1
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Wei J, Chen X, Li Y, Li R, Bao K, Liao L, Xie Y, Yang T, Zhu J, Mao F, Ni S, Jia R, Xu X, Li J. Cucurbitacin B-induced G2/M cell cycle arrest of conjunctival melanoma cells mediated by GRP78–FOXM1–KIF20A pathway. Acta Pharm Sin B 2022; 12:3861-3876. [PMID: 36213538 PMCID: PMC9532536 DOI: 10.1016/j.apsb.2022.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Conjunctival melanoma (CM) is a rare and fatal malignant eye tumor. In this study, we deciphered a novel anti-CM mechanism of a natural tetracyclic compound named as cucurbitacin B (CuB). We found that CuB remarkably inhibited the proliferation of CM cells including CM-AS16, CRMM1, CRMM2 and CM2005.1, without toxicity to normal cells. CuB can also induce CM cells G2/M cell cycle arrest. RNA-seq screening identified KIF20A, a key downstream effector of FOXM1 pathway, was abolished by CuB treatment. Further target identification by activity-based protein profiling chemoproteomic approach revealed that GRP78 is a potential target of CuB. Several lines of evidence demonstrated that CuB interacted with GRP78 and bound with a Kd value of 0.11 μmol/L. Furthermore, ATPase activity evaluation showed that CuB suppressed GRP78 both in human recombinant GRP78 protein and cellular lysates. Knockdown of the GRP78 gene significantly induced the downregulation of FOXM1 and related pathway proteins including KIF20A, underlying an interesting therapeutic perspective. Finally, CuB significantly inhibited tumor progression in NCG mice without causing obvious side effects in vivo. Taken together, our current work proved that GRP78–FOXM1–KIF20A as a promising pathway for CM therapy, and the traditional medicine CuB as a candidate drug to hinder this pathway.
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2
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Holland DO, Gotea V, Fedkenheuer K, Jaiswal SK, Baugher C, Tan H, Fedkenheuer M, Elnitski L. Characterization and clustering of kinase isoform expression in metastatic melanoma. PLoS Comput Biol 2022; 18:e1010065. [PMID: 35560144 PMCID: PMC9132324 DOI: 10.1371/journal.pcbi.1010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/25/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations to the human kinome are known to play causal roles in cancer. The kinome regulates numerous cell processes including growth, proliferation, differentiation, and apoptosis. In addition to aberrant expression, aberrant alternative splicing of cancer-driver genes is receiving increased attention as it could lead to loss or gain of functional domains, altering a kinase's downstream impact. The present study quantifies changes in gene expression and isoform ratios in the kinome of metastatic melanoma cells relative to primary tumors. We contrast 538 total kinases and 3,040 known kinase isoforms between 103 primary tumor and 367 metastatic samples from The Cancer Genome Atlas (TCGA). We find strong evidence of differential expression (DE) at the gene level in 123 kinases (23%). Additionally, of the 468 kinases with alternative isoforms, 60 (13%) had significant difference in isoform ratios (DIR). Notably, DE and DIR have little correlation; for instance, although DE highlights enrichment in receptor tyrosine kinases (RTKs), DIR identifies altered splicing in non-receptor tyrosine kinases (nRTKs). Using exon junction mapping, we identify five examples of splicing events favored in metastatic samples. We demonstrate differential apoptosis and protein localization between SLK isoforms in metastatic melanoma. We cluster isoform expression data and identify subgroups that correlate with genomic subtypes and anatomic tumor locations. Notably, distinct DE and DIR patterns separate samples with BRAF hotspot mutations and (N/K/H)RAS hotspot mutations, the latter of which lacks effective kinase inhibitor treatments. DE in RAS mutants concentrates in CMGC kinases (a group including cell cycle and splicing regulators) rather than RTKs as in BRAF mutants. Furthermore, isoforms in the RAS kinase subgroup show enrichment for cancer-related processes such as angiogenesis and cell migration. Our results reveal a new approach to therapeutic target identification and demonstrate how different mutational subtypes may respond differently to treatments highlighting possible new driver events in cancer.
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Affiliation(s)
- David O. Holland
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Fedkenheuer
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sushil K. Jaiswal
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Catherine Baugher
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hua Tan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Fedkenheuer
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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3
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Tatli O, Dinler Doganay G. Recent Developments in Targeting RAS Downstream Effectors for RAS-Driven Cancer Therapy. Molecules 2021; 26:molecules26247561. [PMID: 34946644 PMCID: PMC8703923 DOI: 10.3390/molecules26247561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Aberrant activity of oncogenic rat sarcoma virus (RAS) protein promotes tumor growth and progression. RAS-driven cancers comprise more than 30% of all human cancers and are refractory to frontline treatment strategies. Since direct targeting of RAS has proven challenging, efforts have been centered on the exploration of inhibitors for RAS downstream effector kinases. Two major RAS downstream signaling pathways, including the Raf/MEK/Erk cascade and the phosphatidylinositol-3-kinase (PI3K) pathway, have become compelling targets for RAS-driven cancer therapy. However, the main drawback in the blockade of a single RAS effector is the multiple levels of crosstalk and compensatory mechanisms between these two pathways that contribute to drug resistance against monotherapies. A growing body of evidence reveals that the sequential or synergistic inhibition of multiple RAS effectors is a more convenient route for the efficacy of cancer therapy. Herein, we revisit the recent developments and discuss the most promising modalities targeting canonical RAS downstream effectors for the treatment of RAS-driven cancers.
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Affiliation(s)
- Ozge Tatli
- Department of Molecular Biology, Genetics-Biotechnology, Graduate School, Istanbul Technical University, Istanbul 34469, Turkey;
- Department of Molecular Biology and Genetics, Istanbul Medeniyet University, Istanbul 34720, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology, Genetics-Biotechnology, Graduate School, Istanbul Technical University, Istanbul 34469, Turkey;
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
- Correspondence: ; Tel.: +90-2122-857-256
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4
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LC-MS/MS bioanalytical method for quantification of binimetinib and venetoclax, and their pharmacokinetic interaction. Bioanalysis 2021; 14:75-86. [PMID: 34841894 DOI: 10.4155/bio-2021-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: Because of several prospective benefits, binimetinib (BMT)-venetoclax (VTC) combination can be a better therapeutic strategy to treat cancer. Results: An LC-MS/MS method for simultaneous quantification of BMT and VTC in rat plasma has been developed and validated. Specificity, accuracy, precision and stability results met the acceptance criteria for validation. Accuracy and precisions at all quality control levels were <15%. The study revealed that co-administration of BMT and VTC has no significant effect on their pharmacokinetics. Conclusion: The developed method can provide accurate results for quantification of BMT and VTC over the range of 5-500 ng/ml. The reported pharmacokinetic interaction study results will be useful for future consideration of the combined treatment of BMT and VTC in anticancer chemotherapy regimens.
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5
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Martínez-Fernández P, Pose P, Dolz-Gaitón R, García A, Trigo-Sánchez I, Rodríguez-Zarco E, Garcia-Ruiz MJ, Barba I, Izquierdo-García M, Valero-Garcia J, Ruiz C, Lázaro M, Carbonell P, Gargallo P, Méndez C, Ríos-Martín JJ, Palmeiro-Uriach A, Camarasa-Lillo N, Forteza-Vila J, Calabria I. Comprehensive NGS Panel Validation for the Identification of Actionable Alterations in Adult Solid Tumors. J Pers Med 2021; 11:jpm11050360. [PMID: 33947144 PMCID: PMC8145002 DOI: 10.3390/jpm11050360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023] Open
Abstract
The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx's utility in adult solid tumors.
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Affiliation(s)
- Paula Martínez-Fernández
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Patricia Pose
- Servicio de Anatomía Patológica, Hospital Universitario de la Ribera, 46600 Alcira, Spain; (P.P.); (R.D.-G.)
| | - Raquel Dolz-Gaitón
- Servicio de Anatomía Patológica, Hospital Universitario de la Ribera, 46600 Alcira, Spain; (P.P.); (R.D.-G.)
| | - Arantxa García
- Servicio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia, 15009 A Coruña, Spain;
| | - Inmaculada Trigo-Sánchez
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - Enrique Rodríguez-Zarco
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - MJose Garcia-Ruiz
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Ibon Barba
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Marta Izquierdo-García
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Jennifer Valero-Garcia
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Carlos Ruiz
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Marián Lázaro
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Paula Carbonell
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Pablo Gargallo
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Carlos Méndez
- Servicio de Oncología Médica, Centro Oncológico de Galicia, 15009 A Coruña, Spain;
| | - Juan José Ríos-Martín
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - Alberto Palmeiro-Uriach
- Laboratorio de Anatomía Patológica, Hospital General Universitario de Castellón, 12004 Castellón, Spain;
| | | | - Jerónimo Forteza-Vila
- Anatomía Patológica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain;
| | - Inés Calabria
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
- Correspondence:
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6
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Bao K, Li Y, Wei J, Li R, Yang J, Shi J, Li B, Zhu J, Mao F, Jia R, Li J. Fangchinoline suppresses conjunctival melanoma by directly binding FUBP2 and inhibiting the homologous recombination pathway. Cell Death Dis 2021; 12:380. [PMID: 33828201 PMCID: PMC8027391 DOI: 10.1038/s41419-021-03653-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 01/13/2023]
Abstract
Conjunctival melanoma (CM) is a rare and fatal ocular tumour with poor prognosis. There is an urgent need of effective therapeutic drugs against CM. Here, we reported the discovery of a novel potential therapeutic target for CM. Through phenotypic screening of our in-house library, fangchinoline was discovered to significantly inhibit the growth of CM cells including CM-AS16, CRMM1, CRMM2 and CM2005.1. Further mechanistic experiments indicated that fangchinoline suppressed the homologous recombination (HR)-directed DNA repair by binding with far upstream element binding protein 2 (FUBP2) and downregulating the expression of HR factors BRCA1 and RAD51. In vitro and in vivo antitumour experiments revealed that fangchinoline increased the efficacy of cisplatin by blocking HR factors and reduced the drug dose and toxicity. In conclusion, our work provides a promising therapeutic strategy for the treatment of CM that is worthy of extensive preclinical investigation.
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Affiliation(s)
- Keting Bao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Jinlian Wei
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Ruoxi Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Jiahao Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Baoli Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jin Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Fei Mao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China.
| | - Jian Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China. .,College of Pharmacy and Chemistry, Dali University, 5 Xue Ren Road, Dali, Yunnan, 671000, China. .,Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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7
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Dong J, Li S, Liu G. Binimetinib Is a Potent Reversible and Time-Dependent Inhibitor of Cytochrome P450 1A2. Chem Res Toxicol 2021; 34:1169-1174. [PMID: 33728909 DOI: 10.1021/acs.chemrestox.1c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binimetinib is a selective MEK1/2 inhibitor, which is indicative of melanoma. We aimed to investigate the inhibitory effect of binimetinib on cytochrome P450 using human liver microsomes. Binimetinib was demonstrated to display reversible and time-dependent inhibitory effects on human CYP1A2. Binimetinib can inhibit the activity of phenacetin deethylation with IC50 of 5.6 μM. A 30 min preincubation of binimetinib with NADPH-supplemented human liver microsomes raised a significant left IC50 shift (6.5-fold), from 5.69-0.88 μM. The inactivation parameters Kinact and KI were 0.063 min-1 and 15.47 μM, and the half-life of inactivation was 11 min. Glutathione (GSH) and catalase/superoxide exhibited minor or no protective effect on binimetinib-induced enzyme inactivation. Trapping experiment by GSH induced a detection of GSH adduct, of which the formation was believed to be through the oxidation of electron-rich 1,4-benzenediamine to reactive 1,4-diiminoquinone species. Cytochrome P450 3A4, 2C9, and 2D6 were involved in the bioactivation of binimetinib. In conclusion, binimetinib was proven to display reversible and time-dependent inhibitory effect on CYP1A2, which may have implications for the toxicity of binimetinib.
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Affiliation(s)
- Jiangnan Dong
- Department of Pharmacy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China
| | - Su Li
- Department of Pharmacy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China
| | - Guangxuan Liu
- Department of Pharmacy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China
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8
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Zhao J, Galvez C, Beckermann KE, Johnson DB, Sosman JA. Novel insights into the pathogenesis and treatment of NRAS mutant melanoma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021; 6:281-294. [PMID: 34485698 PMCID: PMC8415440 DOI: 10.1080/23808993.2021.1938545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION NRAS was the first mutated oncogene identified in melanoma and is currently the second most common driver mutation in this malignancy. For patients with NRASmutant advanced stage melanoma refractory to immunotherapy or with contraindications to immune-based regimens, there are few therapeutic options including low-efficacy chemotherapy regimens and binimetinib monotherapy. Here, we review recent advances in preclinical studies of molecular targets for NRAS mutant melanoma as well as the failures and successes of early-phase clinical trials. While there are no targeted therapies for NRAS-driven melanoma, there is great promise in approaches combining MEK inhibition with inhibitors of the focal adhesion kinase (FAK), inhibitors of autophagy pathways, and pan-RAF inhibitors. AREAS COVERED This review surveys new developments in all aspects of disease pathogenesis and potential treatment - including those that have failed, stalled, or progressed through various phases of preclinical and clinical development. EXPERT OPINION There are no currently approved targeted therapies for BRAF wild-type melanoma patients harboring NRAS driver mutations though an array of agents are in early phase clinical trials. The diverse strategies taken exploit combined MAP kinase signaling blockade with inhibition of cell cycle mediators, inhibition of the autophagy pathway, and alteration of kinases involved in actin cytoskeleton signaling. Future advances of developmental therapeutics into late stage trials may yield new options beyond immunotherapy for patients with advanced stage disease and NRAS mutation status.
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Affiliation(s)
- Jeffrey Zhao
- Northwestern University Feinberg School of Medicine
| | - Carlos Galvez
- Northwestern Medicine, Division of Hematology and Oncology.,Robert H. Lurie Comprehensive Cancer Center
| | - Kathryn Eby Beckermann
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology and Oncology, 1301 Medical Center Drive, Nashville, 37232, USA
| | - Douglas B Johnson
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology and Oncology, 1301 Medical Center Drive, Nashville, 37232, USA
| | - Jeffrey A Sosman
- Northwestern Medicine, Division of Hematology and Oncology.,Robert H. Lurie Comprehensive Cancer Center
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9
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Ribaudo G, Ongaro A, Oselladore E, Zagotto G, Memo M, Gianoncelli A. A computational approach to drug repurposing against SARS-CoV-2 RNA dependent RNA polymerase (RdRp). J Biomol Struct Dyn 2020; 40:1101-1108. [PMID: 32948103 PMCID: PMC7544925 DOI: 10.1080/07391102.2020.1822209] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused a worldwide outbreak of coronavirus disease 19 (COVID-19), which rapidly evolved as a global concern. The efforts of the scientific community are pointed towards the identification of promptly available therapeutic options. RNA-dependent RNA polymerase (RdRp) is a promising target for developing small molecules to contrast SARS-CoV-2 replication. Modern computational tools can boost identification and repurposing of known drugs targeting RdRp. We here report the results regarding the screening of a database containing more than 8800 molecules, including approved, experimental, nutraceutical, illicit, withdrawn and investigational compounds. The molecules were docked against the cryo-electron microscopy structure of SARS-CoV-2 RdRp, optimized by means of molecular dynamics (MD) simulations. The adopted three-stage ensemble docking study underline that compounds formerly developed as kinase inhibitors may interact with RdRp. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Erika Oselladore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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10
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Drosten M, Barbacid M. Targeting the MAPK Pathway in KRAS-Driven Tumors. Cancer Cell 2020; 37:543-550. [PMID: 32289276 DOI: 10.1016/j.ccell.2020.03.013] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022]
Abstract
KRAS mutations occur in a quarter of all of human cancers, yet no selective drug has been approved to treat these tumors. Despite the recent development of drugs that block KRASG12C, the majority of KRAS oncoproteins remain undruggable. Here, we review recent efforts to validate individual components of the mitogen-activated protein kinase (MAPK) pathway as targets to treat KRAS-mutant cancers by comparing genetic information derived from experimental mouse models of KRAS-driven lung and pancreatic tumors with the outcome of selective MAPK inhibitors in clinical trials. We also review the potential of RAF1 as a key target to block KRAS-mutant cancers.
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Affiliation(s)
- Matthias Drosten
- Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
| | - Mariano Barbacid
- Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
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11
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Kim Y, Bismeijer T, Zwart W, Wessels LFA, Vis DJ. Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo. Nat Commun 2019; 10:5034. [PMID: 31695042 PMCID: PMC6834616 DOI: 10.1038/s41467-019-13027-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/10/2019] [Indexed: 01/20/2023] Open
Abstract
Integrative analyses that summarize and link molecular data to treatment sensitivity are crucial to capture the biological complexity which is essential to further precision medicine. We introduce Weighted Orthogonal Nonnegative parallel factor analysis (WON-PARAFAC), a data integration method that identifies sparse and interpretable factors. WON-PARAFAC summarizes the GDSC1000 cell line compendium in 130 factors. We interpret the factors based on their association with recurrent molecular alterations, pathway enrichment, cancer type, and drug-response. Crucially, the cell line derived factors capture the majority of the relevant biological variation in Patient-Derived Xenograft (PDX) models, strongly suggesting our factors capture invariant and generalizable aspects of cancer biology. Furthermore, drug response in cell lines is better and more consistently translated to PDXs using factor-based predictors as compared to raw feature-based predictors. WON-PARAFAC efficiently summarizes and integrates multiway high-dimensional genomic data and enhances translatability of drug response prediction from cell lines to patient-derived xenografts.
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Affiliation(s)
- Yongsoo Kim
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.
| | - Daniel J Vis
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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12
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Exacerbation of skin psoriasis when associating an MEK inhibitor with anti-PD1 immunotherapy for metastatic melanoma. Melanoma Res 2019; 29:447-448. [PMID: 31246728 DOI: 10.1097/cmr.0000000000000601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Savoia P, Fava P, Casoni F, Cremona O. Targeting the ERK Signaling Pathway in Melanoma. Int J Mol Sci 2019; 20:ijms20061483. [PMID: 30934534 PMCID: PMC6472057 DOI: 10.3390/ijms20061483] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/17/2019] [Accepted: 03/19/2019] [Indexed: 12/24/2022] Open
Abstract
The discovery of the role of the RAS/RAF/MEK/ERK pathway in melanomagenesis and its progression have opened a new era in the treatment of this tumor. Vemurafenib was the first specific kinase inhibitor approved for therapy of advanced melanomas harboring BRAF-activating mutations, followed by dabrafenib and encorafenib. However, despite the excellent results of first-generation kinase inhibitors in terms of response rate, the average duration of the response was short, due to the onset of genetic and epigenetic resistance mechanisms. The combination therapy with MEK inhibitors is an excellent strategy to circumvent drug resistance, with the additional advantage of reducing side effects due to the paradoxical reactivation of the MAPK pathway. The recent development of RAS and extracellular signal-related kinases (ERK) inhibitors promises to add new players for the ultimate suppression of this signaling pathway and the control of pathway-related drug resistance. In this review, we analyze the pharmacological, preclinical, and clinical trial data of the various MAPK pathway inhibitors, with a keen interest for their clinical applicability in the management of advanced melanoma.
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Affiliation(s)
- Paola Savoia
- Department of Health Science, University of Eastern Piedmont, via Solaroli 17, 28100 Novara, Italy.
| | - Paolo Fava
- Section of Dermatology, Department of Medical Science, University of Turin, 10124 Turin, Italy.
| | - Filippo Casoni
- San Raffaele Scientific Institute, Division of Neuroscience, via Olgettina 58, 20132 Milano, Italy.
- Università Vita Salute San Raffaele, via Olgettina 58, 20132 Milano, Italy.
| | - Ottavio Cremona
- San Raffaele Scientific Institute, Division of Neuroscience, via Olgettina 58, 20132 Milano, Italy.
- Università Vita Salute San Raffaele, via Olgettina 58, 20132 Milano, Italy.
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14
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Abstract
LEARNING OBJECTIVES After studying this article, the participant should be able to: 1. Summarize the changes to the American Joint Committee on Cancer Eighth Edition Melanoma Staging System. 2. List advances in genetic, molecular, and histopathologic melanoma diagnosis and prognostication. 3. Recommend sentinel lymph node biopsy and appropriate surgical margins based on individualized patient needs. 4. Recognize the currently available treatments for in-transit metastasis and advanced melanoma. 5. Describe current and future therapies for melanoma with distant visceral or brain metastases. SUMMARY Strides in melanoma surveillance, detection, and treatment continue to be made. The American Joint Committee on Cancer Eighth Edition Cancer Staging System has improved risk stratification of patients, introduced new staging categories, and resulted in stage migration of patients with improved outcomes. This review summarizes melanoma advances of the recent years with an emphasis on the surgical advances, including techniques and utility of sentinel node biopsy, controversies in melanoma margin selection, and the survival impact of time-to-treatment metrics. Once a disease manageable only with surgery, a therapeutic paradigm shift has given a more promising outlook to melanoma patients at any stage. Indeed, a myriad of novel, survival-improving immunotherapies have been introduced for metastatic melanoma and more recently in the high-risk adjuvant setting.
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15
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Barclay SF, Inman KW, Luks VL, McIntyre JB, Al-Ibraheemi A, Church AJ, Perez-Atayde AR, Mangray S, Jeng M, Kreimer SR, Walker L, Fishman SJ, Alomari AI, Chaudry G, Trenor Iii CC, Adams D, Kozakewich HPW, Kurek KC. A somatic activating NRAS variant associated with kaposiform lymphangiomatosis. Genet Med 2018; 21:1517-1524. [PMID: 30542204 PMCID: PMC6565516 DOI: 10.1038/s41436-018-0390-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/19/2018] [Indexed: 11/25/2022] Open
Abstract
Purpose: Kaposiform lymphangiomatosis (KLA) is a rare, frequently aggressive, systemic disorder of the lymphatic vasculature, occurring primarily in children. Even with multimodal treatments, KLA has a poor prognosis and high mortality rate secondary to coagulopathy, effusions and systemic involvement. We hypothesized that, as has recently been found for other vascular anomalies, KLA may be caused by somatic mosaic variants affecting vascular development. Methods: We performed exome sequencing of tumor samples from five individuals with KLA, along with samples from uninvolved control tissue in three of the five. We used digital PCR (dPCR) to validate the exome findings and to screen KLA samples from six other individuals. Results: We identified a somatic activating NRAS variant (c.182A>G, p.Q61R) in lesional tissue from 10/11 individuals, at levels ranging from 1–28%, that was absent from the tested control tissues. Conclusion: The activating NRAS p.Q61R variant is a known ‘hotspot’ variant, frequently identified in several types of human cancer, especially melanoma. KLA, therefore, joins a growing group of vascular malformations and tumors caused by somatic activating variants in the RAS/PI3K/mTOR signalling pathways. This discovery will expand treatment options for these high risk patients as there is potential for use of targeted RAS pathway inhibitors.
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Affiliation(s)
- Sarah F Barclay
- Departments of Pathology & Laboratory Medicine and Medical Genetics, Alberta Children's Hospital Research Institute and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Kyle W Inman
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Valerie L Luks
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - John B McIntyre
- Translational Laboratory, Tom Baker Cancer Centre, Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.,Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | | | - Shamlal Mangray
- Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Michael Jeng
- Division of Pediatric Hematology-Oncology, Lucile Salter Packard Children's Hospital, Stanford University, Palo Alto, CA, USA
| | - Sara R Kreimer
- Division of Pediatric Hematology-Oncology, Lucile Salter Packard Children's Hospital, Stanford University, Palo Alto, CA, USA
| | - Lori Walker
- Department of Pediatrics, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Steven J Fishman
- Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Ahmad I Alomari
- Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA.,Division of Interventional Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Gulraiz Chaudry
- Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA.,Division of Interventional Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Cameron C Trenor Iii
- Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA.,Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Denise Adams
- Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA.,Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Harry P W Kozakewich
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.,Vascular Anomalies Center, Boston Children's Hospital, Boston, MA, USA
| | - Kyle C Kurek
- Departments of Pathology & Laboratory Medicine and Medical Genetics, Alberta Children's Hospital Research Institute and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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16
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Ryabaya O, Prokofieva A, Akasov R, Khochenkov D, Emelyanova M, Burov S, Markvicheva E, Inshakov A, Stepanova E. Metformin increases antitumor activity of MEK inhibitor binimetinib in 2D and 3D models of human metastatic melanoma cells. Biomed Pharmacother 2018; 109:2548-2560. [PMID: 30551515 DOI: 10.1016/j.biopha.2018.11.109] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/02/2018] [Accepted: 11/25/2018] [Indexed: 12/29/2022] Open
Abstract
Melanoma is one of the most aggressive and treatment-resistant tumors that responsible for majority of skin-cancer related deaths. Here we propose a combination of MEK inhibitor binimetinib with metformin as a promising therapy against human melanoma cells in vitro, including BRAF -mutated A375, Mel Z, and Mel IL cells, and NRAS-mutated Mel MTP and Mel Me cells. Additionally, we obtained two close to clinical practice models of melanoma progression. The first one was vemurafenib-resistant Mel IL/R melanoma cells with acquired resistance to BRAF inhibition-targeted therapy, and the second one was tumor spheroids, which are 3D in vitro model of small-size solid tumors in vivo. The cytotoxicity of binimetinib and metformin was synergistic in both 2D and 3D melanoma culture and mediated through apoptotic pathway. The combination reduced the number of melanoma-formed colonies, inhibited cell invasion and migration, and led to G0/G1 cell cycle arrest through cyclin D/CDK4/CDK6 pathway. The mechanism of metformin and binimetinib synergy in melanoma cells was associated with increased activation of p-AMPKα and decreased p-ERK, but not with alterations in p-mTOR. In summary, the combination of metformin and binimetinib resulted in stronger anti-proliferative effects on melanoma cells compared to binimetinib alone, and therefore could be promising for clinical applications.
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Affiliation(s)
- Oxana Ryabaya
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Anastasia Prokofieva
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Roman Akasov
- Institute of Molecular Medicine Sechenov First Moscow State Medical University, 119991, 8-2 Trubetskaya street, Moscow, Russia; Cytomed J.S.Co, Russia; Federal Scientific Research Center «Crystallography and Photonics» Russian Academy of Sciences, 117997, 17a Butlerova st, Moscow, Russia.
| | - Dmitry Khochenkov
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Marina Emelyanova
- Department of Biological Microchips Engelhardt Institute of Molecular Biology, 119991, 32 Vavilova street, Moscow, Russia.
| | | | - Elena Markvicheva
- Department of Biomaterials and Biotechnologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Andrey Inshakov
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Evgenia Stepanova
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
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17
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Abstract
Abnormally activated RAS proteins are the main oncogenic driver that governs the functioning of major signaling pathways involved in the initiation and development of human malignancies. Mutations in RAS genes and or its regulators, most frequent in human cancers, are the main force for incessant RAS activation and associated pathological conditions including cancer. In general, RAS is the main upstream regulator of the highly conserved signaling mechanisms associated with a plethora of important cellular activities vital for normal homeostasis. Mutated or the oncogenic RAS aberrantly activates a web of interconnected signaling pathways including RAF-MEK (mitogen-activated protein kinase kinase)-ERK (extracellular signal-regulated kinase), phosphoinositide-3 kinase (PI3K)/AKT (protein kinase B), protein kinase C (PKC) and ral guanine nucleotide dissociation stimulator (RALGDS), etc., leading to uncontrolled transcriptional expression and reprogramming in the functioning of a range of nuclear and cytosolic effectors critically associated with the hallmarks of carcinogenesis. This review highlights the recent literature on how oncogenic RAS negatively use its signaling web in deregulating the expression and functioning of various effector molecules in the pathogenesis of human malignancies.
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18
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Lu B, Huang S, Cao J, Hu Q, Shen R, Wan H, Wang D, Yuan J, Zhang L, Zhang J, Zhang M, Tao W, Zhang L. Discovery of EBI-1051: A novel and orally efficacious MEK inhibitor with benzofuran scaffold. Bioorg Med Chem 2018; 26:581-589. [DOI: 10.1016/j.bmc.2017.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/09/2017] [Accepted: 12/12/2017] [Indexed: 10/18/2022]
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