d2 (i.e., distances coordinating the Pβ atom of the GTP ligand with two key residues, T35 and G60), shown to correlate closely with activities of WT and mutated K-Ras4B. However, our new K-Ras4B conformational kinetics study reveals a more complex network of equilibrium Markovian states. We show that a new reaction coordinate is required to account for the orientation of acidic K-Ras4B sidechains such as D38 with respect to the interface with binding effector RAF1 and rationalize the activation/inactivation propensities and the corresponding molecular binding mechanisms. We use this understanding to unveil how a relatively conservative mutation (i.e., D33E, in the switch I region) can lead to significantly different activation propensities compared with WT K-Ras4B. Our study sheds new light on the ability of residues near the K-Ras4B-RAF1 interface to modulate the network of salt bridges at the binding interface with the RAF1 downstream effector and, thus, to influence the underlying GTP-dependent activation/inactivation mechanism. Altogether, our hybrid MD-docking modeling approach enables the development of new in silico methods for quantitative assessment of activation propensity changes (e.g., due to mutations or local binding environment). It also unveils the underlying molecular mechanisms and facilitates the rational design of new cancer drugs.
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Affiliation(s)
- Brajesh Narayan
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Christina Kiel
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
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Wang G, Bai Y, Cui J, Zong Z, Gao Y, Zheng Z. Computer-Aided Drug Design Boosts RAS Inhibitor Discovery. Molecules 2022; 27:molecules27175710. [PMID: 36080477 PMCID: PMC9457765 DOI: 10.3390/molecules27175710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/13/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
The Rat Sarcoma (RAS) family (NRAS, HRAS, and KRAS) is endowed with GTPase activity to regulate various signaling pathways in ubiquitous animal cells. As proto-oncogenes, RAS mutations can maintain activation, leading to the growth and proliferation of abnormal cells and the development of a variety of human cancers. For the fight against tumors, the discovery of RAS-targeted drugs is of high significance. On the one hand, the structural properties of the RAS protein make it difficult to find inhibitors specifically targeted to it. On the other hand, targeting other molecules in the RAS signaling pathway often leads to severe tissue toxicities due to the lack of disease specificity. However, computer-aided drug design (CADD) can help solve the above problems. As an interdisciplinary approach that combines computational biology with medicinal chemistry, CADD has brought a variety of advances and numerous benefits to drug design, such as the rapid identification of new targets and discovery of new drugs. Based on an overview of RAS features and the history of inhibitor discovery, this review provides insight into the application of mainstream CADD methods to RAS drug design.
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Affiliation(s)
- Ge Wang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Yuhao Bai
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Jiarui Cui
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Zirui Zong
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Yuan Gao
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Zhen Zheng
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence:
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Li M, Wang Y, Fan J, Zhuang H, Liu Y, Ji D, Lu S. Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading. J Mol Biol 2022; 434:167730. [PMID: 35872068 DOI: 10.1016/j.jmb.2022.167730] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 01/17/2023]
Abstract
Allosteric regulation is the most direct and efficient way of regulating protein function, wherein proteins transmit the perturbations at one site to another distinct functional site. Deciphering the mechanism of allosteric regulation is of vital importance for the comprehension of both physiological and pathological events in vivo as well as the rational allosteric drug design. However, it remains challenging to elucidate dominant allosteric signal transduction pathways, especially for large and multi-component protein machineries where long-range allosteric regulation exits. One of the quintessential examples having long-range allosteric regulation is the ternary complex, SPRED1-RAS-neurofibromin type 1 (NF1, a RAS GTPase-activating protein), in which SPRED1 facilitates RAS-GTP hydrolysis by interacting with NF1 at a distal, allosteric site from the RAS binding site. To address the underlying mechanism, we performed extensive Gaussian accelerated molecular dynamics simulations and Markov state model analysis of KRAS-NF1 complex in the presence and absence of SPRED1. Our findings suggested that SPRED1 loading allosterically enhanced KRAS-NF1 binding, but hindered conformational transformation of the NF1 catalytic center for RAS hydrolysis. Moreover, we unveiled the possible allosteric pathways upon SPRED1 binding through difference contact network analysis. This study not only provided an in-depth mechanistic insight into the allosteric regulation of KRAS by SPRED1, but also shed light on the investigation of long-range allosteric regulation among complex macromolecular systems.
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Affiliation(s)
- Minyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Haiming Zhuang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, Navy Medical University, Shanghai 200433, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
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12
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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] [Key Words] [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
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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13
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Xiong Y, Zeng J, Xia F, Cui Q, Deng X, Xu X. Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process. J Comput Chem 2022; 43:906-916. [PMID: 35324017 PMCID: PMC9191747 DOI: 10.1002/jcc.26846] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022]
Abstract
The human Son of Sevenless (SOS) activates the signal-transduction protein Ras by forming the complex SOS·Ras and accelerating the guanosine triphosphate (GTP) exchange in Ras. Inhibition of SOS·Ras could regulate the function of Ras in cells and has emerged as an effective strategy for battling Ras related cancers. A key factor to the success of this approach is to understand the conformational change of Ras during the GTP exchange process. In this study, we perform an extensive molecular dynamics simulation to characterize the specific conformations of Ras without and with guanine nucleotide exchange factors (GEFs) of SOS, especially for the substates of State 1 of HRasGTP∙Mg2+ . The potent binding pockets on the surfaces of the RasGDP∙Mg2+ , the S1.1 and S1.2 substates in State 1 of RasGTP∙Mg2+ and the ternary complexes with SOS are predicted, including the binding sites of other domains of SOS. These findings help to obtain a more thorough understanding of Ras functions in the GTP cycling process and provide a structural foundation for future drug design.
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Affiliation(s)
- Yuqing Xiong
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai, China
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai, China
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14
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Ilter M, Kasmer R, Jalalypour F, Atilgan C, Topcu O, Karakas N, Sensoy O. Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS. eLife 2022; 11:79747. [PMID: 36458814 PMCID: PMC9762712 DOI: 10.7554/elife.79747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.
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Affiliation(s)
- Metehan Ilter
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol UniversityIstanbulTurkey
| | - Ramazan Kasmer
- Medical Biology and Genetics Program, Graduate School for Health Sciences, Istanbul Medipol UniversityIstanbulTurkey,Cancer Research Center, Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
| | - Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbulTurkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbulTurkey
| | - Ozan Topcu
- Medical Biology and Genetics Program, Graduate School for Health Sciences, Istanbul Medipol UniversityIstanbulTurkey
| | - Nihal Karakas
- Medical Biology and Genetics Program, Graduate School for Health Sciences, Istanbul Medipol UniversityIstanbulTurkey,Department of Medical Biology, International School of Medicine, Istanbul Medipol UniversityIstanbulTurkey
| | - Ozge Sensoy
- Department of Computer Engineering, School of Engineering and Natural Sciences, Istanbul Medipol UniversityIstanbulTurkey,Regenerative and Restorative Medicine Research Center (REMER), Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
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15
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Hu HF, Ye Z, Qin Y, Xu XW, Yu XJ, Zhuo QF, Ji SR. Mutations in key driver genes of pancreatic cancer: molecularly targeted therapies and other clinical implications. Acta Pharmacol Sin 2021; 42:1725-1741. [PMID: 33574569 PMCID: PMC8563973 DOI: 10.1038/s41401-020-00584-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/16/2020] [Indexed: 02/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, with a minimal difference between its incidence rate and mortality rate. Advances in oncology over the past several decades have dramatically improved the overall survival of patients with multiple cancers due to the implementation of new techniques in early diagnosis, therapeutic drugs, and personalized therapy. However, pancreatic cancers remain recalcitrant, with a 5-year relative survival rate of <9%. The lack of measures for early diagnosis, strong resistance to chemotherapy, ineffective adjuvant chemotherapy and the unavailability of molecularly targeted therapy are responsible for the high mortality rate of this notorious disease. Genetically, PDAC progresses as a complex result of the activation of oncogenes and inactivation of tumor suppressors. Although next-generation sequencing has identified numerous new genetic alterations, their clinical implications remain unknown. Classically, oncogenic mutations in genes such as KRAS and loss-of-function mutations in tumor suppressors, such as TP53, CDNK2A, DPC4/SMAD4, and BRCA2, are frequently observed in PDAC. Currently, research on these key driver genes is still the main focus. Therefore, studies assessing the functions of these genes and their potential clinical implications are of paramount importance. In this review, we summarize the biological function of key driver genes and pharmaceutical targets in PDAC. In addition, we conclude the results of molecularly targeted therapies in clinical trials and discuss how to utilize these genetic alterations in further clinical practice.
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Affiliation(s)
- Hai-feng Hu
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Zeng Ye
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Yi Qin
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Xiao-wu Xu
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Xian-jun Yu
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Qi-feng Zhuo
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Shun-rong Ji
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
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16
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Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
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17
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Coley AB, Ward A, Keeton AB, Chen X, Maxuitenko Y, Prakash A, Li F, Foote JB, Buchsbaum DJ, Piazza GA. Pan-RAS inhibitors: Hitting multiple RAS isozymes with one stone. Adv Cancer Res 2021; 153:131-168. [PMID: 35101229 DOI: 10.1016/bs.acr.2021.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mutations in the three RAS oncogenes are present in approximately 30% of all human cancers that drive tumor growth and metastasis by aberrant activation of RAS-mediated signaling. Despite the well-established role of RAS in tumorigenesis, past efforts to develop small molecule inhibitors have failed for various reasons leading many to consider RAS as "undruggable." Advances over the past decade with KRAS(G12C) mutation-specific inhibitors have culminated in the first FDA-approved RAS drug, sotorasib. However, the patient population that stands to benefit from KRAS(G12C) inhibitors is inherently limited to those patients harboring KRAS(G12C) mutations. Additionally, both intrinsic and acquired mechanisms of resistance have been reported that indicate allele-specificity may afford disadvantages. For example, the compensatory activation of uninhibited wild-type (WT) NRAS and HRAS isozymes can rescue cancer cells harboring KRAS(G12C) mutations from allele-specific inhibition or the occurrence of other mutations in KRAS. It is therefore prudent to consider alternative drug discovery strategies that may overcome these potential limitations. One such approach is pan-RAS inhibition, whereby all RAS isozymes co-expressed in the tumor cell population are targeted by a single inhibitor to block constitutively activated RAS regardless of the underlying mutation. This chapter provides a review of past and ongoing strategies to develop pan-RAS inhibitors in detail and seeks to outline the trajectory of this promising strategy of RAS inhibition.
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Affiliation(s)
- Alexander B Coley
- Department of Pharmacology, University of South Alabama, Mobile, AL, United States; Mitchell Cancer Institute, Mobile, AL, United States
| | - Antonio Ward
- Department of Pharmacology, University of South Alabama, Mobile, AL, United States; Mitchell Cancer Institute, Mobile, AL, United States
| | - Adam B Keeton
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | - Xi Chen
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | - Yulia Maxuitenko
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | - Aishwarya Prakash
- Mitchell Cancer Institute, Mobile, AL, United States; Department of Biochemistry & Molecular Biology, University of South Alabama, Mobile, AL, United States
| | - Feng Li
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | - Jeremy B Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Donald J Buchsbaum
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gary A Piazza
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States.
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18
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Rio-Vilariño A, del Puerto-Nevado L, García-Foncillas J, Cebrián A. Ras Family of Small GTPases in CRC: New Perspectives for Overcoming Drug Resistance. Cancers (Basel) 2021; 13:3757. [PMID: 34359657 PMCID: PMC8345156 DOI: 10.3390/cancers13153757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer remains among the cancers with the highest incidence, prevalence, and mortality worldwide. Although the development of targeted therapies against the EGFR and VEGFR membrane receptors has considerably improved survival in these patients, the appearance of resistance means that their success is still limited. Overactivation of several members of the Ras-GTPase family is one of the main actors in both tumour progression and the lack of response to cytotoxic and targeted therapies. This fact has led many resources to be devoted over the last decades to the development of targeted therapies against these proteins. However, they have not been as successful as expected in their move to the clinic so far. In this review, we will analyse the role of these Ras-GTPases in the emergence and development of colorectal cancer and their relationship with resistance to targeted therapies, as well as the status and new advances in the design of targeted therapies against these proteins and their possible clinical implications.
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Affiliation(s)
| | | | - Jesús García-Foncillas
- Translational Oncology Division, Hospital Universitario Fundación Jimenez Diaz, 28040 Madrid, Spain; (A.R.-V.); (L.d.P.-N.)
| | - Arancha Cebrián
- Translational Oncology Division, Hospital Universitario Fundación Jimenez Diaz, 28040 Madrid, Spain; (A.R.-V.); (L.d.P.-N.)
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19
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Moghadamchargari Z, Shirzadeh M, Liu C, Schrecke S, Packianathan C, Russell DH, Zhao M, Laganowsky A. Molecular assemblies of the catalytic domain of SOS with KRas and oncogenic mutants. Proc Natl Acad Sci U S A 2021; 118:e2022403118. [PMID: 33723061 PMCID: PMC8000204 DOI: 10.1073/pnas.2022403118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ras is regulated by a specific guanine nucleotide exchange factor Son of Sevenless (SOS), which facilitates the exchange of inactive, GDP-bound Ras with GTP. The catalytic activity of SOS is also allosterically modulated by an active Ras (Ras-GTP). However, it remains poorly understood how oncogenic Ras mutants interact with SOS and modulate its activity. Here, native ion mobility-mass spectrometry is employed to monitor the assembly of the catalytic domain of SOS (SOScat) with KRas and three cancer-associated mutants (G12C, G13D, and Q61H), leading to the discovery of different molecular assemblies and distinct conformers of SOScat engaging KRas. We also find KRasG13D exhibits high affinity for SOScat and is a potent allosteric modulator of its activity. A structure of the KRasG13D•SOScat complex was determined using cryogenic electron microscopy providing insight into the enhanced affinity of the mutant protein. In addition, we find that KRasG13D-GTP can allosterically increase the nucleotide exchange rate of KRas at the active site more than twofold compared to KRas-GTP. Furthermore, small-molecule Ras•SOS disruptors fail to dissociate KRasG13D•SOScat complexes, underscoring the need for more potent disruptors. Taken together, a better understanding of the interaction between oncogenic Ras mutants and SOS will provide avenues for improved therapeutic interventions.
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Affiliation(s)
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Chang Liu
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Samantha Schrecke
- 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
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843;
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20
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Tian X, Xu WH, Anwaier A, Wang HK, Wan FN, Cao DL, Luo WJ, Shi GH, Qu YY, Zhang HL, Ye DW. Construction of a robust prognostic model for adult adrenocortical carcinoma: Results from bioinformatics and real-world data. J Cell Mol Med 2021; 25:3898-3911. [PMID: 33626208 PMCID: PMC8051734 DOI: 10.1111/jcmm.16323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/24/2020] [Accepted: 01/09/2021] [Indexed: 12/27/2022] Open
Abstract
This study aims to construct a robust prognostic model for adult adrenocortical carcinoma (ACC) by large‐scale multiomics analysis and real‐world data. The RPPA data, gene expression profiles and clinical information of adult ACC patients were obtained from The Cancer Proteome Atlas (TCPA), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Integrated prognosis‐related proteins (IPRPs) model was constructed. Immunohistochemistry was used to validate the prognostic value of the IPRPs model in Fudan University Shanghai Cancer Center (FUSCC) cohort. 76 ACC cases from TCGA and 22 ACC cases from GSE10927 in NCBI’s GEO database with full data for clinical information and gene expression were utilized to validate the effectiveness of the IPRPs model. Higher FASN (P = .039), FIBRONECTIN (P < .001), TFRC (P < .001), TSC1 (P < .001) expression indicated significantly worse overall survival for adult ACC patients. Risk assessment suggested significantly a strong predictive capacity of IPRPs model for poor overall survival (P < .05). IPRPs model showed a little stronger ability for predicting prognosis than Ki‐67 protein in FUSCC cohort (P = .003, HR = 3.947; P = .005, HR = 3.787). In external validation of IPRPs model using gene expression data, IPRPs model showed strong ability for predicting prognosis in TCGA cohort (P = .005, HR = 3.061) and it exhibited best ability for predicting prognosis in GSE10927 cohort (P = .0898, HR = 2.318). This research constructed IPRPs model for predicting adult ACC patients’ prognosis using proteomic data, gene expression data and real‐world data and this prognostic model showed stronger predictive value than other biomarkers (Ki‐67, Beta‐catenin, etc) in multi‐cohorts.
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Affiliation(s)
- Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong-Kai Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fang-Ning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Jie Luo
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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21
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Veluswamy R, Mack PC, Houldsworth J, Elkhouly E, Hirsch FR. KRAS G12C-Mutant Non-Small Cell Lung Cancer: Biology, Developmental Therapeutics, and Molecular Testing. J Mol Diagn 2021; 23:507-520. [PMID: 33618059 DOI: 10.1016/j.jmoldx.2021.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Mutation in the gene that encodes Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most common oncogenic driver in advanced non-small cell lung cancer, occurring in approximately 30% of lung adenocarcinomas. Over 80% of oncogenic KRAS mutations occur at codon 12, where the glycine residue is substituted by different amino acids, leading to genomic heterogeneity of KRas-mutant tumors. The KRAS glycine-to-cysteine mutation (G12C) composes approximately 44% of KRAS mutations in non-small cell lung cancer, with mutant KRasG12C present in approximately 13% of all patients with lung adenocarcinoma. Mutant KRas has been an oncogenic target for decades, but no viable therapeutic agents were developed until recently. However, advances in KRas molecular modeling have led to the development and clinical testing of agents that directly inhibit mutant KRasG12C. These agents include sotorasib (AMG-510), adagrasib (MRTX-849), and JNJ-74699157. In addition to testing for known actionable oncogenic driver alterations in EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, and NTRK and for the expression of programmed cell-death protein ligand 1, pathologists, medical oncologists, and community practitioners will need to incorporate routine testing for emerging biomarkers such as MET amplification, ERBB2 (alias HER2), and KRAS mutations, particularly KRAS G12C, considering the promising development of direct inhibitors of KRasG12C protein.
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Affiliation(s)
| | - Philip C Mack
- Icahn School of Medicine, The Mount Sinai Hospital, New York, New York
| | - Jane Houldsworth
- Icahn School of Medicine, The Mount Sinai Hospital, New York, New York
| | | | - Fred R Hirsch
- Icahn School of Medicine, The Mount Sinai Hospital, New York, New York.
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22
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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23
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He X, Huang N, Qiu Y, Zhang J, Liu Y, Yin XL, Lu S. Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors. Molecules 2021; 26:962. [PMID: 33670371 PMCID: PMC7918825 DOI: 10.3390/molecules26040962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/31/2022] Open
Abstract
Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.
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Affiliation(s)
- Xinheng He
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (X.H.); (Y.Q.); (J.Z.)
- Zhiyuan Innovative Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ning Huang
- Northern Huashan Hospital, Fudan University, Shanghai 201907, China;
| | - Yuran Qiu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (X.H.); (Y.Q.); (J.Z.)
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (X.H.); (Y.Q.); (J.Z.)
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Xiao-Lan Yin
- Department of Radiotherapy, Changhai Hospital (Hongkou District) Affiliated to Naval Medical University, Shanghai 200081, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (X.H.); (Y.Q.); (J.Z.)
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24
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Wang Y, Ji D, Lei C, Chen Y, Qiu Y, Li X, Li M, Ni D, Pu J, Zhang J, Fu Q, Liu Y, Lu S. Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Comput Struct Biotechnol J 2021; 19:1184-1199. [PMID: 33680360 PMCID: PMC7902900 DOI: 10.1016/j.csbj.2021.01.044] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ras undergoes interconversion between the active GTP-bound state and the inactive GDP-bound state. This GTPase cycle, which controls the activities of Ras, is accelerated by Ras GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (SOS). Oncogenic Ras mutations could affect the GTPase cycle and impair Ras functions. Additionally, Src-induced K-Ras Y32/64 dual phosphorylation has been reported to disrupt GTPase cycle and hinder Ras downstream signaling. However, the underlying mechanisms remain unclear. To address this, we performed molecular dynamics simulations (~30 μs in total) on unphosphorylated and phosphorylated K-Ras4B in GTP- and GDP-bound states, and on their complexes with GTPase cycle regulators (GAP and SOS) and the effector protein Raf. We found that K-Ras4B dual phosphorylation mainly alters the conformation at the nucleotide binding site and creates disorder at the catalytic site, resulting in the enlargement of GDP binding pocket and the retard of Ras-GTP intrinsic hydrolysis. We observed phosphorylation-induced shift in the distribution of Ras-GTP inactive-active sub-states and recognized potential druggable pockets in the phosphorylated Ras-GTP. Moreover, decreased catalytic competence or signal delivery abilities due to reduced binding affinities and/or distorted catalytic conformations of GAP, SOS and Raf were observed. In addition, the allosteric pathway from Ras/Raf interface to the distal Raf L4 loop was compromised by Ras phosphorylation. These results reveal the mechanisms by which phosphorylation influences the intrinsic or GAP/SOS catalyzed transformations between GTP- and GDP-bound states of Ras and its signal transduction to Raf. Our findings project Ras phosphorylation as a target for cancer drug discovery.
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Affiliation(s)
- Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China
| | - Chaoyu Lei
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yingfei Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yuran Qiu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200120, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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25
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Chen H, Smaill JB, Liu T, Ding K, Lu X. Small-Molecule Inhibitors Directly Targeting KRAS as Anticancer Therapeutics. J Med Chem 2020; 63:14404-14424. [PMID: 33225706 DOI: 10.1021/acs.jmedchem.0c01312] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
KRAS, the most frequently mutated oncogene, plays a predominant role in driving initiation and progression of cancers. Decades of effort to target KRAS using small molecules has been unsuccessful, causing KRAS to be considered an "undruggable" cancer target. However, this view began to change recently, as drug discovery techniques have developed several KRAS G12C allosteric inhibitors that are currently being evaluated in clinical trials. Herein we provide an in-depth analysis of the structure and binding pockets of KRAS, medicinal chemistry optimization processes, and the biological characterization of small-molecule inhibitors that directly target KRAS, including covalent allosteric inhibitors specific for the G12C mutant, GTP-competitive inhibitors targeting the nucleotide-binding site, and protein-protein interaction inhibitors that bind in the switch I/II pocket or the A59 site. Additionally, we propose potential challenges faced by these new classes of KRAS inhibitors under clinical evaluation.
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Affiliation(s)
- Hao Chen
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Tongzheng Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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26
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Targeting KRAS mutant cancers by preventing signaling transduction in the MAPK pathway. Eur J Med Chem 2020; 211:113006. [PMID: 33228976 DOI: 10.1016/j.ejmech.2020.113006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
KRAS genes are the most commonly mutated oncogenes in cancer. Unfortunately, effective therapeutic strategies for targeting KRAS mutant cancers have proven to be difficult to obtain. A key reason for this setback is due to the lack of success direct KRAS mutant inhibitors have received. Researchers have turned their efforts away from targeting the KRAS nucleotide-binding site directly and towards targeting other areas of the MAPK signaling pathway to block KRAS function. Researchers found that inhibiting enzymes and protein-protein interactions involved in the MAPK signaling pathway inhibit the activation of KRAS mutant therefore can lead to a potential therapeutic for KRAS mutated cancers. Throughout the past two decades, various indirect inhibitors have been designed and tested. EGFR and MEK inhibitors have presented with less success; however, significant advances have been made when targeting the plasma membrane localization process and the allosteric site of KRAS mutant. Farnesyltransferase and allosteric inhibitors have both advanced to human clinical trials. This comprehensive review presents the most recent developments of direct and indirect KRAS mutant inhibitors. This review summarizes published data on the inhibitory and anti-cancer activity of compounds that target KRAS activation as well as highlights the most promising strategies for targeting KRAS mutant cancers.
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27
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Bhardwaj VK, Singh R, Das P, Purohit R. Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Comput Biol Med 2020; 128:104117. [PMID: 33217661 PMCID: PMC7659809 DOI: 10.1016/j.compbiomed.2020.104117] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/01/2020] [Accepted: 11/07/2020] [Indexed: 12/11/2022]
Abstract
Background The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals. Methods We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 μs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules. Results The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated more deeply inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket. Conclusion The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro. A robust computational strategy applied to identify the potential lead for COVID-19. Repurposed FDA approved antiviral drugs were compared with a set of acridinedione analogs against Mpro of SARS-CoV-2. The acridinedione analogs have acceptable ADMET values and low toxicity profile. In-house synthesized acridinedione analogs showed good amount of interaction with Mpro of SARS-CoV-2.
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Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP, 176061, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP, 176061, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP, 176061, India.
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28
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Baltanás FC, Zarich N, Rojas-Cabañeros JM, Santos E. SOS GEFs in health and disease. Biochim Biophys Acta Rev Cancer 2020; 1874:188445. [PMID: 33035641 DOI: 10.1016/j.bbcan.2020.188445] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
SOS1 and SOS2 are the most universal and widely expressed family of guanine exchange factors (GEFs) capable or activating RAS or RAC1 proteins in metazoan cells. SOS proteins contain a sequence of modular domains that are responsible for different intramolecular and intermolecular interactions modulating mechanisms of self-inhibition, allosteric activation and intracellular homeostasis. Despite their homology, analyses of SOS1/2-KO mice demonstrate functional prevalence of SOS1 over SOS2 in cellular processes including proliferation, migration, inflammation or maintenance of intracellular redox homeostasis, although some functional redundancy cannot be excluded, particularly at the organismal level. Specific SOS1 gain-of-function mutations have been identified in inherited RASopathies and various sporadic human cancers. SOS1 depletion reduces tumorigenesis mediated by RAS or RAC1 in mouse models and is associated with increased intracellular oxidative stress and mitochondrial dysfunction. Since WT RAS is essential for development of RAS-mutant tumors, the SOS GEFs may be considered as relevant biomarkers or therapy targets in RAS-dependent cancers. Inhibitors blocking SOS expression, intrinsic GEF activity, or productive SOS protein-protein interactions with cellular regulators and/or RAS/RAC targets have been recently developed and shown preclinical and clinical effectiveness blocking aberrant RAS signaling in RAS-driven and RTK-driven tumors.
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Affiliation(s)
- Fernando C Baltanás
- Centro de Investigación del Cáncer - IBMCC (CSIC-USAL) and CIBERONC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Natasha Zarich
- Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC) and CIBERONC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Jose M Rojas-Cabañeros
- Unidad Funcional de Investigación de Enfermedades Crónicas (UFIEC) and CIBERONC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - Eugenio Santos
- Centro de Investigación del Cáncer - IBMCC (CSIC-USAL) and CIBERONC, Universidad de Salamanca, 37007 Salamanca, Spain.
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Christopher Jeyaseelan S, Milton Franklin Benial A. Spectroscopic characterization, DFT studies, molecular docking and cytotoxic evaluation of 4-nitro-indole-3-carboxaldehyde: A potent lung cancer agent. J Mol Recognit 2020; 34:e2872. [PMID: 32815220 DOI: 10.1002/jmr.2872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/29/2022]
Abstract
The 4-nitro-1H-indole-carboxaldehyde (NICA) molecule was characterized experimentally using FT-IR, FT-Raman and UV-Vis spectra, and it was studied theoretically using DFT calculations. The optimized structure of the NICA molecule was determined by DFT calculations using B3LYP functional with cc-pVTZ basis set. The electron localization function (ELF) and local orbital localizer (LOL) studies were performed to visualize the electron delocalization in the molecule. The experimental and theoretical wavenumbers of the title molecule were assigned using VEDA 4.0 program. The charge delocalization and stability of the title molecule were investigated using natural bond orbital (NBO) analysis. Frontier molecular orbitals (FMOs) and related molecular properties were calculated. UV-Vis spectrum was calculated theoretically and validated experimentally. The reactive sites of the molecule were studied from the MEP surface and Fukui function analysis. The molecular docking analysis reveals that the NICA ligand shows better inhibitory activity against RAS, which causes lung cancer. The in vitro cytotoxic activity of the molecule against human lung cancer cell lines (A549) was determined by MTT assay. Thus, the NICA molecule can be used as a potential candidate for the development of the drug against lung cancer.
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30
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Liao TJ, Jang H, Fushman D, Nussinov R. SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations. J Chem Phys 2020; 153:045106. [PMID: 32752665 PMCID: PMC7390601 DOI: 10.1063/5.0013926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/12/2020] [Indexed: 12/18/2022] Open
Abstract
Grb2 is an adaptor protein connecting the epidermal growth factor receptor and the downstream Son of sevenless 1 (SOS1), a Ras-specific guanine nucleotide exchange factor (RasGEF), which exchanges GDP by GTP. Grb2 contains three SH domains: N-terminal SH3 (nSH3), SH2, and C-terminal SH3 (cSH3). The C-terminal proline-rich (PR) domain of SOS1 regulates nSH3 open/closed conformations. Earlier, several nSH3 binding motifs were identified in the PR domain. More recently, we characterized by nuclear magnetic resonance and replica exchange simulations possible cSH3 binding regions. Among them, we discovered a cSH3-specific binding region. However, how PR binding at these sites regulates the nSH3/cSH3 conformation has been unclear. Here, we explore the nSH3/cSH3 interaction with linked and truncated PR segments using molecular dynamics simulations. Our 248 μs simulations include 620 distinct trajectories, each 400 ns. We construct the effective free energy landscape to validate the nSH3/cSH3 binding sites. The nSH3/cSH3-SOS1 peptide complex models indicate that strong peptide binders attract the flexible nSH3 n-Src loop, inducing a closed conformation of nSH3; by contrast, the cSH3 conformation remains unchanged. Inhibitors that disrupt the Ras-SOS1 interaction have been designed; the conformational details uncovered here may assist in the design of polypeptides inhibiting Grb2-SOS1 interaction, thus SOS1 recruitment to the membrane where Ras resides.
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Affiliation(s)
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
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31
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Liao TJ, Jang H, Nussinov R, Fushman D. High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1. J Am Chem Soc 2020; 142:3401-3411. [PMID: 31970984 PMCID: PMC8459210 DOI: 10.1021/jacs.9b10710] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Grb2 is an adaptor protein that recruits Ras-specific guanine nucleotide exchange factor, Son of Sevenless 1 (SOS1), to the plasma membrane. SOS1 exchanges GDP by GTP, activating Ras. Grb2 consists of an SH2 domain flanked by N- and C-terminal SH3 domains (nSH3/cSH3). Grb2 nSH3/cSH3 domains have strong binding affinity for the SOS1 proline-rich (PR) domain that mediates the Grb2-SOS1 interaction. The nSH3/cSH3 domains have distinct preferred binding motifs: PxxPxR for nSH3 and PxxxRxxKP for cSH3 (x represents any natural amino acid). Several nSH3-binding motifs have been identified in the SOS1 PR domain but none specific for cSH3 binding. Even though both nSH3 and cSH3 exhibit the strongest binding to the SOS1 peptide PVPPPVPPRRRP, this mutually exclusive binding combined with other potential nSH3/cSH3 binding regions in SOS1 makes understanding the Grb2-SOS1 interaction challenging. To identify the SOS1-cSH3 binding sites, we selected seven potential binding segments in SOS1. The synthesized peptides were tested for their binding to nSH3/cSH3. Our NMR data reveal that the PKLPPKTYKREH peptide has strong binding affinity for cSH3, but very weak for nSH3. The binding specificity suggests that the most likely Grb2-SOS1 binding mode is through nSH3-PVPPPVPPRRRP and cSH3-PKLPPKTYKREH interactions, which is supported by replica-exchange simulations for the Grb2-SOS1 complex models. We propose that nSH3/cSH3 binding peptides, which effectively interrupt Grb2-SOS1 association, can serve as tumor suppressors. The Grb2-SOS1 mechanism outlined here offers new venues for future therapeutic strategies for upstream mutations in cancer, such as in EGFR.
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Affiliation(s)
- Tsung-Jen Liao
- Biophysics Program, Institute for Physical Science and Technology , University of Maryland , College Park , Maryland 20742 , United States
- Computational Structural Biology Section, Basic Science Program , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21702 , United States
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21702 , United States
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21702 , United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine , Tel Aviv University , Tel Aviv 69978 , Israel
| | - David Fushman
- Biophysics Program, Institute for Physical Science and Technology , University of Maryland , College Park , Maryland 20742 , United States
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization , University of Maryland , College Park , Maryland 20742 , United States
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32
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Ni D, Li X, He X, Zhang H, Zhang J, Lu S. Drugging K-Ras G12C through covalent inhibitors: Mission possible? Pharmacol Ther 2019; 202:1-17. [PMID: 31233765 DOI: 10.1016/j.pharmthera.2019.06.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ras, whose mutants are present in approximately 30% of human tumours, is one of the most important oncogenes. Drugging Ras is thus regarded as the quest for the Holy Grail in cancer therapeutics development. Despite more than three decades of efforts, drug discovery targeting Ras constantly fails, rendering Ras undruggable, due to its smooth surface and picomolar affinity towards guanosine substrates. The most frequently mutated isoform of Ras is K-Ras, accounting for >85% of Ras-driven cancers, and one majority of them is the G12C mutation. Recent advances in structural biology shed light on drugging Ras, and one of the cutting-edge breakthroughs is the design of covalent G12C-specific inhibitors targeting the mutated cysteine. This type of inhibitor can be classified into substrate-competitive orthosteric inhibitors and non-competitive allosteric inhibitors. They display improved selectivity and enhanced potency due to their G12-specific and irreversible covalent binding nature. Thus, they represent a new hope for revolutionizing the conventional characterization of Ras as "undruggable" and pave a promising avenue for further drug discovery. Here, we provide comprehensive structural and medicinal chemical insights into K-Ras covalent inhibitors specific for the G12C mutant. We first present an in-depth analysis of the conformations of the inhibitor binding pockets. Then, all the latest covalent ligands selectively inhibiting K-RasG12C are reviewed. Finally, we examine the current challenges faced by this new class of anti-Ras inhibitors.
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Affiliation(s)
- Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinheng He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Hao Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
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Ni D, Lu S, Zhang J. Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Med Res Rev 2019; 39:2314-2342. [PMID: 30957264 DOI: 10.1002/med.21585] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.
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Affiliation(s)
- Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Center for Single-Cell Omics, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019; 15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.
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Prieto-Dominguez N, Parnell C, Teng Y. Drugging the Small GTPase Pathways in Cancer Treatment: Promises and Challenges. Cells 2019; 8:E255. [PMID: 30884855 PMCID: PMC6468615 DOI: 10.3390/cells8030255] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/08/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023] Open
Abstract
Small GTPases are a family of low molecular weight GTP-hydrolyzing enzymes that cycle between an inactive state when bound to GDP and an active state when associated to GTP. Small GTPases regulate key cellular processes (e.g., cell differentiation, proliferation, and motility) as well as subcellular events (e.g., vesicle trafficking), making them key participants in a great array of pathophysiological processes. Indeed, the dysfunction and deregulation of certain small GTPases, such as the members of the Ras and Arf subfamilies, have been related with the promotion and progression of cancer. Therefore, the development of inhibitors that target dysfunctional small GTPases could represent a potential therapeutic strategy for cancer treatment. This review covers the basic biochemical mechanisms and the diverse functions of small GTPases in cancer. We also discuss the strategies and challenges of inhibiting the activity of these enzymes and delve into new approaches that offer opportunities to target them in cancer therapy.
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Affiliation(s)
- Néstor Prieto-Dominguez
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, GA 30912, USA.
- Institute of Biomedicine (IBIOMED), University of León, León 24010, Spain.
| | | | - Yong Teng
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, GA 30912, USA.
- Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
- Department of Medical laboratory, Imaging and Radiologic Sciences, College of Allied Health, Augusta University, Augusta, GA 30912, USA.
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Cheng F, Liang H, Butte AJ, Eng C, Nussinov R. Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health. Pharmacol Rev 2019; 71:1-19. [PMID: 30545954 PMCID: PMC6294046 DOI: 10.1124/pr.118.016253] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent remarkable advances in genome sequencing have enabled detailed maps of identified and interpreted genomic variation, dubbed "mutanomes." The availability of thousands of exome/genome sequencing data has prompted the emergence of new challenges in the identification of novel druggable targets and therapeutic strategies. Typically, mutanomes are viewed as one- or two-dimensional. The three-dimensional protein structural view of personal mutanomes sheds light on the functional consequences of clinically actionable mutations revealed in tumor diagnosis and followed up in personalized treatments, in a mutanome-informed manner. In this review, we describe the protein structural landscape of personal mutanomes and provide expert opinions on rational strategies for more streamlined oncological drug discovery and molecularly targeted therapies for each individual and each tumor. We provide the structural mechanism of orthosteric versus allosteric drugs at the atom-level via targeting specific somatic alterations for combating drug resistance and the "undruggable" challenges in solid and hematologic neoplasias. We discuss computational biophysics strategies for innovative mutanome-informed cancer immunotherapies and combination immunotherapies. Finally, we highlight a personal mutanome infrastructure for the emerging development of personalized cancer medicine using a breast cancer case study.
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Affiliation(s)
- Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute (F.C., C.E.) and Taussig Cancer Institute (C.E.), Cleveland Clinic, Cleveland, Ohio; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio (F.C., C.E.); CASE Comprehensive Cancer Center (F.C., C.E.) and Department of Genetics and Genome Sciences (C.E.), Case Western Reserve University School of Medicine, Cleveland, Ohio; Departments of Bioinformatics and Computational Biology and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (H.L.); Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California (A.J.B.); Center for Data-Driven Insights and Innovation, University of California Health, Oakland, California (A.J.B.); Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland (R.N.); and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel (R.N.)
| | - Han Liang
- Genomic Medicine Institute, Lerner Research Institute (F.C., C.E.) and Taussig Cancer Institute (C.E.), Cleveland Clinic, Cleveland, Ohio; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio (F.C., C.E.); CASE Comprehensive Cancer Center (F.C., C.E.) and Department of Genetics and Genome Sciences (C.E.), Case Western Reserve University School of Medicine, Cleveland, Ohio; Departments of Bioinformatics and Computational Biology and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (H.L.); Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California (A.J.B.); Center for Data-Driven Insights and Innovation, University of California Health, Oakland, California (A.J.B.); Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland (R.N.); and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel (R.N.)
| | - Atul J Butte
- Genomic Medicine Institute, Lerner Research Institute (F.C., C.E.) and Taussig Cancer Institute (C.E.), Cleveland Clinic, Cleveland, Ohio; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio (F.C., C.E.); CASE Comprehensive Cancer Center (F.C., C.E.) and Department of Genetics and Genome Sciences (C.E.), Case Western Reserve University School of Medicine, Cleveland, Ohio; Departments of Bioinformatics and Computational Biology and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (H.L.); Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California (A.J.B.); Center for Data-Driven Insights and Innovation, University of California Health, Oakland, California (A.J.B.); Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland (R.N.); and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel (R.N.)
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute (F.C., C.E.) and Taussig Cancer Institute (C.E.), Cleveland Clinic, Cleveland, Ohio; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio (F.C., C.E.); CASE Comprehensive Cancer Center (F.C., C.E.) and Department of Genetics and Genome Sciences (C.E.), Case Western Reserve University School of Medicine, Cleveland, Ohio; Departments of Bioinformatics and Computational Biology and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (H.L.); Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California (A.J.B.); Center for Data-Driven Insights and Innovation, University of California Health, Oakland, California (A.J.B.); Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland (R.N.); and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel (R.N.)
| | - Ruth Nussinov
- Genomic Medicine Institute, Lerner Research Institute (F.C., C.E.) and Taussig Cancer Institute (C.E.), Cleveland Clinic, Cleveland, Ohio; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio (F.C., C.E.); CASE Comprehensive Cancer Center (F.C., C.E.) and Department of Genetics and Genome Sciences (C.E.), Case Western Reserve University School of Medicine, Cleveland, Ohio; Departments of Bioinformatics and Computational Biology and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas (H.L.); Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California (A.J.B.); Center for Data-Driven Insights and Innovation, University of California Health, Oakland, California (A.J.B.); Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland (R.N.); and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel (R.N.)
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Chen D, Chen Y, Lian F, Chen L, Li Y, Cao D, Wang X, Chen L, Li J, Meng T, Huang M, Geng M, Shen J, Zhang N, Xiong B. Fragment-based drug discovery of triazole inhibitors to block PDEδ-RAS protein-protein interaction. Eur J Med Chem 2018; 163:597-609. [PMID: 30562696 DOI: 10.1016/j.ejmech.2018.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 01/12/2023]
Abstract
Although mutated Ras protein is well recognized as an important drug target, direct targeting Ras has proven to be a daunting task. Recent studies demonstrated that Ras protein needs PDEδ to relocate to plasma membrane to execute its signaling transduction function, which provides a new avenue for modulating the Ras protein. To find small molecules antagonizing the interactions between PDEδ and Ras, here we presented a successful application of fragment-based drug discovery of PDEδ inhibitors. Under the guidance of crystal structures, we are able to quickly optimize the initial fragment into highly potent inhibitors, with more than 2000-fold improvement in binding activity, which further adds to the arsenal towards the inhibition of Ras signaling in cancer therapy.
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Affiliation(s)
- Danqi Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yuehong Chen
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Fulin Lian
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Liu Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yanlian Li
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Danyan Cao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Xin Wang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Lin Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Jian Li
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Tao Meng
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Min Huang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
| | - Meiyu Geng
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Jingkang Shen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Naixia Zhang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
| | - Bing Xiong
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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Chong SJF, Lai JXH, Eu JQ, Bellot GL, Pervaiz S. Reactive Oxygen Species and Oncoprotein Signaling-A Dangerous Liaison. Antioxid Redox Signal 2018; 29:1553-1588. [PMID: 29186971 DOI: 10.1089/ars.2017.7441] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SIGNIFICANCE There is evidence to implicate reactive oxygen species (ROS) in tumorigenesis and its progression. This has been associated with the interplay between ROS and oncoproteins, resulting in enhanced cellular proliferation and survival. Recent Advances: To date, studies have investigated specific contributions of the crosstalk between ROS and signaling networks in cancer initiation and progression. These investigations have challenged the established dogma of ROS as agents of cell death by demonstrating a secondary function that fuels cell proliferation and survival. Studies have thus identified (onco)proteins (Bcl-2, STAT3/5, RAS, Rac1, and Myc) in manipulating ROS level as well as exploiting an altered redox environment to create a milieu conducive for cancer formation and progression. CRITICAL ISSUES Despite these advances, drug resistance and its association with an altered redox metabolism continue to pose a challenge at the mechanistic and clinical levels. Therefore, identifying specific signatures, altered protein expressions, and modifications as well as protein-protein interplay/function could not only enhance our understanding of the redox networks during cancer initiation and progression but will also provide novel targets for designing specific therapeutic strategies. FUTURE DIRECTIONS Not only a heightened realization is required to unravel various gene/protein networks associated with cancer formation and progression, particularly from the redox standpoint, but there is also a need for developing more sensitive tools for assessing cancer redox metabolism in clinical settings. This review attempts to summarize our current knowledge of the crosstalk between oncoproteins and ROS in promoting cancer cell survival and proliferation and treatment strategies employed against these oncoproteins. Antioxid. Redox Signal.
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Affiliation(s)
- Stephen Jun Fei Chong
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore
| | - Jolin Xiao Hui Lai
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore
| | - Jie Qing Eu
- 2 Cancer Science Institute , Singapore, Singapore
| | - Gregory Lucien Bellot
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore .,3 Department of Hand and Reconstructive Microsurgery, National University Health System , Singapore, Singapore
| | - Shazib Pervaiz
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore .,4 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore , Singapore, Singapore .,5 National University Cancer Institute, National University Health System , Singapore, Singapore .,6 School of Biomedical Sciences, Curtin University , Perth, Australia
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Damani Shah H, Saranath D, Das S, Kharkar P, Karande A. In‐silico identification of small molecules targeting H‐Ras and in‐vitro cytotoxicity with caspase‐mediated apoptosis in carcinoma cells. J Cell Biochem 2018; 120:5519-5530. [PMID: 30367521 DOI: 10.1002/jcb.27836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/14/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Hetal Damani Shah
- Department of Biological Sciences, Sunandan Divatia School of Science Narsee Monjee Institute of Management Studies (deemed‐to‐be) University Mumbai India
| | - Dhananjaya Saranath
- Department of Biological Sciences, Sunandan Divatia School of Science Narsee Monjee Institute of Management Studies (deemed‐to‐be) University Mumbai India
| | - Soma Das
- Department of Biochemistry Indian Institute of Science Bangalore India
| | - Prashant Kharkar
- Department of Pharmaceutical Chemistry Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, Narsee Monjee Institute of Management Studies (deemed‐to‐be) University Mumbai India
| | - Anjali Karande
- Department of Biochemistry Indian Institute of Science Bangalore India
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Stout MC, Campbell PM. RASpecting the oncogene: New pathways to therapeutic advances. Biochem Pharmacol 2018; 158:217-228. [PMID: 30352234 DOI: 10.1016/j.bcp.2018.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022]
Abstract
RAS is the most commonly mutated driver of tumorigenesis, seen in about 30% of all cancer cases. There is a subset of tumors termed RAS-driven cancers in which RAS mutation or overactivation is evident, including as much as 95% in pancreatic and 50% in colon cancer. RAS is a family of small membrane bound GTPases that act as a signaling node to control both normal and cancer biology. Since the discovery of RAS' overall prominence in many tumor types and specifically in RAS-dependent cancers, it has been an obvious therapeutic target for drug development. However, RAS has proved a very elusive target, and after a few prominent RAS targeted drugs failed in clinical trials after decades of research, RAS was termed "undruggable" and research in this field was greatly hampered. An increase in knowledge about basic RAS biology has led to a resurgence in the generation of novel therapeutics targeting RAS signaling utilizing various and distinct approaches. These new drugs target RAS activation directly, block downstream signaling effectors and inhibit proper post-translational processing and trafficking/recycling of RAS. This review will cover how these new drugs were developed and how they have fared in preclinical and early phase clinical trials.
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Affiliation(s)
- Matthew C Stout
- Department of Pharmacology and Physiology, College of Medicine, Drexel University, USA; Cancer Biology Program and The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, USA
| | - Paul M Campbell
- Cancer Biology Program and The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, USA.
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Liao TJ, Jang H, Fushman D, Nussinov R. Allosteric KRas4B Can Modulate SOS1 Fast and Slow Ras Activation Cycles. Biophys J 2018; 115:629-641. [PMID: 30097175 PMCID: PMC6103739 DOI: 10.1016/j.bpj.2018.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 01/08/2023] Open
Abstract
Membrane-anchored Ras family proteins are activated by guanine nucleotide exchange factors such as SOS1. The CDC25 domain of SOS1 catalyzes GDP-to-GTP exchange, thereby activating Ras. Here, we aim to decipher the activation mechanism of KRas4B, a significantly mutated oncogene. We perform large-scale molecular dynamics simulations on 12 SOS1 systems, scrutinizing each step in two possible KRas4B activation cycles, fast and slow. To activate KRas4B at the CDC25 catalytic site, the allosteric site in the Ras exchanger motif (REM) domain of SOS1 needs to recruit a (nucleotide-bound) KRas4B molecule. Our simulations indicate that KRas4B-GTP interacts with the REM allosteric site more strongly than with the CDC25 catalytic site, consistent with its allosteric role in the GDP-to-GTP exchange. In the fast cycle, the allosteric KRas4B-GTP induces conformational change at the catalytic site. The conformational change facilitates loading KRas4B-GDP at the catalytic site and opening the KRas4B nucleotide-binding site for GDP release and GTP binding. GTP binding reduces the affinity of KRas4B-GTP to the CDC25 catalytic site, resulting in its release. By contrast, in the slow cycle, KRas4B-GDP binds at the allosteric REM site. The limited, altered conformational change that it induces prevents the exact alignments of switch I and II of KRas4B. The increasing binding strength at both binding sites due to interactions of regions other than switch I and II retards GDP release from the catalytic KRas4B, thus KRas4B activation. The accelerated activation cycle supports a positive feedback loop with allosteric signals communicating between the two Ras molecules and is the predominant, native function of SOS. SOS1 activation details may help drug discovery to inhibit Ras activation.
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Affiliation(s)
- Tsung-Jen Liao
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Biophysics Program
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - David Fushman
- Biophysics Program; Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Liu F, Yang X, Geng M, Huang M. Targeting ERK, an Achilles' Heel of the MAPK pathway, in cancer therapy. Acta Pharm Sin B 2018; 8:552-562. [PMID: 30109180 PMCID: PMC6089851 DOI: 10.1016/j.apsb.2018.01.008] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/11/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022] Open
Abstract
The mitogen-activated protein kinases (MAPK) pathway, often known as the RAS-RAF-MEK-ERK signal cascade, functions to transmit upstream signals to its downstream effectors to regulate physiological process such as cell proliferation, differentiation, survival and death. As the most frequently mutated signaling pathway in human cancer, targeting the MAPK pathway has long been considered a promising strategy for cancer therapy. Substantial efforts in the past decades have led to the clinical success of BRAF and MEK inhibitors. However, the clinical benefits of these inhibitors are compromised by the frequently occurring acquired resistance due to cancer heterogeneity and genomic instability. This review briefly introduces the key protein kinases involved in this pathway as well as their activation mechanisms. We also generalize the correlations between mutations of MAPK members and human cancers, followed by a summarization of progress made on the development of small molecule MAPK kinases inhibitors. In particular, this review highlights the potential advantages of ERK inhibitors in overcoming resistance to upstream targets and proposes that targeting ERK kinase may hold a promising prospect for cancer therapy.
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Nussinov R, Zhang M, Tsai CJ, Jang H. Calmodulin and IQGAP1 activation of PI3Kα and Akt in KRAS, HRAS and NRAS-driven cancers. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2304-2314. [DOI: 10.1016/j.bbadis.2017.10.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 02/06/2023]
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44
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Gebregiworgis T, Marshall CB, Nishikawa T, Radulovich N, Sandí MJ, Fang Z, Rottapel R, Tsao MS, Ikura M. Multiplexed Real-Time NMR GTPase Assay for Simultaneous Monitoring of Multiple Guanine Nucleotide Exchange Factor Activities from Human Cancer Cells and Organoids. J Am Chem Soc 2018. [PMID: 29543440 DOI: 10.1021/jacs.7b13703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Small GTPases (sGTPases) are critical switch-like regulators that mediate several important cellular functions and are often mutated in human cancers. They are activated by guanine nucleotide exchange factors (GEFs), which specifically catalyze the exchange of GTP for GDP. GEFs coordinate signaling networks in normal cells, and are frequently deregulated in cancers. sGTPase signaling pathways are complex and interconnected; however, most GEF assays do not reveal such complexity. In this Communication, we describe the development of a unique real-time NMR-based multiplexed GEF assay that employs distinct isotopic labeling schemes for each sGTPase protein to enable simultaneous observation of six proteins of interest. We monitor nucleotide exchange of KRas, Rheb, RalB, RhoA, Cdc42 and Rac1 in a single system, and assayed the activities of GEFs in lysates of cultured human cells and 3D organoids derived from pancreatic cancer patients. We observed potent activation of RhoA by lysates of HEK293a cells transfected with GEF-H1, along with weak stimulation of Rac1, which we showed is indirect. Our functional analyses of pancreatic cancer-derived organoids revealed higher GEF activity for RhoA than other sGTPases, in line with RNA-seq data indicating high expression of RhoA-specific GEFs.
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Affiliation(s)
- Teklab Gebregiworgis
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Tadateru Nishikawa
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - María-José Sandí
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
| | - Robert Rottapel
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A1 , Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario M5G 1L7 , Canada.,Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
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45
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Marín-Ramos NI, Ortega-Gutiérrez S, López-Rodríguez ML. Blocking Ras inhibition as an antitumor strategy. Semin Cancer Biol 2018; 54:91-100. [PMID: 29409706 DOI: 10.1016/j.semcancer.2018.01.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/17/2022]
Abstract
Ras proteins are among the most frequently mutated drivers in human cancer and remain an elusive pharmaceutical targeting. Previous studies have improved the understanding of Ras structure, processing, and signaling pathways in cancer cells and have opened new possibilities for inhibiting Ras function. In this review we discuss the most recent advances towards inhibiting Ras activity with small molecules, highlighting the two approaches: (i) compounds that bind directly to Ras protein and (ii) inhibitors of the enzymes involved in the post-translational modifications of Ras. In the former, we analyze the most recent contributions in each of the main classes of Ras direct binders, including the different types of nucleotide exchange inhibitors, allosteric compounds, and molecules that interfere with the interaction between Ras and its effectors. In the latter, we examine the compounds that inhibit Ras activation by blocking any of its post-translational modifications. Also, a special focus is made on those molecules that have progressed the farthest from medicinal chemistry and drug development points of view. Finally, the current scene regarding the clinical trials of Ras inhibitors, together with the future promising avenues for further development of the challenging Ras field are reviewed.
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Affiliation(s)
- Nagore I Marín-Ramos
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silvia Ortega-Gutiérrez
- Department of Organic Chemistry I, Universidad Complutense de Madrid, Av. Complutense s/n, E-28040 Madrid, Spain
| | - María L López-Rodríguez
- Department of Organic Chemistry I, Universidad Complutense de Madrid, Av. Complutense s/n, E-28040 Madrid, Spain.
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Computational Insights into the Interactions between Calmodulin and the c/nSH2 Domains of p85α Regulatory Subunit of PI3Kα: Implication for PI3Kα Activation by Calmodulin. Int J Mol Sci 2018; 19:ijms19010151. [PMID: 29300353 PMCID: PMC5796100 DOI: 10.3390/ijms19010151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/18/2017] [Accepted: 12/26/2017] [Indexed: 12/15/2022] Open
Abstract
Calmodulin (CaM) and phosphatidylinositide-3 kinase (PI3Kα) are well known for their multiple roles in a series of intracellular signaling pathways and in the progression of several human cancers. Crosstalk between CaM and PI3Kα has been an area of intensive research. Recent experiments have shown that in adenocarcinoma, K-Ras4B is involved in the CaM-PI3Kα crosstalk. Based on experimental results, we have recently put forward a hypothesis that the coordination of CaM and PI3Kα with K-Ras4B forms a CaM-PI3Kα-K-Ras4B ternary complex, which leads to the formation of pancreatic ductal adenocarcinoma. However, the mechanism for the CaM-PI3Kα crosstalk is unresolved. Based on molecular modeling and molecular dynamics simulations, here we explored the potential interactions between CaM and the c/nSH2 domains of p85α subunit of PI3Kα. We demonstrated that CaM can interact with the c/nSH2 domains and the interaction details were unraveled. Moreover, the possible modes for the CaM-cSH2 and CaM-nSH2 interactions were uncovered and we used them to construct a complete CaM-PI3Kα complex model. The structural model of CaM-PI3Kα interaction not only offers a support for our previous ternary complex hypothesis, but also is useful for drug design targeted at CaM-PI3Kα protein-protein interactions.
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Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation. Int J Mol Sci 2017; 18:ijms18112249. [PMID: 29072601 PMCID: PMC5713219 DOI: 10.3390/ijms18112249] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/13/2017] [Accepted: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras–NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras.
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Nussinov R, Jang H, Tsai CJ, Liao TJ, Li S, Fushman D, Zhang J. Intrinsic protein disorder in oncogenic KRAS signaling. Cell Mol Life Sci 2017; 74:3245-3261. [PMID: 28597297 PMCID: PMC11107717 DOI: 10.1007/s00018-017-2564-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022]
Abstract
How Ras, and in particular its most abundant oncogenic isoform K-Ras4B, is activated and signals in proliferating cells, poses some of the most challenging questions in cancer cell biology. In this paper, we ask how intrinsically disordered regions in K-Ras4B and its effectors help promote proliferative signaling. Conformational disorder allows spanning long distances, supports hinge motions, promotes anchoring in membranes, permits segments to fulfil multiple roles, and broadly is crucial for activation mechanisms and intensified oncogenic signaling. Here, we provide an overview illustrating some of the key mechanisms through which conformational disorder can promote oncogenesis, with K-Ras4B signaling serving as an example. We discuss (1) GTP-bound KRas4B activation through membrane attachment; (2) how farnesylation and palmitoylation can promote isoform functional specificity; (3) calmodulin binding and PI3K activation; (4) how Ras activates its RASSF5 cofactor, thereby stimulating signaling of the Hippo pathway and repressing proliferation; and (5) how intrinsically disordered segments in Raf help its attachment to the membrane and activation. Collectively, we provide the first inclusive review of the roles of intrinsic protein disorder in oncogenic Ras-driven signaling. We believe that a broad picture helps to grasp and formulate key mechanisms in Ras cancer biology and assists in therapeutic intervention.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Tsung-Jen Liao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Shuai Li
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Jian Zhang
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
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Yoshizawa R, Umeki N, Yanagawa M, Murata M, Sako Y. Single-molecule fluorescence imaging of RalGDS on cell surfaces during signal transduction from Ras to Ral. Biophys Physicobiol 2017; 14:75-84. [PMID: 28744424 PMCID: PMC5515350 DOI: 10.2142/biophysico.14.0_75] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/29/2017] [Indexed: 01/28/2023] Open
Abstract
RalGDS is one of the Ras effectors and functions as a guanine nucleotide exchange factor for the small G-protein, Ral, which regulates membrane trafficking and cytoskeletal remodeling. The translocation of RalGDS from the cytoplasm to the plasma membrane is required for Ral activation. In this study, to understand the mechanism of Ras–Ral signaling we performed a single-molecule fluorescence analysis of RalGDS and its functional domains (RBD and REMCDC) on the plasma membranes of living HeLa cells. Increased molecular density of RalGDS and RBD, but not REMCDC, was observed on the plasma membrane after EGF stimulation of the cells to induce Ras activation, suggesting that the translocation of RalGDS involves an interaction between the GTP-bound active form of Ras and the RBD of RalGDS. Whereas the RBD played an important role in increasing the association rate constant between RalGDS and the plasma membrane, the REMCDC domain affected the dissociation rate constant from the membrane, which decreased after Ras activation or the hyperexpression of Ral. The Y64 residue of Ras and clusters of RalGDS molecules were involved in this reduction. From these findings, we infer that Ras activation not merely increases the cell-surface density of RalGDS, but actively stimulates the RalGDS–Ral interaction through a structural change in RalGDS and/or the accumulation of Ral, as well as the GTP–Ras/RalGDS clusters, to induce the full activation of Ral.
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Affiliation(s)
- Ryo Yoshizawa
- Cellular Informatics Lab., RIKEN, Wako, Saitama 351-0198, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Lab., RIKEN, Wako, Saitama 351-0198, Japan
| | | | - Masayuki Murata
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Yasushi Sako
- Cellular Informatics Lab., RIKEN, Wako, Saitama 351-0198, Japan
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50
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Nussinov R, Tsai CJ, Jang H. A New View of Pathway-Driven Drug Resistance in Tumor Proliferation. Trends Pharmacol Sci 2017; 38:427-437. [PMID: 28245913 PMCID: PMC5403593 DOI: 10.1016/j.tips.2017.02.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/25/2017] [Accepted: 02/01/2017] [Indexed: 12/13/2022]
Abstract
Defeating drug resistance in tumor cell proliferation is challenging. We propose that signaling in cell proliferation takes place via two core pathways, each embodying multiple alternative pathways. We consider drug resistance through an alternative proliferation pathway - within the same or within the other core pathway. Most drug combinations target only one core pathway; blocking both can restrain proliferation. We define core pathways as independent and acting similarly in cell-cycle control, which can explain why their products (e.g., ERK and YAP1) can substitute for each other in resistance. Core pathways can forecast possible resistance because acquired resistance frequently occurs through alternative proliferation pathways. This concept may help to predict the efficacy of drug combinations. The selection of distinct combinations for specific mutated pathways would be guided by clinical diagnosis.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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