1
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Teo MYM, Fong JY, Lim WM, In LLA. Current Advances and Trends in KRAS Targeted Therapies for Colorectal Cancer. Mol Cancer Res 2021; 20:30-44. [PMID: 34462329 DOI: 10.1158/1541-7786.mcr-21-0248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/25/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022]
Abstract
Kirsten Rat Sarcoma (KRAS) gene somatic point mutations is one of the most prominently mutated proto-oncogenes known to date, and accounts for approximately 60% of all colorectal cancer cases. One of the most exciting drug development areas against colorectal cancer is the targeting of undruggable kinases and kinase-substrate molecules, although whether and how they can be integrated with other therapies remains a question. Current clinical trial data have provided supporting evidence on the use of combination treatment involving MEK inhibitors and either one of the PI3K inhibitors for patients with metastatic colorectal cancer to avoid the development of resistance and provide effective therapeutic outcome rather than using a single agent alone. Many clinical trials are also ongoing to evaluate different combinations of these pathway inhibitors in combination with immunotherapy for patients with colorectal cancer whose current palliative treatment options are limited. Nevertheless, continued assessment of these targeted cancer therapies will eventually allow patients with colorectal cancer to be treated using a personalized medicine approach. In this review, the most recent scientific approaches and clinical trials targeting KRAS mutations directly or indirectly for the management of colorectal cancer are discussed.
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Affiliation(s)
- Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Jung Yin Fong
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Wan Ming Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia.
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2
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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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3
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Tisi R, Spinelli M, Palmioli A, Airoldi C, Cazzaniga P, Besozzi D, Nobile MS, Mazzoleni E, Arnhold S, De Gioia L, Grandori R, Peri F, Vanoni M, Sacco E. The Multi-Level Mechanism of Action of a Pan-Ras Inhibitor Explains its Antiproliferative Activity on Cetuximab-Resistant Cancer Cells. Front Mol Biosci 2021; 8:625979. [PMID: 33681292 PMCID: PMC7925909 DOI: 10.3389/fmolb.2021.625979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/11/2021] [Indexed: 12/04/2022] Open
Abstract
Ras oncoproteins play a crucial role in the onset, maintenance, and progression of the most common and deadly human cancers. Despite extensive research efforts, only a few mutant-specific Ras inhibitors have been reported. We show that cmp4–previously identified as a water-soluble Ras inhibitor– targets multiple steps in the activation and downstream signaling of different Ras mutants and isoforms. Binding of this pan-Ras inhibitor to an extended Switch II pocket on HRas and KRas proteins induces a conformational change that down-regulates intrinsic and GEF-mediated nucleotide dissociation and exchange and effector binding. A mathematical model of the Ras activation cycle predicts that the inhibitor severely reduces the proliferation of different Ras-driven cancer cells, effectively cooperating with Cetuximab to reduce proliferation even of Cetuximab-resistant cancer cell lines. Experimental data confirm the model prediction, indicating that the pan-Ras inhibitor is an appropriate candidate for medicinal chemistry efforts tailored at improving its currently unsatisfactory affinity.
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Affiliation(s)
- Renata Tisi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.,SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.,SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | - Paolo Cazzaniga
- SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre - B4, Milano, Italy
| | - Daniela Besozzi
- SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre - B4, Milano, Italy
| | - Marco S Nobile
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre - B4, Milano, Italy.,Department of Industrial Engineering and Innovation Sciences, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Elisa Mazzoleni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Simone Arnhold
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.,SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Francesco Peri
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.,SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
| | - Elena Sacco
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy.,SYSBIO-ISBE-IT-Candidate National Node of Italy for ISBE, Research Infrastructure for Systems Biology Europe, Milan, Italy
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4
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Abstract
RAS proteins control a number of essential cellular processes as molecular switches in the human body. Presumably due to their important signalling role, RAS proteins are among the most frequently mutated oncogenes in human cancers. Hence, numerous efforts were done to develop appropriate therapies for RAS-mutant cancers in the last three decades. This review aimed to collect all of the reported small molecules that affect RAS signalling. These molecules can be divided in four main branches. First, we address approaches blocking RAS membrane association. Second, we focus on the stabilization efforts of non-productive RAS complexes. Third, we examine the approach to block RAS downstream signalling through disturbance of RAS-effector complex formation. Finally, we discuss direct inhibition; particularly the most recently reported covalent inhibitors, which are already advanced to human clinical trials.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, Budapest, H-1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, Budapest, H-1117, Hungary.
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5
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Röth S, Macartney TJ, Konopacka A, Chan KH, Zhou H, Queisser MA, Sapkota GP. Targeting Endogenous K-RAS for Degradation through the Affinity-Directed Protein Missile System. Cell Chem Biol 2020; 27:1151-1163.e6. [PMID: 32668202 PMCID: PMC7505679 DOI: 10.1016/j.chembiol.2020.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/12/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022]
Abstract
K-RAS is known as the most frequently mutated oncogene. However, the development of conventional K-RAS inhibitors has been extremely challenging, with a mutation-specific inhibitor reaching clinical trials only recently. Targeted proteolysis has emerged as a new modality in drug discovery to tackle undruggable targets. Our laboratory has developed a system for targeted proteolysis using peptidic high-affinity binders, called “AdPROM.” Here, we used CRISPR/Cas9 technology to knock in a GFP tag on the native K-RAS gene in A549 adenocarcinoma (A549GFPKRAS) cells and constructed AdPROMs containing high-affinity GFP or H/K-RAS binders. Expression of GFP-targeting AdPROM in A549GFPKRAS led to robust proteasomal degradation of endogenous GFP-K-RAS, while expression of anti-HRAS-targeting AdPROM in different cell lines resulted in the degradation of both GFP-tagged and untagged K-RAS, and untagged H-RAS. Our findings imply that endogenous RAS proteins can be targeted for proteolysis, supporting the idea of an alternative therapeutic approach to these undruggable targets. Generation of A549 cells with a homozygous knockin of GFP tag on the KRAS gene Proteasomal degradation of endogenous GFP-K-RAS using a VHL-GFP-nanobody fusion Proteasomal degradation of endogenous H/K-RAS using VHL-H/K-RAS-monobody fusion
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Affiliation(s)
- Sascha Röth
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Thomas J Macartney
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Agnieszka Konopacka
- GlaxoSmithKline, Protein Degradation Group, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | - Kwok-Ho Chan
- GlaxoSmithKline, Protein Degradation Group, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | - Houjiang Zhou
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Markus A Queisser
- GlaxoSmithKline, Protein Degradation Group, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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6
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Mattox TE, Chen X, Maxuitenko YY, Keeton AB, Piazza GA. Exploiting RAS Nucleotide Cycling as a Strategy for Drugging RAS-Driven Cancers. Int J Mol Sci 2019; 21:ijms21010141. [PMID: 31878223 PMCID: PMC6982188 DOI: 10.3390/ijms21010141] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Oncogenic mutations in RAS genes result in the elevation of cellular active RAS protein levels and increased signal propagation through downstream pathways that drive tumor cell proliferation and survival. These gain-of-function mutations drive over 30% of all human cancers, presenting promising therapeutic potential for RAS inhibitors. However, many have deemed RAS “undruggable” after nearly 40 years of failed drug discovery campaigns aimed at identifying a RAS inhibitor with clinical activity. Here we review RAS nucleotide cycling and the opportunities that RAS biochemistry presents for developing novel RAS inhibitory compounds. Additionally, compounds that have been identified to inhibit RAS by exploiting various aspects of RAS biology and biochemistry will be covered. Our current understanding of the biochemical properties of RAS, along with reports of direct-binding inhibitors, both provide insight on viable strategies for the discovery of novel clinical candidates with RAS inhibitory activity.
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Affiliation(s)
- Tyler E. Mattox
- Drug Discovery Research Center, University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA; (X.C.); (Y.Y.M.); (A.B.K.); (G.A.P.)
- Correspondence:
| | - Xi Chen
- Drug Discovery Research Center, University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA; (X.C.); (Y.Y.M.); (A.B.K.); (G.A.P.)
- ADT Pharmaceuticals, Orange Beach, AL 36561, USA
| | - Yulia Y. Maxuitenko
- Drug Discovery Research Center, University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA; (X.C.); (Y.Y.M.); (A.B.K.); (G.A.P.)
| | - Adam B. Keeton
- Drug Discovery Research Center, University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA; (X.C.); (Y.Y.M.); (A.B.K.); (G.A.P.)
- ADT Pharmaceuticals, Orange Beach, AL 36561, USA
| | - Gary A. Piazza
- Drug Discovery Research Center, University of South Alabama Mitchell Cancer Institute, Mobile, AL 36604, USA; (X.C.); (Y.Y.M.); (A.B.K.); (G.A.P.)
- ADT Pharmaceuticals, Orange Beach, AL 36561, USA
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7
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Tsubamoto M, Le TK, Li M, Watanabe T, Matsumi C, Parvatkar P, Fujii H, Kato N, Sun J, Ohkanda J. A Guanidyl-Based Bivalent Peptidomimetic Inhibits K-Ras Prenylation and Association with c-Raf. Chemistry 2019; 25:13531-13536. [PMID: 31393030 DOI: 10.1002/chem.201903129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/07/2019] [Indexed: 01/06/2023]
Abstract
Unusual lipid modification of K-Ras makes Ras-directed cancer therapy a challenging task. Aiming to disrupt electrostatic-driven protein-protein interactions (PPIs) of K-Ras with FTase and GGTase I, a series of bivalent dual inhibitors that recognize the active pocket and the common acidic surface of FTase and GGTase I were designed. The structure-activity-relationship study resulted in 8 b, in which a biphenyl-based peptidomimetic FTI-277 was attached to a guanidyl-containing gallate moiety through an alkyl linker. Cell-based evaluation demonstrated that 8 b exhibited substantial inhibition of K-Ras processing without apparent interference with Rap-1A processing. Fluorescent imaging showed that 8 b disrupts localization of K-Ras to the plasma membrane and impairs interaction with c-Raf, whereas only FTI-277 was found to be inactive. These results suggest that targeting the PPI interface of K-Ras may provide an alternative method of inhibiting K-Ras.
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Affiliation(s)
- Mai Tsubamoto
- The Institute of Scientific Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Toan Khanh Le
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Minghua Li
- Department of Pharmaceutical Science, University of South Florida, Tampa, Florida, 33612, USA
| | - Taku Watanabe
- Ina Laboratory, Medical & Biological Laboratories, CO., Ltd., Ina, Nagano, 396-0002, Japan
| | - Chiemi Matsumi
- Ina Laboratory, Medical & Biological Laboratories, CO., Ltd., Ina, Nagano, 396-0002, Japan
| | - Prakash Parvatkar
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Hiroshi Fujii
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Nobuo Kato
- The Institute of Scientific Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Jiazhi Sun
- Department of Pharmaceutical Science, University of South Florida, Tampa, Florida, 33612, USA
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
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8
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Saliani M, Jalal R, Ahmadian MR. From basic researches to new achievements in therapeutic strategies of KRAS-driven cancers. Cancer Biol Med 2019; 16:435-461. [PMID: 31565476 PMCID: PMC6743616 DOI: 10.20892/j.issn.2095-3941.2018.0530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022] Open
Abstract
Among the numerous oncogenes involved in human cancers, KRAS represents the most studied and best characterized cancer-related genes. Several therapeutic strategies targeting oncogenic KRAS (KRAS onc ) signaling pathways have been suggested, including the inhibition of synthetic lethal interactions, direct inhibition of KRAS onc itself, blockade of downstream KRAS onc effectors, prevention of post-translational KRAS onc modifications, inhibition of the induced stem cell-like program, targeting of metabolic peculiarities, stimulation of the immune system, inhibition of inflammation, blockade of upstream signaling pathways, targeted RNA replacement, and oncogene-induced senescence. Despite intensive and continuous efforts, KRAS onc remains an elusive target for cancer therapy. To highlight the progress to date, this review covers a collection of studies on therapeutic strategies for KRAS published from 1995 to date. An overview of the path of progress from earlier to more recent insights highlight novel opportunities for clinical development towards KRASonc-signaling targeted therapeutics.
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Affiliation(s)
- Mahsa Saliani
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Razieh Jalal
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
- Department of Research Cell and Molecular Biology, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine University, Düsseldorf 40225, Germany
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9
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Bery N, Rabbitts TH. Bioluminescence Resonance Energy Transfer 2 (BRET2)-Based RAS Biosensors to Characterize RAS Inhibitors. ACTA ACUST UNITED AC 2019; 83:e83. [PMID: 30768855 DOI: 10.1002/cpcb.83] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Protein-protein interactions (PPIs) are principle biological processes that control normal cell growth, differentiation, and homeostasis but are also crucial in diseases such as malignancy, neuropathy, and infection. Despite the importance of PPIs in biology, this target class has been very challenging to convert to therapeutics. In the last decade, much progress has been made in the inhibition of PPIs involved in diseases, but many remain difficult such as RAS-effector interactions in cancers. We describe here a protocol for using Bioluminescence Resonance Energy Transfer 2 (BRET2)-based RAS biosensors to detect and characterize RAS PPI inhibition by macromolecules and small molecules. This method could be extended to any other small GTPases or any other PPIs of interest. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Terence H Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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10
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Hodges TR, Abbott JR, Little AJ, Sarkar D, Salovich JM, Howes JE, Akan DT, Sai J, Arnold AL, Browning C, Burns MC, Sobolik T, Sun Q, Beesetty Y, Coker JA, Scharn D, Stadtmueller H, Rossanese OW, Phan J, Waterson AG, McConnell DB, Fesik SW. Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS. J Med Chem 2018; 61:8875-8894. [PMID: 30205005 PMCID: PMC8314423 DOI: 10.1021/acs.jmedchem.8b01108] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.
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Affiliation(s)
- Timothy R. Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jason R. Abbott
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Andrew J. Little
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Dhruba Sarkar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - James M. Salovich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jennifer E. Howes
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Denis T. Akan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Allison L. Arnold
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Carrie Browning
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Michael C. Burns
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Tammy Sobolik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Qi Sun
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Yugandhar Beesetty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jesse A. Coker
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Heinz Stadtmueller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Olivia W. Rossanese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Alex G. Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, USA
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, USA
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11
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Ras proteins as therapeutic targets. Biochem Soc Trans 2018; 46:1303-1311. [PMID: 30154091 DOI: 10.1042/bst20170529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/25/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
Oncogenic mutations in RAS genes underlie the pathogenesis of many human tumours, and there has been intense effort for over 30 years to develop effective and tolerated targeted therapeutics for patients with Ras-driven cancers. This review summarises the progress made in Ras drug discovery, highlighting some of the recent developments in directly targeting Ras through advances in small molecule drug design and novel therapeutic strategies.
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12
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García-Gómez R, Bustelo XR, Crespo P. Protein-Protein Interactions: Emerging Oncotargets in the RAS-ERK Pathway. Trends Cancer 2018; 4:616-633. [PMID: 30149880 DOI: 10.1016/j.trecan.2018.07.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/03/2018] [Accepted: 07/08/2018] [Indexed: 12/20/2022]
Abstract
Given the implication of aberrant RAS-extracellular signal-regulated kinase (ERK) signaling in the development of a large number of tumor types, this route is under intense scrutiny to identify new anticancer drugs. Most avenues in that direction have been primarily focused on the inhibition of the catalytic activity of the kinases that participate in this pathway. Although promising, the efficacy of these therapies is short lived due to undesired toxicity and/or drug resistance problems. As an alternative path, new efforts are now being devoted to the targeting of protein-protein interactions (PPIs) involved in the flow of RAS-ERK signals. Many of these efforts have shown promising results in preclinical models. In this review, we summarize recent progress made in this area.
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Affiliation(s)
- Rocío García-Gómez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander 39011, Spain
| | - Xosé R Bustelo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain; Centro de Investigación del Cáncer, Universidad de Salamanca, Salamanca 37007, Spain; Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca 37007, Spain
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Cantabria, Santander 39011, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain.
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13
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Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment. Nat Commun 2018; 9:3169. [PMID: 30093669 PMCID: PMC6085350 DOI: 10.1038/s41467-018-05707-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
Targeting specific protein–protein interactions (PPIs) is an attractive concept for drug development, but hard to implement since intracellular antibodies do not penetrate cells and most small-molecule drugs are considered unsuitable for PPI inhibition. A potential solution to these problems is to select intracellular antibody fragments to block PPIs, use these antibody fragments for target validation in disease models and finally derive small molecules overlapping the antibody-binding site. Here, we explore this strategy using an anti-mutant RAS antibody fragment as a competitor in a small-molecule library screen for identifying RAS-binding compounds. The initial hits are optimized by structure-based design, resulting in potent RAS-binding compounds that interact with RAS inside the cells, prevent RAS-effector interactions and inhibit endogenous RAS-dependent signalling. Our results may aid RAS-dependent cancer drug development and demonstrate a general concept for developing small compounds to replace intracellular antibody fragments, enabling rational drug development to target validated PPIs. Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells.
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14
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Abbott JR, Hodges TR, Daniels RN, Patel PA, Kennedy JP, Howes JE, Akan DT, Burns MC, Sai J, Sobolik T, Beesetty Y, Lee T, Rossanese OW, Phan J, Waterson AG, Fesik SW. Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling. J Med Chem 2018; 61:6002-6017. [PMID: 29856609 DOI: 10.1021/acs.jmedchem.8b00360] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS activity is to target and affect the activity of proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report on structure-activity relationships (SAR) in an indole series of compounds. Using structure-based design, we systematically explored substitution patterns on the indole nucleus, the pendant amino acid moiety, and the linker unit that connects these two fragments. Best-in-class compounds activate the nucleotide exchange process at submicromolar concentrations in vitro, increase levels of active RAS-GTP in HeLa cells, and elicit signaling changes in the mitogen-activated protein kinase-extracellular regulated kinase (MAPK-ERK) pathway, resulting in a decrease in pERK1/2T202/Y204 protein levels at higher compound concentrations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Alex G Waterson
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States
| | - Stephen W Fesik
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States
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15
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Bery N, Cruz-Migoni A, Bataille CJ, Quevedo CE, Tulmin H, Miller A, Russell A, Phillips SE, Carr SB, Rabbitts TH. BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions. eLife 2018; 7:37122. [PMID: 29989546 PMCID: PMC6039175 DOI: 10.7554/elife.37122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/16/2018] [Indexed: 12/13/2022] Open
Abstract
The RAS family of proteins is amongst the most highly mutated in human cancers and has so far eluded drug therapy. Currently, much effort is being made to discover mutant RAS inhibitors and in vitro screening for RAS-binding drugs must be followed by cell-based assays. Here, we have developed a robust set of bioluminescence resonance energy transfer (BRET)-based RAS biosensors that enable monitoring of RAS-effector interaction inhibition in living cells. These include KRAS, HRAS and NRAS and a variety of different mutations that mirror those found in human cancers with the major RAS effectors such as CRAF, PI3K and RALGDS. We highlighted the utility of these RAS biosensors by showing a RAS-binding compound is a potent pan-RAS-effector interactions inhibitor in cells. The RAS biosensors represent a useful tool to investigate and characterize the potency of anti-RAS inhibitors in cells and more generally any RAS protein-protein interaction (PPI) in cells. A group of proteins known as the RAS family plays a critical role in controlling animal cell growth and division. RAS proteins are normally active only some of the time, but genetic mutations can create permanently active forms of the proteins. These constantly interact with other proteins called effectors. In response, cells multiply uncontrollably and give rise to cancers. In an attempt to find new cancer treatments, researchers across the globe are trying to develop inhibitor drugs that prevent RAS and effector proteins from interacting. New drugs are often tested in laboratory experiments that directly apply the drugs to the proteins that they are designed to work on. But in some cases a drug may work wellin the laboratory but fail to work when used in cells. Unfortunately, there are few ways to judge how well inhibitor drugs work inside living cells. Bery et al. have now developed RAS biosensors – a collection of proteins that bind to RAS and produce light more brightly when RAS interacts with effector proteins in living cells. Tests on cells treated with an antibody that works inside cells and is known to prevent interactions between RAS and effector proteins confirmed that the RAS biosensors work well. Bery et al. then used the RAS biosensors to show that a new RAS inhibitor works in human cancer cells. The RAS biosensors are available upon request to researchers across the globe. They should form an important tool for testing potential treatments for cancers that contain mutated RAS proteins.
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Affiliation(s)
- Nicolas Bery
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Abimael Cruz-Migoni
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | - Camilo E Quevedo
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Hanna Tulmin
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ami Miller
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Simon Ev Phillips
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Stephen B Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom.,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Terence H Rabbitts
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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16
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Stefan E, Troppmair J, Bister K. Targeting the Architecture of Deregulated Protein Complexes in Cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 111:101-132. [PMID: 29459029 DOI: 10.1016/bs.apcsb.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The architectures of central signaling hubs are precisely organized by static and dynamic protein-protein interactions (PPIs). Upon deregulation, these PPI platforms are capable to propagate or initiate pathophysiological signaling events. This causes the acquisition of molecular features contributing to the etiology or progression of many diseases, including cancer, where deregulated molecular interactions of signaling proteins have been best studied. The reasons for PPI-dependent reprogramming of cancer-initiating cells are manifold; in many cases, mutations perturb PPIs, enzyme activities, protein abundance, or protein localization. Consequently, the pharmaceutical targeting of PPIs promises to be of remarkable therapeutic value. For this review we have selected three key players of oncogenic signaling which are differently affected by PPI deregulation: two (the small G proteins of the RAS family and the transcription factor MYC) are considered "undruggable" using classical drug discovery approaches and in the case of the third protein discussed here, PKA, standard kinase inhibitors, may be unsuitable in the clinic. These circumstances require alternative strategies, which may lie in pharmaceutical drug interference of critical PPIs accountable for oncogenic signaling.
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Affiliation(s)
- Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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17
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Liu LJ, Wang W, Huang SY, Hong Y, Li G, Lin S, Tian J, Cai Z, Wang HMD, Ma DL, Leung CH. Inhibition of the Ras/Raf interaction and repression of renal cancer xenografts in vivo by an enantiomeric iridium(iii) metal-based compound. Chem Sci 2017; 8:4756-4763. [PMID: 28959398 PMCID: PMC5603957 DOI: 10.1039/c7sc00311k] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/08/2017] [Indexed: 01/09/2023] Open
Abstract
Targeting protein-protein interactions (PPIs) offers tantalizing opportunities for therapeutic intervention for the treatment of human diseases. Modulating PPI interfaces with organic small molecules has been found to be exceptionally challenging, and few candidates have been successfully developed into clinical drugs. Meanwhile, the striking array of distinctive properties exhibited by metal compounds renders them attractive scaffolds for the development of bioactive leads. Here, we report the identification of iridium(iii) compounds as inhibitors of the H-Ras/Raf-1 PPI. The lead iridium(iii) compound 1 exhibited potent inhibitory activity against the H-Ras/Raf-1 interaction and its signaling pathway in vitro and in vivo, and also directly engaged both H-Ras and Raf-1-RBD in cell lysates. Moreover, 1 repressed tumor growth in a mouse renal xenograft tumor model. Intriguingly, the Δ-enantiomer of 1 showed superior potency in the biological assays compared to Λ-1 or racemic 1. These compounds could potentially be used as starting scaffolds for the development of more potent Ras/Raf PPI inhibitors for the treatment of kidney cancer or other proliferative diseases.
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Affiliation(s)
- Li-Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Wanhe Wang
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Shi-Ying Huang
- College of Oceanology and Food Science , Quanzhou Normal University , Quanzhou 362000 , China
- Key Laboratory for the Development of Bioactive Material from Marine Algae , Quanzhou 362000 , China
| | - Yanjun Hong
- Partner State Key Laboratory of Environmental and Biological Analysis , Department of Chemistry , Hong Kong Baptist University , 224 Waterloo Road , Kowloon Tong , Hong Kong SAR , P. R. China .
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Sheng Lin
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Jinglin Tian
- Partner State Key Laboratory of Environmental and Biological Analysis , Department of Chemistry , Hong Kong Baptist University , 224 Waterloo Road , Kowloon Tong , Hong Kong SAR , P. R. China .
| | - Zongwei Cai
- Partner State Key Laboratory of Environmental and Biological Analysis , Department of Chemistry , Hong Kong Baptist University , 224 Waterloo Road , Kowloon Tong , Hong Kong SAR , P. R. China .
| | - Hui-Min David Wang
- Graduate Institute of Biomedical Engineering , National Chung Hsing University , Taichung 402 , Taiwan .
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
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18
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Levinson AM, McGee JH, Roberts AG, Creech GS, Wang T, Peterson MT, Hendrickson RC, Verdine GL, Danishefsky SJ. Total Chemical Synthesis and Folding of All-l and All-d Variants of Oncogenic KRas(G12V). J Am Chem Soc 2017; 139:7632-7639. [PMID: 28448128 PMCID: PMC5606205 DOI: 10.1021/jacs.7b02988] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Ras proteins are essential GTPases involved in the regulation of cell proliferation and survival. Mutated oncogenic forms of Ras alter effector binding and innate GTPase activity, leading to deregulation of downstream signal transduction. Mutated forms of Ras are involved in approximately 30% of human cancers. Despite decades of effort to develop direct Ras inhibitors, Ras has long been considered "undruggable" due to its high affinity for GTP and its lack of hydrophobic binding pockets. Herein, we report a total chemical synthesis of all-l- and all-d-amino acid biotinylated variants of oncogenic mutant KRas(G12V). The protein is synthesized using Fmoc-based solid-phase peptide synthesis and assembled using combined native chemical ligation and isonitrile-mediated activation strategies. We demonstrate that both KRas(G12V) enantiomers can successfully fold and bind nucleotide substrates and binding partners with observable enantiodiscrimination. By demonstrating the functional competency of a mirror-image form of KRas bound to its corresponding enantiomeric nucleotide triphosphate, this study sets the stage for further biochemical studies with this material. In particular, this protein will enable mirror-image yeast surface display experiments to identify all-d peptide ligands for oncogenic KRas, providing a useful tool in the search for new therapeutics against this challenging disease target.
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Affiliation(s)
- Adam M. Levinson
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - John H. McGee
- Departments of Molecular and Cellular Biology, Stem Cell and Regenerative Biology, and Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, MA 02138
| | - Andrew G. Roberts
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Gardner S. Creech
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Ting Wang
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Michael T. Peterson
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Ronald C. Hendrickson
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
| | - Gregory L. Verdine
- Departments of Molecular and Cellular Biology, Stem Cell and Regenerative Biology, and Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, MA 02138
| | - Samuel J. Danishefsky
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States of America
- Department of Chemistry, Columbia University, Havemeyer Hall, 3000 Broadway, New York, New York 10027, United States of America
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19
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Abstract
The study of oncogenic RAS mutations has led to crucial discoveries regarding cancer molecular biology and behavior and has been integral in shaping the era of targeted cancer therapy. RAS mutations are one of the most common oncogenic drivers in human cancer, and intense efforts to find a clinically effective inhibitor are ongoing. Despite these efforts, targeting RAS mutations has remained elusive, so much so that some have termed oncogenic RAS mutations as "undruggable." In this review, we will summarize current understanding of RAS biology, explore strategies to inhibit RAS oncoproteins and its downstream effectors, and discuss recently described complexities that have shed new light on this pursuit.
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20
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Badshah SL, Mabkhot Y. Arresting kinase suppressor of Ras in an inactive state. CHINESE JOURNAL OF CANCER 2017; 36:5. [PMID: 28069069 PMCID: PMC5223383 DOI: 10.1186/s40880-017-0181-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 11/17/2016] [Indexed: 02/03/2023]
Abstract
Ras protein signaling pathways are important in controlling the plight of different types of cancer. Here we discussed the paper entitled “Small molecule stabilization of the KSR inactive state antagonizes oncogenic Ras signalling” published in Nature journal on inactivating the kinase suppressor of Ras (KSR) protein using a small molecule as an inhibitor by Dhawan et al. A biphenyl ether analogue of a quinazoline binds in one of the binding pockets of KSR and results in stabilization of its inactive state. In this inactive state, KSR is unable to take part in the cascade of protein association to perform the signalling process.
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Affiliation(s)
- Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Khyber Pukhtoonkhwa, 25120, Pakistan.
| | - Yahia Mabkhot
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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21
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Keeton AB, Salter EA, Piazza GA. The RAS-Effector Interaction as a Drug Target. Cancer Res 2017; 77:221-226. [PMID: 28062402 DOI: 10.1158/0008-5472.can-16-0938] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 09/22/2016] [Accepted: 10/08/2016] [Indexed: 12/21/2022]
Abstract
About a third of all human cancers harbor mutations in one of the K-, N-, or HRAS genes that encode an abnormal RAS protein locked in a constitutively activated state to drive malignant transformation and tumor growth. Despite more than three decades of intensive research aimed at the discovery of RAS-directed therapeutics, there are no FDA-approved drugs that are broadly effective against RAS-driven cancers. Although RAS proteins are often said to be "undruggable," there is mounting evidence suggesting it may be feasible to develop direct inhibitors of RAS proteins. Here, we review this evidence with a focus on compounds capable of inhibiting the interaction of RAS proteins with their effectors that transduce the signals of RAS and that drive and sustain malignant transformation and tumor growth. These reports of direct-acting RAS inhibitors provide valuable insight for further discovery and development of clinical candidates for RAS-driven cancers involving mutations in RAS genes or otherwise activated RAS proteins. Cancer Res; 77(2); 221-6. ©2017 AACR.
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Affiliation(s)
- Adam B Keeton
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama. .,ADT Pharmaceuticals Inc., Orange Beach, Alabama
| | - E Alan Salter
- Department of Chemistry, University of South Alabama, Mobile, Alabama
| | - Gary A Piazza
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama.,ADT Pharmaceuticals Inc., Orange Beach, Alabama
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22
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Muhoza D, Adams PD. Two Small Molecules, ZCL278 and AZA197 Show Promise in Influencing Protein Interactions Involving the Ras-Related Protein Cell division cycle 42 [Cdc42] to Modulate Its Oncogenic Potential. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ojbiphy.2017.73006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Lu S, Jang H, Gu S, Zhang J, Nussinov R. Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. Chem Soc Rev 2016; 45:4929-52. [PMID: 27396271 PMCID: PMC5021603 DOI: 10.1039/c5cs00911a] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ras proteins are small GTPases, cycling between inactive GDP-bound and active GTP-bound states. Through these switches they regulate signaling that controls cell growth and proliferation. Activating Ras mutations are associated with approximately 30% of human cancers, which are frequently resistant to standard therapies. Over the past few years, structural biology and in silico drug design, coupled with improved screening technology, led to a handful of promising inhibitors, raising the possibility of drugging Ras proteins. At the same time, the invariable emergence of drug resistance argues for the critical importance of additionally honing in on signaling pathways which are likely to be involved. Here we overview current advances in Ras structural knowledge, including the conformational dynamic of full-length Ras in solution and at the membrane, therapeutic inhibition of Ras activity by targeting its active site, allosteric sites, and Ras-effector protein-protein interfaces, Ras dimers, the K-Ras4B/calmodulin/PI3Kα trimer, and targeting Ras with siRNA. To mitigate drug resistance, we propose signaling pathways that can be co-targeted along with Ras and explain why. These include pathways leading to the expression (or activation) of YAP1 and c-Myc. We postulate that these and Ras signaling pathways, MAPK/ERK and PI3K/Akt/mTOR, act independently and in corresponding ways in cell cycle control. The structural data are instrumental in the discovery and development of Ras inhibitors for treating RAS-driven cancers. Together with the signaling blueprints through which drug resistance can evolve, this review provides a comprehensive and innovative master plan for tackling mutant Ras proteins.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Shuo Gu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Children’s Medical Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, U.S.A
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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24
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Ostrem JML, Shokat KM. Direct small-molecule inhibitors of KRAS: from structural insights to mechanism-based design. Nat Rev Drug Discov 2016; 15:771-785. [PMID: 27469033 DOI: 10.1038/nrd.2016.139] [Citation(s) in RCA: 400] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
KRAS is the most frequently mutated oncogene in human cancer. In addition to holding this distinction, unsuccessful attempts to target this protein have led to the characterization of RAS as 'undruggable'. However, recent advances in technology and novel approaches to drug discovery have renewed hope that a direct KRAS inhibitor may be on the horizon. In this Review, we provide an in-depth analysis of the structure, dynamics, mutational activation and inactivation, and signalling mechanisms of RAS. From this perspective, we then consider potential mechanisms of action for effective RAS inhibitors. Finally, we examine each of the many recent reports of direct RAS inhibitors and discuss promising avenues for further development.
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Affiliation(s)
- Jonathan M L Ostrem
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA
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25
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Abstract
The RAL GTPases have emerged as important drivers of tumor growth and metastasis in lung, colon, pancreatic and other cancers. We recently developed the first small molecule inhibitors of RAL that exhibited antitumor activity in human lung cancer cell lines. These compounds are non-competitive inhibitors that bind to the allosteric site of GDP-bound RAL. The RAL inhibitors have the potential to be used in combination therapy with other inhibitors of the RAS signaling pathway. They also provide insights toward directly targeting other GTPases.
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Affiliation(s)
- Chao Yan
- a Departments of Surgery (Urology) and Pharmacology ; University of Colorado ; Aurora , CO USA
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26
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Marcus K, Mattos C. Direct Attack on RAS: Intramolecular Communication and Mutation-Specific Effects. Clin Cancer Res 2016; 21:1810-8. [PMID: 25878362 DOI: 10.1158/1078-0432.ccr-14-2148] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The crystal structure of RAS was first solved 25 years ago. In spite of tremendous and sustained efforts, there are still no drugs in the clinic that directly target this major driver of human cancers. Recent success in the discovery of compounds that bind RAS and inhibit signaling has fueled renewed enthusiasm, and in-depth understanding of the structure and function of RAS has opened new avenues for direct targeting. To succeed, we must focus on the molecular details of the RAS structure and understand at a high-resolution level how the oncogenic mutants impair function. Structural networks of intramolecular communication between the RAS active site and membrane-interacting regions on the G-domain are disrupted in oncogenic mutants. Although conserved across the isoforms, these networks are near hot spots of protein-ligand interactions with amino acid composition that varies among RAS proteins. These differences could have an effect on stabilization of conformational states of interest in attenuating signaling through RAS. The development of strategies to target these novel sites will add a fresh direction in the quest to conquer RAS-driven cancers. Clin Cancer Res; 21(8); 1810-8. ©2015 AACR. See all articles in this CCR Focus section, "Targeting RAS-Driven Cancers."
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Affiliation(s)
- Kendra Marcus
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.
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27
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Trinh TB, Upadhyaya P, Qian Z, Pei D. Discovery of a Direct Ras Inhibitor by Screening a Combinatorial Library of Cell-Permeable Bicyclic Peptides. ACS COMBINATORIAL SCIENCE 2016; 18:75-85. [PMID: 26645887 PMCID: PMC4710893 DOI: 10.1021/acscombsci.5b00164] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Cyclic
peptides have great potential as therapeutic agents and research tools.
However, their applications against intracellular targets have been
limited, because cyclic peptides are generally impermeable to the
cell membrane. It was previously shown that fusion of cyclic peptides
with a cyclic cell-penetrating peptide resulted in cell-permeable
bicyclic peptides that are proteolytically stable and biologically
active in cellular assays. In this work, we tested the generality
of the bicyclic approach by synthesizing a combinatorial library of
5.7 × 106 bicyclic peptides featuring a degenerate
sequence in the first ring and an invariant cell-penetrating peptide
in the second ring. Screening of the library against oncoprotein K-Ras
G12V followed by hit optimization produced a moderately potent and
cell-permeable K-Ras inhibitor, which physically blocks the Ras-effector
interactions in vitro, inhibits the signaling events downstream of
Ras in cancer cells, and induces apoptosis of the cancer cells. Our
approach should be generally applicable to developing cell-permeable
bicyclic peptide inhibitors against other intracellular proteins.
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Affiliation(s)
- Thi B. Trinh
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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8-Hydroxyquinoline-based inhibitors of the Rce1 protease disrupt Ras membrane localization in human cells. Bioorg Med Chem 2015; 24:160-78. [PMID: 26706114 DOI: 10.1016/j.bmc.2015.11.043] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 01/05/2023]
Abstract
Ras converting enzyme 1 (Rce1) is an endoprotease that catalyzes processing of the C-terminus of Ras protein by removing -aaX from the CaaX motif. The activity of Rce1 is crucial for proper localization of Ras to the plasma membrane where it functions. Ras is responsible for transmitting signals related to cell proliferation, cell cycle progression, and apoptosis. The disregulation of these pathways due to constitutively active oncogenic Ras can ultimately lead to cancer. Ras, its effectors and regulators, and the enzymes that are involved in its maturation process are all targets for anti-cancer therapeutics. Key enzymes required for Ras maturation and localization are the farnesyltransferase (FTase), Rce1, and isoprenylcysteine carboxyl methyltransferase (ICMT). Among these proteins, the physiological role of Rce1 in regulating Ras and other CaaX proteins has not been fully explored. Small-molecule inhibitors of Rce1 could be useful as chemical biology tools to understand further the downstream impact of Rce1 on Ras function and serve as potential leads for cancer therapeutics. Structure-activity relationship (SAR) analysis of a previously reported Rce1 inhibitor, NSC1011, has been performed to generate a new library of Rce1 inhibitors. The new inhibitors caused a reduction in Rce1 in vitro activity, exhibited low cell toxicity, and induced mislocalization of EGFP-Ras from the plasma membrane in human colon carcinoma cells giving rise to a phenotype similar to that observed with siRNA knockdowns of Rce1 expression. Several of the new inhibitors were more effective at mislocalizing K-Ras compared to a potent farnesyltransferase inhibitor (FTI), which is significant because of the preponderance of K-Ras mutations in cancer.
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Novel Activities of Select NSAID R-Enantiomers against Rac1 and Cdc42 GTPases. PLoS One 2015; 10:e0142182. [PMID: 26558612 PMCID: PMC4641600 DOI: 10.1371/journal.pone.0142182] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/19/2015] [Indexed: 01/02/2023] Open
Abstract
Rho family GTPases (including Rac, Rho and Cdc42) collectively control cell proliferation, adhesion and migration and are of interest as functional therapeutic targets in numerous epithelial cancers. Based on high throughput screening of the Prestwick Chemical Library® and cheminformatics we identified the R-enantiomers of two approved drugs (naproxen and ketorolac) as inhibitors of Rac1 and Cdc42. The corresponding S-enantiomers are considered the active component in racemic drug formulations, acting as non-steroidal anti-inflammatory drugs (NSAIDs) with selective activity against cyclooxygenases. Here, we show that the S-enantiomers of naproxen and ketorolac are inactive against the GTPases. Additionally, more than twenty other NSAIDs lacked inhibitory action against the GTPases, establishing the selectivity of the two identified NSAIDs. R-naproxen was first identified as a lead compound and tested in parallel with its S-enantiomer and the non-chiral 6-methoxy-naphthalene acetic acid (active metabolite of nabumetone, another NSAID) as a structural series. Cheminformatics-based substructure analyses—using the rotationally constrained carboxylate in R-naproxen—led to identification of racemic [R/S] ketorolac as a suitable FDA-approved candidate. Cell based measurement of GTPase activity (in animal and human cell lines) demonstrated that the R-enantiomers specifically inhibit epidermal growth factor stimulated Rac1 and Cdc42 activation. The GTPase inhibitory effects of the R-enantiomers in cells largely mimic those of established Rac1 (NSC23766) and Cdc42 (CID2950007/ML141) specific inhibitors. Docking predicts that rotational constraints position the carboxylate moieties of the R-enantiomers to preferentially coordinate the magnesium ion, thereby destabilizing nucleotide binding to Rac1 and Cdc42. The S-enantiomers can be docked but are less favorably positioned in proximity to the magnesium. R-naproxen and R-ketorolac have potential for rapid translation and efficacy in the treatment of several epithelial cancer types on account of established human toxicity profiles and novel activities against Rho-family GTPases.
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direkte Modulation von Aktivität und Funktion kleiner GTPasen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direct Modulation of Small GTPase Activity and Function. Angew Chem Int Ed Engl 2015; 54:13516-37. [DOI: 10.1002/anie.201504357] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/19/2022]
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Shima F, Matsumoto S, Yoshikawa Y, Kawamura T, Isa M, Kataoka T. Current status of the development of Ras inhibitors. J Biochem 2015; 158:91-9. [DOI: 10.1093/jb/mvv060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
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Sudhakar G, Reddy KJ, Nanubolu JB. Nazarov cyclization of dienylaziridines: synthesis of cyclopentadienyl/hydrinedienyl/indenyl glycines. Org Biomol Chem 2015. [DOI: 10.1039/c5ob01219h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclopentadienyl, hydrinedienyl, and indenyl glycines were synthesized by the Nazarov cyclization of dienylaziridines for the first time. Several substrates were synthesized to demonstrate the compatibility of this reaction. Asymmetric synthesis of these amino acids was also developed to show the additional scope of this method.
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Affiliation(s)
- Gangarajula Sudhakar
- Division of CPC (Organic Chemistry-II)
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
- Academy of Scientific and Innovative Research
| | - Karla Janardhan Reddy
- Division of CPC (Organic Chemistry-II)
- CSIR-Indian Institute of Chemical Technology
- Hyderabad-500007
- India
- Academy of Scientific and Innovative Research
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Upadhyaya P, Qian Z, Habir NAA, Pei D. Direct Ras Inhibitors Identified from a Structurally Rigidified Bicyclic Peptide Library. Tetrahedron 2014; 70:7714-7720. [PMID: 25284901 PMCID: PMC4180945 DOI: 10.1016/j.tet.2014.05.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A one-bead-two-compound (OBTC) library of structurally rigidified bicyclic peptides was chemically synthesized on TentaGel microbeads (90 μm), with each bead displaying a unique bicyclic peptide on its surface and a linear encoding peptide of the same sequence in its interior. Screening of the library against oncogenic K-Ras G12V mutant identified two classes of Ras ligands. The class I ligands apparently bind to the effector-binding site and inhibit the Ras-Raf interaction, whereas the class II ligand appears to bind to a yet unidentified site different from the effector-binding site. These Ras ligands provide useful research tools and may be further developed into therapeutic agents.
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Affiliation(s)
- Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
| | - Nurlaila A. A. Habir
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
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Abstract
Despite more than three decades of intensive effort, no effective pharmacological inhibitors of the RAS oncoproteins have reached the clinic, prompting the widely held perception that RAS proteins are 'undruggable'. However, recent data from the laboratory and the clinic have renewed our hope for the development of RAS-inhibitory molecules. In this Review, we summarize the progress and the promise of five key approaches. Firstly, we focus on the prospects of using direct inhibitors of RAS. Secondly, we address the issue of whether blocking RAS membrane association is a viable approach. Thirdly, we assess the status of targeting RAS downstream effector signalling, which is arguably the most favourable current approach. Fourthly, we address whether the search for synthetic lethal interactors of mutant RAS still holds promise. Finally, RAS-mediated changes in cell metabolism have recently been described and we discuss whether these changes could be exploited for new therapeutic directions. We conclude with perspectives on how additional complexities, which are not yet fully understood, may affect each of these approaches.
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Düppe PM, Tran Thi Phuong T, Autzen J, Schöpel M, Yip KT, Stoll R, Scherkenbeck J. Sequence-selective molecular recognition of the C-terminal CaaX-boxes of Rheb and related Ras-proteins by synthetic receptors. ACS Chem Biol 2014; 9:1755-63. [PMID: 24856002 DOI: 10.1021/cb5002075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Constitutive activation of Ras-proteins plays an important role in the development of aggressive colorectal carcinomas and several other types of cancer. Despite some progress in recent years in the case of K-Ras4B, until now not a single small molecule inhibitor has been identified that binds efficiently to Rheb and interrupts the protein-protein interactions with mTOR. We describe here a complementary approach that aims at inhibiting membrane insertion of Rheb and related Ras proteins by masking the crucial C-terminal CaaX-box with peptidomimetic receptors identified in combinatorial solid-phase libraries.
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Affiliation(s)
- Peter M. Düppe
- University of Wuppertal, Gaußstraße
20, D-42119 Wuppertal, Germany
| | | | - Jasmin Autzen
- University of Wuppertal, Gaußstraße
20, D-42119 Wuppertal, Germany
| | - Miriam Schöpel
- Ruhr-University of Bochum, Universitätsstraße
150, D-44780 Bochum, Germany
| | - King Tuo Yip
- Ruhr-University of Bochum, Universitätsstraße
150, D-44780 Bochum, Germany
| | - Raphael Stoll
- Ruhr-University of Bochum, Universitätsstraße
150, D-44780 Bochum, Germany
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Small-molecule modulation of Ras signaling. Nat Chem Biol 2014; 10:613-22. [PMID: 24929527 DOI: 10.1038/nchembio.1560] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/21/2014] [Indexed: 12/19/2022]
Abstract
Despite intense efforts in pharmaceutical industry and academia, a therapeutic grip on oncogenic Ras proteins has remained elusive. Mutated Ras is associated with ~20-30% of all human cancers often not responsive to established therapies. In particular, K-Ras, the most frequently mutated Ras isoform, is considered one of the most important but 'undruggable' targets in cancer research. Recently, new cavities on Ras for small-molecule ligands were identified, and selective direct targeting of mutated K-Ras(G12C) has become possible for what is to our knowledge the first time. In addition, impairment of Ras spatial organization, in particular via targeting the prenyl-binding Ras chaperone PDEδ, has opened a fresh perspective in anticancer research. These recent advances fuel hopes for the development of new drugs targeting Ras.
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Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. Proc Natl Acad Sci U S A 2014; 111:3401-6. [PMID: 24550516 DOI: 10.1073/pnas.1315798111] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aberrant activation of the small GTPase Ras by oncogenic mutation or constitutively active upstream receptor tyrosine kinases results in the deregulation of cellular signals governing growth and survival in ∼30% of all human cancers. However, the discovery of potent inhibitors of Ras has been difficult to achieve. Here, we report the identification of small molecules that bind to a unique pocket on the Ras:Son of Sevenless (SOS):Ras complex, increase the rate of SOS-catalyzed nucleotide exchange in vitro, and modulate Ras signaling pathways in cells. X-ray crystallography of Ras:SOS:Ras in complex with these molecules reveals that the compounds bind in a hydrophobic pocket in the CDC25 domain of SOS adjacent to the Switch II region of Ras. The structure-activity relationships exhibited by these compounds can be rationalized on the basis of multiple X-ray cocrystal structures. Mutational analyses confirmed the functional relevance of this binding site and showed it to be essential for compound activity. These molecules increase Ras-GTP levels and disrupt MAPK and PI3K signaling in cells at low micromolar concentrations. These small molecules represent tools to study the acute activation of Ras and highlight a pocket on SOS that may be exploited to modulate Ras signaling.
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Chandrashekar R, Adams PD. Prospective Development of Small Molecule Targets to Oncogenic Ras Proteins. ACTA ACUST UNITED AC 2013; 3:207-211. [PMID: 25392746 PMCID: PMC4226270 DOI: 10.4236/ojbiphy.2013.34025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Abnormal expression or mutations in Ras proteins has been found in up to 30% of cancer cell types, making them excellent protein models to probe structure-function relationships of cell-signaling processes that mediate cell transformtion. Yet, there has been very little development of therapies to help tackle Ras-related diseased states. The development of small molecules to target Ras proteins to potentially inhibit abnormal Ras-stimulated cell signaling has been conceptualized and some progress has been made over the last 16 or so years. Here, we briefly review studies characterizing Ras protein-small molecule interactions to show the importance and potential that these small molecules may have for Ras-related drug discovery. We summarize recent results, highlighting small molecules that can be directly targeted to Ras using Structure-Based Drug Design (SBDD) and Fragment-Based Lead Discovery (FBLD) methods. The inactivation of Ras oncogenic signaling in vitro by small molecules is currently an attractive hurdle to try to and leap over in order to attack the oncogenic state. In this regard, important features of previously characterized properties of small molecule Ras targets, as well as a current understanding of conformational and dynamics changes seen for Ras-related mutants, relative to wild type, must be taken into account as newer small molecule design strategies towards Ras are developed.
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Affiliation(s)
- Reena Chandrashekar
- Department of Chemistry and Biochemistry, The University of Arkansas, Fayetteville, USA
| | - Paul D Adams
- Department of Chemistry and Biochemistry, The University of Arkansas, Fayetteville, USA
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40
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Sugar-Based Inhibitors of Ras Activation. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/b978-0-12-416749-0.00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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41
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42
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Johnson CW, Mattos C. The Allosteric Switch and Conformational States in Ras GTPase Affected by Small Molecules. INHIBITORS OF THE RAS SUPERFAMILY G-PROTEINS, PART A 2013; 33 Pt A:41-67. [DOI: 10.1016/b978-0-12-416749-0.00003-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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43
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Rosnizeck IC, Spoerner M, Harsch T, Kreitner S, Filchtinski D, Herrmann C, Engel D, König B, Kalbitzer HR. Metal-Bis(2-picolyl)amine Complexes as State 1(T) Inhibitors of Activated Ras Protein. Angew Chem Int Ed Engl 2012; 51:10647-51. [DOI: 10.1002/anie.201204148] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Indexed: 11/10/2022]
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44
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Rosnizeck IC, Spoerner M, Harsch T, Kreitner S, Filchtinski D, Herrmann C, Engel D, König B, Kalbitzer HR. Metall-Bis(2-picolyl)amin-Komplexe als Zustand-1(T)-Inhibitoren für aktiviertes Ras-Protein. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204148] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Ras inhibition via direct Ras binding--is there a path forward? Bioorg Med Chem Lett 2012; 22:5766-76. [PMID: 22902659 DOI: 10.1016/j.bmcl.2012.07.082] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/18/2012] [Accepted: 07/24/2012] [Indexed: 12/18/2022]
Abstract
Three decades after identification of the Ras oncogene, no effective treatments for Ras mutant tumors are available despite intensive drug discovery efforts. Here we critically review the attempts to inhibit Ras function via direct binding of small molecules at the Ras surface with the aim to disrupt its interaction with other proteins. Multiple binders at different binding sites have been discovered, and recent efforts afforded crystal structures of Ras-binder complexes. Albeit with low affinities, many of the binders were shown to impart inhibitory activities, and inhibition of nucleotide exchange as a consequence of disrupting the Ras-SOS interaction has been the most commonly identified mode of action. We see two key challenges in the development of these early starting points: Enhancing binding affinities and achieving selectivity, both against other GTPases and for mutant Ras over the wildtype form. In light of the large unmet medical need, we encourage the continued search for functionally active Ras binders, and we believe that integrated use of biophysical and biochemical tools will provide the highest chances for success. Given the failures experienced in the past and the significant hurdles ahead, we propose that this challenge be tackled through alliances between industry and academia.
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Grimme D, González-ruiz D, Gohlke* H. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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47
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Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. Proc Natl Acad Sci U S A 2012; 109:5299-304. [PMID: 22431598 DOI: 10.1073/pnas.1116510109] [Citation(s) in RCA: 460] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory effects have not been uncovered to date. Through an NMR-based fragment screen, we identified a group of small molecules that all bind to a common site on Ras. High-resolution cocrystal structures delineated a unique ligand-binding pocket on the Ras protein that is adjacent to the switch I/II regions and can be expanded upon compound binding. Structure analysis predicts that compound-binding interferes with the Ras/SOS interactions. Indeed, selected compounds inhibit SOS-mediated nucleotide exchange and prevent Ras activation by blocking the formation of intermediates of the exchange reaction. The discovery of a small-molecule binding pocket on Ras with functional significance provides a new direction in the search of therapeutically effective inhibitors of the Ras oncoprotein.
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48
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Mesquida N, López-Pérez S, Dinarès I, Alcalde E. Synthetic approaches to multifunctional indenes. Beilstein J Org Chem 2012; 7:1739-44. [PMID: 22238553 PMCID: PMC3252879 DOI: 10.3762/bjoc.7.204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 12/10/2011] [Indexed: 11/23/2022] Open
Abstract
The synthesis of multifunctional indenes with at least two different functional groups has not yet been extensively explored. Among the plausible synthetic routes to 3,5-disubstituted indenes bearing two different functional groups, such as the [3-(aminoethyl)inden-5-yl)]amines, a reasonable pathway involves the (5-nitro-3-indenyl)acetamides as key intermediates. Although several multistep synthetic approaches can be applied to obtain these advanced intermediates, we describe herein their preparation by an aldol-type reaction between 5-nitroindan-1-ones and the lithium salt of N,N-disubstituted acetamides, followed immediately by dehydration with acid. This classical condensation process, which is neither simple nor trivial despite its apparent directness, permits an efficient entry to a variety of indene-based molecular modules, which could be adapted to a range of functionalized indanones.
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Affiliation(s)
- Neus Mesquida
- Laboratori de Química Orgànica, Departament de Farmacologia i Química Terapèutica, Facultat de Farmàcia, Universitat de Barcelona, Avda. Joan XXIII s/n, 08028 Barcelona, Spain
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Sacco E, Metalli D, Spinelli M, Manzoni R, Samalikova M, Grandori R, Morrione A, Traversa S, Alberghina L, Vanoni M. Novel RasGRF1-derived Tat-fused peptides inhibiting Ras-dependent proliferation and migration in mouse and human cancer cells. Biotechnol Adv 2011; 30:233-43. [PMID: 21620943 DOI: 10.1016/j.biotechadv.2011.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
Abstract
Mutations of RAS genes are critical events in the pathogenesis of different human tumors and Ras proteins represent a major clinical target for the development of specific inhibitors to use as anticancer agents. Here we present RasGRF1-derived peptides displaying both in vitro and in vivo Ras inhibitory properties. These peptides were designed on the basis of the down-sizing of dominant negative full-length RasGRF1 mutants. The over-expression of these peptides can revert the phenotype of K-RAS transformed mouse fibroblasts to wild type, as monitored by several independent biological readouts, including Ras-GTP intracellular levels, ERK activity, morphology, proliferative potential and anchorage independent growth. Fusion of the RasGRF1-derived peptides with the Tat protein transduction domain allows their uptake into mammalian cells. Chemically synthesized Tat-fused peptides, reduced to as small as 30 residues on the basis of structural constraints, retain Ras inhibitory activity. These small peptides interfere in vitro with the GEF catalyzed nucleotide dissociation and exchange on Ras, reduce cell proliferation of K-RAS transformed mouse fibroblasts, and strongly reduce Ras-dependent IGF-I-induced migration and invasion of human bladder cancer cells. These results support the use of RasGRF1-derived peptides as model compounds for the development of Ras inhibitory anticancer agents.
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Affiliation(s)
- Elena Sacco
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
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Amyloid beta 42 peptide (Abeta42)-lowering compounds directly bind to Abeta and interfere with amyloid precursor protein (APP) transmembrane dimerization. Proc Natl Acad Sci U S A 2010; 107:14597-602. [PMID: 20679249 DOI: 10.1073/pnas.1003026107] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Following ectodomain shedding by beta-secretase, successive proteolytic cleavages within the transmembrane sequence (TMS) of the amyloid precursor protein (APP) catalyzed by gamma-secretase result in the release of amyloid-beta (Abeta) peptides of variable length. Abeta peptides with 42 amino acids appear to be the key pathogenic species in Alzheimer's disease, as they are believed to initiate neuronal degeneration. Sulindac sulfide, which is known as a potent gamma-secretase modulator (GSM), selectively reduces Abeta42 production in favor of shorter Abeta species, such as Abeta38. By studying APP-TMS dimerization we previously showed that an attenuated interaction similarly decreased Abeta42 levels and concomitantly increased Abeta38 levels. However, the precise molecular mechanism by which GSMs modulate Abeta production is still unclear. In this study, using a reporter gene-based dimerization assay, we found that APP-TMS dimers are destabilized by sulindac sulfide and related Abeta42-lowering compounds in a concentration-dependent manner. By surface plasmon resonance analysis and NMR spectroscopy, we show that sulindac sulfide and novel sulindac-derived compounds directly bind to the Abeta sequence. Strikingly, the attenuated APP-TMS interaction by GSMs correlated strongly with Abeta42-lowering activity and binding strength to the Abeta sequence. Molecular docking analyses suggest that certain GSMs bind to the GxxxG dimerization motif in the APP-TMS. We conclude that these GSMs decrease Abeta42 levels by modulating APP-TMS interactions. This effect specifically emphasizes the importance of the dimeric APP-TMS as a promising drug target in Alzheimer's disease.
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