1
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Steffen CL, Manoharan GB, Pavic K, Yeste-Vázquez A, Knuuttila M, Arora N, Zhou Y, Härmä H, Gaigneaux A, Grossmann TN, Abankwa DK. Identification of an H-Ras nanocluster disrupting peptide. Commun Biol 2024; 7:837. [PMID: 38982284 PMCID: PMC11233548 DOI: 10.1038/s42003-024-06523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Hyperactive Ras signalling is found in most cancers. Ras proteins are only active in membrane nanoclusters, which are therefore potential drug targets. We previously showed that the nanocluster scaffold galectin-1 (Gal1) enhances H-Ras nanoclustering via direct interaction with the Ras binding domain (RBD) of Raf. Here, we establish that the B-Raf preference of Gal1 emerges from the divergence of the Raf RBDs at their proposed Gal1-binding interface. We then identify the L5UR peptide, which disrupts this interaction by binding with low micromolar affinity to the B- and C-Raf-RBDs. Its 23-mer core fragment is sufficient to interfere with H-Ras nanoclustering, modulate Ras-signalling and moderately reduce cell viability. These latter two phenotypic effects may also emerge from the ability of L5UR to broadly engage with several RBD- and RA-domain containing Ras interactors. The L5UR-peptide core fragment is a starting point for the development of more specific reagents against Ras-nanoclustering and -interactors.
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Affiliation(s)
- Candy Laura Steffen
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Matias Knuuttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Harri Härmä
- Chemistry of Drug Development, Department of Chemistry, University of Turku, 20500, Turku, Finland
| | - Anthoula Gaigneaux
- Bioinformatics Core, Department of Life Sciences and Medicine, University of Luxembourg, 4367, Esch-sur-Alzette, Luxembourg
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
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2
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Shen L, Zhang C, Cui K, Liang X, Zhu G, Hong L. Fer-mediated activation of the Ras-MAPK signaling pathway drives the proliferation, migration, and invasion of endometrial carcinoma cells. Mol Cell Biochem 2024; 479:1787-1799. [PMID: 38017327 DOI: 10.1007/s11010-023-04890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND The role of Feline sarcoma-related protein (Fer) in various cancers has been extensively studied, but its specific involvement and underlying mechanisms in the progression of endometrial carcinoma (EC) are yet to be fully understood. METHODS The expression levels of Fer were assessed in EC tissues and cell lines using real-time quantitative PCR and western blot analysis. CCK-8 assay, Edu staining, transwell assays, and flow cytometry, were conducted to evaluate the impact of Fer on EC cells. Furthermore, a mice xenograft model and immunohistochemistry (IHC) staining were utilized for in vivo analysis. The levels of Ras, pMek1/2, and pErk1/2 were determined by western blot assay. Ras-MAPK signaling pathway inhibitor was utilized to study the regulatory role of Fer on EC cells. RESULTS Our findings revealed that Fer exhibited upregulation in both EC tissues and cell lines, concomitant with the activation of the Ras-MAPK signaling pathway. Silencing of Fer resulted in the suppression of cell proliferation, migration, invasion, and Ras-MAPK signaling pathway, while promoted hypoxia-induced apoptosis in RL95-2 and KLE cells. Fer overexpression stimulated cell proliferation, migration, invasion, and Ras-MAPK signaling pathway in Ishikawa and AN3-CA cells, which were reversed after treatment with either Ras or MAPK inhibitor. Moreover, silencing of Fer suppressed tumor growth and downregulated the expression of Ki-67, Ras, pMek1/2, and pErk1/2, but had no significant effect on Mek1/2 and Erk1/2, while upregulated caspase-3 expression in vivo. CONCLUSION In summary, the upregulation of Fer in EC cells resulted in the enhancement of cell proliferation, migration, and invasion through the activation of the Ras-MAPK signaling pathway.
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Affiliation(s)
- Lifan Shen
- Department of Gynecology, Surgery Building, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), 19Th Xiuhua Road, Xiuying District, Haikou, 570000, China
| | - Chen Zhang
- Department of Central Lab, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Kaiying Cui
- Department of Gynecology, Surgery Building, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), 19Th Xiuhua Road, Xiuying District, Haikou, 570000, China
| | - Xin Liang
- Department of Gynecology, Surgery Building, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), 19Th Xiuhua Road, Xiuying District, Haikou, 570000, China
| | - Genhai Zhu
- Department of Gynecology, Surgery Building, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), 19Th Xiuhua Road, Xiuying District, Haikou, 570000, China
| | - Lan Hong
- Department of Gynecology, Surgery Building, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), 19Th Xiuhua Road, Xiuying District, Haikou, 570000, China.
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3
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Lin Y, Pal DS, Banerjee P, Banerjee T, Qin G, Deng Y, Borleis J, Iglesias PA, Devreotes PN. Ras suppression potentiates rear actomyosin contractility-driven cell polarization and migration. Nat Cell Biol 2024; 26:1062-1076. [PMID: 38951708 DOI: 10.1038/s41556-024-01453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/31/2024] [Indexed: 07/03/2024]
Abstract
Ras has been extensively studied as a promoter of cell proliferation, whereas few studies have explored its role in migration. To investigate the direct and immediate effects of Ras activity on cell motility or polarity, we focused on RasGAPs, C2GAPB in Dictyostelium amoebae and RASAL3 in HL-60 neutrophils and macrophages. In both cellular systems, optically recruiting the respective RasGAP to the cell front extinguished pre-existing protrusions and changed migration direction. However, when these respective RasGAPs were recruited uniformly to the membrane, cells polarized and moved more rapidly, whereas targeting to the back exaggerated these effects. These unexpected outcomes of attenuating Ras activity naturally had strong, context-dependent consequences for chemotaxis. The RasGAP-mediated polarization depended critically on myosin II activity and commenced with contraction at the cell rear, followed by sustained mTORC2-dependent actin polymerization at the front. These experimental results were captured by computational simulations in which Ras levels control front- and back-promoting feedback loops. The discovery that inhibiting Ras activity can produce counterintuitive effects on cell migration has important implications for future drug-design strategies targeting oncogenic Ras.
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Affiliation(s)
- Yiyan Lin
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Dhiman Sankar Pal
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Parijat Banerjee
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA
| | - Tatsat Banerjee
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guanghui Qin
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yu Deng
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jane Borleis
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pablo A Iglesias
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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4
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Hossain MA. Targeting the RAS upstream and downstream signaling pathway for Cancer treatment. Eur J Pharmacol 2024:176727. [PMID: 38866361 DOI: 10.1016/j.ejphar.2024.176727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Cancer often involves the overactivation of RAS/RAF/MEK/ERK (MAPK) and PI3K-Akt-mTOR pathways due to mutations in genes like RAS, RAF, PTEN, and PIK3CA. Various strategies are employed to address the overactivation of these pathways, among which targeted therapy emerges as a promising approach. Directly targeting specific proteins, leads to encouraging results in cancer treatment. For instance, RTK inhibitors such as imatinib and afatinib selectively target these receptors, hindering ligand binding and reducing signaling initiation. These inhibitors have shown potent efficacy against Non-Small Cell Lung Cancer. Other inhibitors, like lonafarnib targeting Farnesyltransferase and GGTI 2418 targeting geranylgeranyl Transferase, disrupt post-translational modifications of proteins. Additionally, inhibition of proteins like SOS, SH2 domain, and Ras demonstrate promising anti-tumor activity both in vivo and in vitro. Targeting downstream components with RAF inhibitors such as vemurafenib, dabrafenib, and sorafenib, along with MEK inhibitors like trametinib and binimetinib, has shown promising outcomes in treating cancers with BRAF-V600E mutations, including myeloma, colorectal, and thyroid cancers. Furthermore, inhibitors of PI3K (e.g., apitolisib, copanlisib), AKT (e.g., ipatasertib, perifosine), and mTOR (e.g., sirolimus, temsirolimus) exhibit promising efficacy against various cancers such as Invasive Breast Cancer, Lymphoma, Neoplasms, and hematological malignancies. This review offers an overview of small molecule inhibitors targeting specific proteins within the RAS upstream and downstream signaling pathways in cancer.
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Affiliation(s)
- Md Arafat Hossain
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh;.
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5
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Bao H, Wang W, Sun H, Chen J. The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes. J Biomol Struct Dyn 2024; 42:3363-3381. [PMID: 37216340 DOI: 10.1080/07391102.2023.2213355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Point mutations play a vital role in the conformational transformation of HRAS. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by constructions of free energy landscapes (FELs) were adopted to explore the effect of mutations D33K, A59T and L120A on conformation states of the GDP-bound HRAS. The results from the post-processing analyses on GaMD trajectories suggest that mutations alter the flexibility and motion modes of the switch domains from HRAS. The analyses from FELs show that mutations induce more disordered states of the switch domains and affect interactions of GDP with HRAS, implying that mutations yield a vital effect on the binding of HRAS to effectors. The GDP-residue interaction network revealed by our current work indicates that salt bridges and hydrogen bonding interactions (HBIs) play key roles in the binding of GDP to HRAS. Furthermore, instability in the interactions of magnesium ions and GDP with the switch SI leads to the extreme disorder of the switch domains. This study is expected to provide the energetic basis and molecular mechanism for further understanding the function of HRAS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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6
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Yu Z, Wang Z, Cui X, Cao Z, Zhang W, Sun K, Hu G. Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics. Molecules 2024; 29:645. [PMID: 38338389 PMCID: PMC10856033 DOI: 10.3390/molecules29030645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/01/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The HRAS protein is considered a critical target for drug development in cancers. It is vital for effective drug development to understand the effects of mutations on the binding of GTP and GDP to HRAS. We conducted Gaussian accelerated molecular dynamics (GaMD) simulations and free energy landscape (FEL) calculations to investigate the impacts of two mutations (A59E and K117R) on GTP and GDP binding and the conformational states of the switch domain. Our findings demonstrate that these mutations not only modify the flexibility of the switch domains, but also affect the correlated motions of these domains. Furthermore, the mutations significantly disrupt the dynamic behavior of the switch domains, leading to a conformational change in HRAS. Additionally, these mutations significantly impact the switch domain's interactions, including their hydrogen bonding with ligands and electrostatic interactions with magnesium ions. Since the switch domains are crucial for the binding of HRAS to effectors, any alterations in their interactions or conformational states will undoubtedly disrupt the activity of HRAS. This research provides valuable information for the design of drugs targeting HRAS.
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Affiliation(s)
- Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
| | - Zhen Wang
- Pingyin People’s Hospital, Jinan 250400, China; (Z.W.); (X.C.)
| | - Xiuzhen Cui
- Pingyin People’s Hospital, Jinan 250400, China; (Z.W.); (X.C.)
| | - Zanxia Cao
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
| | - Wanyunfei Zhang
- School of Science, Xi’an Polytechnic University, Xi’an 710048, China; (W.Z.); (K.S.)
| | - Kunxiao Sun
- School of Science, Xi’an Polytechnic University, Xi’an 710048, China; (W.Z.); (K.S.)
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
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7
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Chen J, Cui L, Lu S, Xu S. Amino acid metabolism in tumor biology and therapy. Cell Death Dis 2024; 15:42. [PMID: 38218942 PMCID: PMC10787762 DOI: 10.1038/s41419-024-06435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Amino acid metabolism plays important roles in tumor biology and tumor therapy. Accumulating evidence has shown that amino acids contribute to tumorigenesis and tumor immunity by acting as nutrients, signaling molecules, and could also regulate gene transcription and epigenetic modification. Therefore, targeting amino acid metabolism will provide new ideas for tumor treatment and become an important therapeutic approach after surgery, radiotherapy, and chemotherapy. In this review, we systematically summarize the recent progress of amino acid metabolism in malignancy and their interaction with signal pathways as well as their effect on tumor microenvironment and epigenetic modification. Collectively, we also highlight the potential therapeutic application and future expectation.
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Affiliation(s)
- Jie Chen
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China
| | - Likun Cui
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China
| | - Shaoteng Lu
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China
| | - Sheng Xu
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China.
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
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8
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Bahar ME, Kim HJ, Kim DR. Targeting the RAS/RAF/MAPK pathway for cancer therapy: from mechanism to clinical studies. Signal Transduct Target Ther 2023; 8:455. [PMID: 38105263 PMCID: PMC10725898 DOI: 10.1038/s41392-023-01705-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 12/19/2023] Open
Abstract
Metastatic dissemination of solid tumors, a leading cause of cancer-related mortality, underscores the urgent need for enhanced insights into the molecular and cellular mechanisms underlying metastasis, chemoresistance, and the mechanistic backgrounds of individuals whose cancers are prone to migration. The most prevalent signaling cascade governed by multi-kinase inhibitors is the mitogen-activated protein kinase (MAPK) pathway, encompassing the RAS-RAF-MAPK kinase (MEK)-extracellular signal-related kinase (ERK) pathway. RAF kinase is a primary mediator of the MAPK pathway, responsible for the sequential activation of downstream targets, such as MEK and the transcription factor ERK, which control numerous cellular and physiological processes, including organism development, cell cycle control, cell proliferation and differentiation, cell survival, and death. Defects in this signaling cascade are associated with diseases such as cancer. RAF inhibitors (RAFi) combined with MEK blockers represent an FDA-approved therapeutic strategy for numerous RAF-mutant cancers, including melanoma, non-small cell lung carcinoma, and thyroid cancer. However, the development of therapy resistance by cancer cells remains an important barrier. Autophagy, an intracellular lysosome-dependent catabolic recycling process, plays a critical role in the development of RAFi resistance in cancer. Thus, targeting RAF and autophagy could be novel treatment strategies for RAF-mutant cancers. In this review, we delve deeper into the mechanistic insights surrounding RAF kinase signaling in tumorigenesis and RAFi-resistance. Furthermore, we explore and discuss the ongoing development of next-generation RAF inhibitors with enhanced therapeutic profiles. Additionally, this review sheds light on the functional interplay between RAF-targeted therapies and autophagy in cancer.
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Affiliation(s)
- Md Entaz Bahar
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea.
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9
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Stanfill SB, Hecht SS, Joerger AC, González PJ, Maia LB, Rivas MG, Moura JJG, Gupta AK, Le Brun NE, Crack JC, Hainaut P, Sparacino-Watkins C, Tyx RE, Pillai SD, Zaatari GS, Henley SJ, Blount BC, Watson CH, Kaina B, Mehrotra R. From cultivation to cancer: formation of N-nitrosamines and other carcinogens in smokeless tobacco and their mutagenic implications. Crit Rev Toxicol 2023; 53:658-701. [PMID: 38050998 DOI: 10.1080/10408444.2023.2264327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/20/2023] [Indexed: 12/07/2023]
Abstract
Tobacco use is a major cause of preventable morbidity and mortality globally. Tobacco products, including smokeless tobacco (ST), generally contain tobacco-specific N-nitrosamines (TSNAs), such as N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-butanone (NNK), which are potent carcinogens that cause mutations in critical genes in human DNA. This review covers the series of biochemical and chemical transformations, related to TSNAs, leading from tobacco cultivation to cancer initiation. A key aim of this review is to provide a greater understanding of TSNAs: their precursors, the microbial and chemical mechanisms that contribute to their formation in ST, their mutagenicity leading to cancer due to ST use, and potential means of lowering TSNA levels in tobacco products. TSNAs are not present in harvested tobacco but can form due to nitrosating agents reacting with tobacco alkaloids present in tobacco during certain types of curing. TSNAs can also form during or following ST production when certain microorganisms perform nitrate metabolism, with dissimilatory nitrate reductases converting nitrate to nitrite that is then released into tobacco and reacts chemically with tobacco alkaloids. When ST usage occurs, TSNAs are absorbed and metabolized to reactive compounds that form DNA adducts leading to mutations in critical target genes, including the RAS oncogenes and the p53 tumor suppressor gene. DNA repair mechanisms remove most adducts induced by carcinogens, thus preventing many but not all mutations. Lastly, because TSNAs and other agents cause cancer, previously documented strategies for lowering their levels in ST products are discussed, including using tobacco with lower nornicotine levels, pasteurization and other means of eliminating microorganisms, omitting fermentation and fire-curing, refrigerating ST products, and including nitrite scavenging chemicals as ST ingredients.
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Affiliation(s)
- Stephen B Stanfill
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andreas C Joerger
- Structural Genomics Consortium (SGC), Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pablo J González
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - Luisa B Maia
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | - Maria G Rivas
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - José J G Moura
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | | | - Nick E Le Brun
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Grenoble Alpes University, Grenoble, France
| | - Courtney Sparacino-Watkins
- University of Pittsburgh, School of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, PA, USA
| | - Robert E Tyx
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suresh D Pillai
- Department of Food Science & Technology, National Center for Electron Beam Research, Texas A&M University, College Station, TX, USA
| | - Ghazi S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - S Jane Henley
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin C Blount
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clifford H Watson
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Ravi Mehrotra
- Centre for Health, Innovation and Policy Foundation, Noida, India
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10
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Gomez-Gutierrez P, Rubio-Martinez J, Perez JJ. Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening. J Chem Inf Model 2023; 63:6412-6422. [PMID: 37824186 PMCID: PMC10598794 DOI: 10.1021/acs.jcim.3c01212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Indexed: 10/13/2023]
Abstract
Mutants of Ras are oncogenic drivers of a large number of human tumors. Despite being recognized as an attractive target for the treatment of cancer, the high affinity for its substrate tagged the protein as undruggable for a few years. The identification of cryptic pockets on the protein surface gave the opportunity to identify molecules capable of acting as allosteric modulators. Several molecules were disclosed in recent years, with sotorasib and adagrasib already approved for clinical use. The present study makes use of computational methods to characterize eight prospective allosteric pockets (P1-P8) in K-Ras, four of which (P1-P4) were previously characterized in the literature. The present study also describes the results of a virtual screening study focused on the discovery of hit compounds, binders of the P4 site that can be considered as peptidomimetics of a fragment of the SOS αI helix, a guanine exchange factor of Ras. After a detailed description of the computational procedure followed, we disclose five hit compounds, prospective binders of the P4 allosteric site that exhibit an inhibitory capability higher than 30% in a cell proliferation assay at 50 μM.
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Affiliation(s)
- Patricia Gomez-Gutierrez
- Department
of Chemical Engineering. ETSEIB, Universitat
Politecnica de Catalunya, Av. Diagonal, 647, Barcelona 08028, Spain
- Allinky
Biopharma, Madrid Scientific Park, Faraday, 7, Madrid 28049, Spain
| | - Jaime Rubio-Martinez
- Department
of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica
i Computacional (IQTCUB), Marti i Franques, 1, Barcelona 08028, Spain
| | - Juan J. Perez
- Department
of Chemical Engineering. ETSEIB, Universitat
Politecnica de Catalunya, Av. Diagonal, 647, Barcelona 08028, Spain
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11
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Sanz M, Weideman AMK, Ward AR, Clohosey ML, Garcia-Recio S, Selitsky SR, Mann BT, Iannone MA, Whitworth CP, Chitrakar A, Garrido C, Kirchherr J, Coffey AR, Tsai YH, Samir S, Xu Y, Copertino D, Bosque A, Jones BR, Parker JS, Hudgens MG, Goonetilleke N, Soriano-Sarabia N. Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1. Front Immunol 2023; 14:1219250. [PMID: 37744358 PMCID: PMC10516574 DOI: 10.3389/fimmu.2023.1219250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.
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Affiliation(s)
- Marta Sanz
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Ann Marie K. Weideman
- Biostatistics Core, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Adam R. Ward
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
- Department of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Matthew L. Clohosey
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sara R. Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Brendan T. Mann
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Marie Anne Iannone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Chloe P. Whitworth
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alisha Chitrakar
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Carolina Garrido
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jennifer Kirchherr
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alisha R. Coffey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yi- Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shahryar Samir
- Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yinyan Xu
- Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dennis Copertino
- Department of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Alberto Bosque
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
| | - Brad R. Jones
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
- Department of Infectious Diseases, Weill Cornell Medicine, New York, NY, United States
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michael G. Hudgens
- Biostatistics Core, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nilu Goonetilleke
- Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Natalia Soriano-Sarabia
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington, DC, United States
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12
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Lin Y, Pal DS, Banerjee P, Banerjee T, Qin G, Deng Y, Borleis J, Iglesias PA, Devreotes PN. Ras-mediated homeostatic control of front-back signaling dictates cell polarity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555648. [PMID: 37693515 PMCID: PMC10491231 DOI: 10.1101/2023.08.30.555648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Studies in the model systems, Dictyostelium amoebae and HL-60 neutrophils, have shown that local Ras activity directly regulates cell motility or polarity. Localized Ras activation on the membrane is spatiotemporally regulated by its activators, RasGEFs, and inhibitors, RasGAPs, which might be expected to create a stable 'front' and 'back', respectively, in migrating cells. Focusing on C2GAPB in amoebae and RASAL3 in neutrophils, we investigated how Ras activity along the cortex controls polarity. Since existing gene knockout and overexpression studies can be circumvented, we chose optogenetic approaches to assess the immediate, local effects of these Ras regulators on the cell cortex. In both cellular systems, optically targeting the respective RasGAPs to the cell front extinguished existing protrusions and changed the direction of migration, as might be expected. However, when the expression of C2GAPB was induced globally, amoebae polarized within hours. Furthermore, within minutes of globally recruiting either C2GAPB in amoebae or RASAL3 in neutrophils, each cell type polarized and moved more rapidly. Targeting the RasGAPs to the cell backs exaggerated these effects on migration and polarity. Overall, in both cell types, RasGAP-mediated polarization was brought about by increased actomyosin contractility at the back and sustained, localized F-actin polymerization at the front. These experimental results were accurately captured by computational simulations in which Ras levels control front and back feedback loops. The discovery that context-dependent Ras activity on the cell cortex has counterintuitive, unanticipated effects on cell polarity can have important implications for future drug-design strategies targeting oncogenic Ras.
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13
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Zhou X, Ji Y, Zhou J. Multiple Strategies to Develop Small Molecular KRAS Directly Bound Inhibitors. Molecules 2023; 28:molecules28083615. [PMID: 37110848 PMCID: PMC10146153 DOI: 10.3390/molecules28083615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
KRAS gene mutation is widespread in tumors and plays an important role in various malignancies. Targeting KRAS mutations is regarded as the "holy grail" of targeted cancer therapies. Recently, multiple strategies, including covalent binding strategy, targeted protein degradation strategy, targeting protein and protein interaction strategy, salt bridge strategy, and multivalent strategy, have been adopted to develop KRAS direct inhibitors for anti-cancer therapy. Various KRAS-directed inhibitors have been developed, including the FDA-approved drugs sotorasib and adagrasib, KRAS-G12D inhibitor MRTX1133, and KRAS-G12V inhibitor JAB-23000, etc. The different strategies greatly promote the development of KRAS inhibitors. Herein, the strategies are summarized, which would shed light on the drug discovery for both KRAS and other "undruggable" targets.
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Affiliation(s)
- Xile Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
| | - Yang Ji
- Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Jinming Zhou
- Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
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14
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Jiang H, Fan Y, Wang X, Wang J, Yang H, Fan W, Tang C. Design, Synthesis and Biological Evaluation of Quinazoline SOS1 Inhibitors. Bioorg Med Chem Lett 2023; 88:129265. [PMID: 37011767 DOI: 10.1016/j.bmcl.2023.129265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Son of sevenless 1 (SOS1) is a vital guanine nucleotide exchange factor (GEFs) that activates rat sarcoma (Ras) protein in cells. SOS1 inhibitors can effectively inhibit the expression of downstream signaling pathways by blocking the interaction between SOS1 and Ras protein. Here, we designed and synthesized a series of quinazoline-based compounds, and conducted subsequent evaluations of their biological activities. Among them, the comparable compounds I-2 (IC50=20nM, against SOS1) I-5 (IC50=18nM, against SOS1) and I-10 (IC50=8.5nM, against SOS1) have kinase activity equivalent to BAY-293 (IC50=6.6nM, against SOS1), and I-10 also has cell activity equivalent to BAY-293, providing a theoretical reference for subsequent related researches on SOS1 inhibitors.
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15
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Sanz M, Weideman AMK, Ward AR, Clohosey ML, Garcia-Recio S, Selitsky SR, Mann BT, Iannone MA, Whitworth CP, Chitrakar A, Garrido C, Kirchherr J, Coffey AR, Tsai YH, Samir S, Xu Y, Copertino D, Bosque A, Jones BR, Parker JS, Hudgens MG, Goonetilleke N, Soriano-Sarabia N. Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527421. [PMID: 36798291 PMCID: PMC9934553 DOI: 10.1101/2023.02.07.527421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.
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Affiliation(s)
- Marta Sanz
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Ann Marie K. Weideman
- Department of Biostatistics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Adam R. Ward
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
- Department of Infectious Diseases, Weill Cornell Medicine, New York, USA
| | - Matthew L. Clohosey
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Sara R. Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Brendan T. Mann
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Marie Anne Iannone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Chloe P. Whitworth
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Alisha Chitrakar
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Carolina Garrido
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- UNC HIV-1 Cure Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Alisha R. Coffey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Shahryar Samir
- Microbiology & Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Yinyan Xu
- Microbiology & Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Dennis Copertino
- Department of Infectious Diseases, Weill Cornell Medicine, New York, USA
| | - Alberto Bosque
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
| | - Brad R. Jones
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
- Department of Infectious Diseases, Weill Cornell Medicine, New York, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Michael G. Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- Microbiology & Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Natalia Soriano-Sarabia
- Department of Microbiology Immunology and Tropical Medicine, the George Washington University, Washington DC, USA
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16
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Paulussen FM, Grossmann TN. Peptide-based covalent inhibitors of protein-protein interactions. J Pept Sci 2023; 29:e3457. [PMID: 36239115 PMCID: PMC10077911 DOI: 10.1002/psc.3457] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPI) are involved in all cellular processes and many represent attractive therapeutic targets. However, the frequently rather flat and large interaction areas render the identification of small molecular PPI inhibitors very challenging. As an alternative, peptide interaction motifs derived from a PPI interface can serve as starting points for the development of inhibitors. However, certain proteins remain challenging targets when applying inhibitors with a competitive mode of action. For that reason, peptide-based ligands with an irreversible binding mode have gained attention in recent years. This review summarizes examples of covalent inhibitors that employ peptidic binders and have been tested in a biological context.
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Affiliation(s)
- Felix M Paulussen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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17
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Rangel M, Kong J, Bhatt V, Khayati K, Guo JY. Autophagy and tumorigenesis. FEBS J 2022; 289:7177-7198. [PMID: 34270851 PMCID: PMC8761221 DOI: 10.1111/febs.16125] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/28/2021] [Accepted: 07/15/2021] [Indexed: 01/13/2023]
Abstract
Autophagy is a catabolic process that captures cellular waste and degrades them in the lysosome. The main functions of autophagy are quality control of cytosolic proteins and organelles, and intracellular recycling of nutrients in order to maintain cellular homeostasis. Autophagy is upregulated in many cancers to promote cell survival, proliferation, and metastasis. Both cell-autonomous autophagy (also known as tumor autophagy) and non-cell-autonomous autophagy (also known as host autophagy) support tumorigenesis through different mechanisms, including inhibition of p53 activation, sustaining redox homeostasis, maintenance of essential amino acids levels in order to support energy production and biosynthesis, and inhibition of antitumor immune responses. Therefore, autophagy may serve as a tumor-specific vulnerability and targeting autophagy could be a novel strategy in cancer treatment.
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Affiliation(s)
- Michael Rangel
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA
| | - Jerry Kong
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA
| | - Vrushank Bhatt
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA
| | - Khoosheh Khayati
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA,Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA,Department of Chemical Biology, Rutgers Ernest Mario School of Pharmacy, Piscataway, NJ, USA
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18
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Yu Z, Su H, Chen J, Hu G. Deciphering Conformational Changes of the GDP-Bound NRAS Induced by Mutations G13D, Q61R, and C118S through Gaussian Accelerated Molecular Dynamic Simulations. Molecules 2022; 27:molecules27175596. [PMID: 36080363 PMCID: PMC9457619 DOI: 10.3390/molecules27175596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
The conformational changes in switch domains significantly affect the activity of NRAS. Gaussian-accelerated molecular dynamics (GaMD) simulations of three separate replicas were performed to decipher the effects of G13D, Q16R, and C118S on the conformational transformation of the GDP-bound NRAS. The analyses of root-mean-square fluctuations and dynamics cross-correlation maps indicated that the structural flexibility and motion modes of the switch domains involved in the binding of NRAS to effectors are highly altered by the G13D, Q61R, and C118Smutations. The free energy landscapes (FELs) suggested that mutations induce more energetic states in NRAS than the GDP-bound WT NRAS and lead to high disorder in the switch domains. The FELs also indicated that the different numbers of sodium ions entering the GDP binding regions compensate for the changes in electrostatic environments caused by mutations, especially for G13D. The GDP–residue interactions revealed that the disorder in the switch domains was attributable to the unstable hydrogen bonds between GDP and two residues, V29 and D30. This work is expected to provide information on the energetic basis and dynamics of conformational changes in switch domains that can aid in deeply understanding the target roles of NRAS in anticancer treatment.
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Affiliation(s)
- Zhiping Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Hongyi Su
- Laoling People's Hospital, Dezhou 253600, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- Laoling People's Hospital, Dezhou 253600, China
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19
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20
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Armijo ME, Escalona E, Peña D, Farias A, Morin V, Baumann M, Klebl BM, Pincheira R, Castro AF. Blocking the Farnesyl Pocket of PDEδ Reduces Rheb-Dependent mTORC1 Activation and Survival of Tsc2-Null Cells. Front Pharmacol 2022; 13:912688. [PMID: 35814251 PMCID: PMC9260180 DOI: 10.3389/fphar.2022.912688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022] Open
Abstract
Rheb is a small GTPase member of the Ras superfamily and an activator of mTORC1, a protein complex master regulator of cell metabolism, growth, and proliferation. Rheb/mTORC1 pathway is hyperactivated in proliferative diseases, such as Tuberous Sclerosis Complex syndrome and cancer. Therefore, targeting Rheb-dependent signaling is a rational strategy for developing new drug therapies. Rheb activates mTORC1 in the cytosolic surface of lysosomal membranes. Rheb’s farnesylation allows its anchorage on membranes, while its proper localization depends on the prenyl-binding chaperone PDEδ. Recently, the use of PDEδ inhibitors has been proposed as anticancer agents because they interrupted KRas signaling leading to antiproliferative effects in KRas-dependent pancreatic cancer cells. However, the effect of PDEδ inhibition on the Rheb/mTORC1 pathway has been poorly investigated. Here, we evaluated the impact of a new PDEδ inhibitor, called Deltasonamide 1, in Tsc2-null MEFs, a Rheb-dependent overactivated mTORC1 cell line. By using a yeast two-hybrid assay, we first validated that Deltasonamide 1 disrupts Rheb-PDEδ interaction. Accordingly, we found that Deltasonamide 1 reduces mTORC1 targets activation. In addition, our results showed that Deltasonamide 1 has antiproliferative and cytotoxic effects on Tsc2-null MEFs but has less effect on Tsc2-wild type MEFs viability. This work proposes the pharmacological PDEδ inhibition as a new approach to target the abnormal Rheb/mTORC1 activation in Tuberous Sclerosis Complex cells.
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Affiliation(s)
- Marisol Estrella Armijo
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Emilia Escalona
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Daniela Peña
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Alejandro Farias
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Violeta Morin
- Laboratorio de Proteasas y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | | | - Roxana Pincheira
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- *Correspondence: Roxana Pincheira, ; Ariel Fernando Castro,
| | - Ariel Fernando Castro
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- *Correspondence: Roxana Pincheira, ; Ariel Fernando Castro,
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21
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Learte-Aymamí S, Martin-Malpartida P, Roldán-Martín L, Sciortino G, Couceiro JR, Maréchal JD, Macias MJ, Mascareñas JL, Vázquez ME. Controlling oncogenic KRAS signaling pathways with a Palladium-responsive peptide. Commun Chem 2022; 5:75. [PMID: 36697641 PMCID: PMC9814687 DOI: 10.1038/s42004-022-00691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/10/2022] [Indexed: 01/28/2023] Open
Abstract
RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed bis-histidine peptide derived from the αH helix of the cofactor SOS1 binds to KRAS with high affinity upon coordination to Pd(II). NMR spectroscopy and MD studies demonstrate that Pd(II) has a nucleating effect that facilitates the access to the bioactive α-helical conformation. The binding can be suppressed by an external metal chelator and recovered again by the addition of more Pd(II), making this system the first switchable KRAS binder, and demonstrates that folding-upon-binding mechanisms can operate in metal-nucleated peptides. In vitro experiments show that the metallopeptide can efficiently internalize into living cells and inhibit the MAPK kinase cascade.
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Affiliation(s)
- Soraya Learte-Aymamí
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Pau Martin-Malpartida
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain
| | - Lorena Roldán-Martín
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Giuseppe Sciortino
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain ,grid.473715.30000 0004 6475 7299Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, 43007 Spain
| | - José R. Couceiro
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Jean-Didier Maréchal
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Maria J. Macias
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010 Spain
| | - José L. Mascareñas
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - M. Eugenio Vázquez
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
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22
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Manoharan GB, Okutachi S, Abankwa D. Potential of phenothiazines to synergistically block calmodulin and reactivate PP2A in cancer cells. PLoS One 2022; 17:e0268635. [PMID: 35617282 PMCID: PMC9135253 DOI: 10.1371/journal.pone.0268635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/04/2022] [Indexed: 11/19/2022] Open
Abstract
Phenothiazines (PTZ) were developed as inhibitors of monoamine neurotransmitter receptors, notably dopamine receptors. Because of this activity they have been used for decades as antipsychotic drugs. In addition, they possess significant anti-cancer properties and several attempts for their repurposing were made. However, their incompletely understood polypharmacology is challenging. Here we examined the potential of the PTZ fluphenazine (Flu) and its mustard derivative (Flu-M) to synergistically act on two cancer associated targets, calmodulin (CaM) and the tumor suppressor protein phosphatase 2A (PP2A). Both proteins are known to modulate the Ras- and MAPK-pathway, cell viability and features of cancer cell stemness. Consistently, we show that the combination of a CaM inhibitor and the PP2A activator DT-061 synergistically inhibited the 3D-spheroid formation of MDA-MB-231 (K-Ras-G13D), NCI-H358 (K-Ras-G12C) and A375 (B-raf-V600E) cancer cells, and increased apoptosis in MDA-MB-231. We reasoned that these activities remain combined in PTZ, which were the starting point for PP2A activator development, while several PTZ are known CaM inhibitors. We show that both Flu and Flu-M retained CaM inhibitory activity in vitro and in cells, with a higher potency of the mustard derivative in cells. In line with the CaM dependence of Ras plasma membrane organization, the mustard derivative potently reduced the functional membrane organization of oncogenic Ras, while DT-061 had a negligible effect. Like DT-061, both PTZ potently decreased c-MYC levels, a hallmark of PP2A activation. Benchmarking against the KRAS-G12C specific inhibitor AMG-510 in MIA PaCa-2 cells revealed a higher potency of Flu-M than combinations of DT-061 and a CaM inhibitor on MAPK-output and a strong effect on cell proliferation. While our study is limited, our results suggest that improved PTZ derivatives that retain both, their CaM inhibitory and PP2A activating properties, but have lost their neurological side-effects, may be interesting to pursue further as anti-cancer agents.
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Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sunday Okutachi
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- * E-mail:
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23
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Hossain MS, Zhang Z, Ashok S, Jenks AR, Lynch CJ, Hougland JL, Mozhdehi D. Temperature-Responsive Nano-Biomaterials from Genetically Encoded Farnesylated Disordered Proteins. ACS APPLIED BIO MATERIALS 2022; 5:1846-1856. [PMID: 35044146 PMCID: PMC9115796 DOI: 10.1021/acsabm.1c01162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
Despite broad interest in understanding the biological implications of protein farnesylation in regulating different facets of cell biology, the use of this post-translational modification to develop protein-based materials and therapies remains underexplored. The progress has been slow due to the lack of accessible methodologies to generate farnesylated proteins with broad physicochemical diversities rapidly. This limitation, in turn, has hindered the empirical elucidation of farnesylated proteins' sequence-structure-function rules. To address this gap, we genetically engineered prokaryotes to develop operationally simple, high-yield biosynthetic routes to produce farnesylated proteins and revealed determinants of their emergent material properties (nano-aggregation and phase-behavior) using scattering, calorimetry, and microscopy. These outcomes foster the development of farnesylated proteins as recombinant therapeutics or biomaterials with molecularly programmable assembly.
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Affiliation(s)
- Md. Shahadat Hossain
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Zhe Zhang
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Sudhat Ashok
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Ashley R. Jenks
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Christopher J. Lynch
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
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24
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AIMP2-DX2 provides therapeutic interface to control KRAS-driven tumorigenesis. Nat Commun 2022; 13:2572. [PMID: 35546148 PMCID: PMC9095880 DOI: 10.1038/s41467-022-30149-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/14/2022] [Indexed: 12/11/2022] Open
Abstract
Recent development of the chemical inhibitors specific to oncogenic KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog) mutants revives much interest to control KRAS-driven cancers. Here, we report that AIMP2-DX2, a variant of the tumor suppressor AIMP2 (aminoacyl-tRNA synthetase-interacting multi-functional protein 2), acts as a cancer-specific regulator of KRAS stability, augmenting KRAS-driven tumorigenesis. AIMP2-DX2 specifically binds to the hypervariable region and G-domain of KRAS in the cytosol prior to farnesylation. Then, AIMP2-DX2 competitively blocks the access of Smurf2 (SMAD Ubiquitination Regulatory Factor 2) to KRAS, thus preventing ubiquitin-mediated degradation. Moreover, AIMP2-DX2 levels are positively correlated with KRAS levels in colon and lung cancer cell lines and tissues. We also identified a small molecule that specifically bound to the KRAS-binding region of AIMP2-DX2 and inhibited the interaction between these two factors. Treatment with this compound reduces the cellular levels of KRAS, leading to the suppression of KRAS-dependent cancer cell growth in vitro and in vivo. These results suggest the interface of AIMP2-DX2 and KRAS as a route to control KRAS-driven cancers. Direct targeting of oncogenic KRAS activity is a challenge. Here the authors report that a splice variant of AIMP2, AIMP2-DX2, enhances KRAS stability by blocking ubiquitin-mediated degradation of KRAS via the E3 ligase, Smurf2, and identify a chemical that can hinder AIMP2-DX2 from interacting with KRAS.
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25
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Li JX, Li RZ, Ma LR, Wang P, Xu DH, Huang J, Li LQ, Tang L, Xie Y, Leung ELH, Yan PY. Targeting Mutant Kirsten Rat Sarcoma Viral Oncogene Homolog in Non-Small Cell Lung Cancer: Current Difficulties, Integrative Treatments and Future Perspectives. Front Pharmacol 2022; 13:875330. [PMID: 35517800 PMCID: PMC9065471 DOI: 10.3389/fphar.2022.875330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 11/15/2022] Open
Abstract
In the past few decades, several gene mutations, including the anaplastic lymphoma kinase, epidermal growth factor receptor, ROS proto-oncogene 1 and rat sarcoma viral oncogene homolog (RAS), have been discovered in non-small cell lung cancer (NSCLC). Kirsten rat sarcoma viral oncogene homolog (KRAS) is the isoform most frequently altered in RAS-mutated NSCLC cases. Due to the structural and biochemical characteristics of the KRAS protein, effective approaches to treating KRAS-mutant NSCLC still remain elusive. Extensive recent research on KRAS-mutant inhibitors has made a breakthrough in identifying the covalent KRASG12C inhibitor as an effective agent for the treatment of NSCLC. This review mainly concentrated on introducing new covalent KRASG12C inhibitors like sotorasib (AMG 510) and adagrasib (MRTX 849); summarizing inhibitors targeting the KRAS-related upstream and downstream effectors in RAF/MEK/ERK pathway and PI3K/AKT/mTOR pathway; exploring the efficacy of immunotherapy and certain emerging immune-related therapeutics such as adoptive cell therapy and cancer vaccines. These inhibitors are being investigated in clinical trials and have exhibited promising effects. On the other hand, naturally extracted compounds, which have exhibited safe and effective properties in treating KRAS-mutant NSCLC through suppressing the MAPK and PI3K/AKT/mTOR signaling pathways, as well as through decreasing PD-L1 expression in preclinical studies, could be expected to enter into clinical studies. Finally, in order to confront the matter of drug resistance, the ongoing clinical trials in combination treatment strategies were summarized herein.
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Affiliation(s)
- Jia-Xin Li
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Run-Ze Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Lin-Rui Ma
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Peng Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Dong-Han Xu
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Jie Huang
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Li-Qi Li
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Ling Tang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, China
- Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou, China
| | - Ying Xie
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
- Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, Zhuhai, China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macao, China
| | - Pei-Yu Yan
- State Key Laboratory of Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao, China
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26
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Zhou Y, Zou Y, Yang M, Mei S, Liu X, Han H, Zhang CD, Niu MM. Highly Potent, Selective, Biostable, and Cell-Permeable Cyclic d-Peptide for Dual-Targeting Therapy of Lung Cancer. J Am Chem Soc 2022; 144:7117-7128. [PMID: 35417174 DOI: 10.1021/jacs.1c12075] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The application of peptide drugs in cancer therapy is impeded by their poor biostability and weak cell permeability. Therefore, it is imperative to find biostable and cell-permeable peptide drugs for cancer treatment. Here, we identified a potent, selective, biostable, and cell-permeable cyclic d-peptide, NKTP-3, that targets NRP1 and KRASG12D using structure-based virtual screening. NKTP-3 exhibited strong biostability and cellular uptake ability. Importantly, it significantly inhibited the growth of A427 cells with the KRASG12D mutation. Moreover, NKTP-3 showed strong antitumor activity against A427 cell-derived xenograft and KRASG12D-driven primary lung cancer models without obvious toxicity. This study demonstrates that the dual NRP1/KRASG12D-targeting cyclic d-peptide NKTP-3 may be used as a potential chemotherapeutic agent for KRASG12D-driven lung cancer treatment.
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Affiliation(s)
- Yunjiang Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Mei Yang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaohao Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huiyun Han
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Chang-Dong Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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27
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Kwan AK, Piazza GA, Keeton AB, Leite CA. The path to the clinic: a comprehensive review on direct KRASG12C inhibitors. J Exp Clin Cancer Res 2022; 41:27. [PMID: 35045886 PMCID: PMC8767686 DOI: 10.1186/s13046-021-02225-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/16/2021] [Indexed: 02/08/2023] Open
Abstract
AbstractThe RAS oncogene is both the most frequently mutated oncogene in human cancer and the first confirmed human oncogene to be discovered in 1982. After decades of research, in 2013, the Shokat lab achieved a seminal breakthrough by showing that the activated KRAS isozyme caused by the G12C mutation in the KRAS gene can be directly inhibited via a newly unearthed switch II pocket. Building upon this groundbreaking discovery, sotorasib (AMG510) obtained approval by the United States Food and Drug Administration in 2021 to become the first therapy to directly target the KRAS oncoprotein in any KRAS-mutant cancers, particularly those harboring the KRASG12C mutation. Adagrasib (MRTX849) and other direct KRASG12C inhibitors are currently being investigated in multiple clinical trials. In this review, we delve into the path leading to the development of this novel KRAS inhibitor, starting with the discovery, structure, and function of the RAS family of oncoproteins. We then examine the clinical relevance of KRAS, especially the KRASG12C mutation in human cancer, by providing an in-depth analysis of its cancer epidemiology. Finally, we review the preclinical evidence that supported the initial development of the direct KRASG12C inhibitors and summarize the ongoing clinical trials of all direct KRASG12C inhibitors.
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28
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Guo M, He S, Cheng J, Li Y, Dong G, Sheng C. Hydrophobic Tagging-Induced Degradation of PDEδ in Colon Cancer Cells. ACS Med Chem Lett 2022; 13:298-303. [PMID: 35178186 PMCID: PMC8842115 DOI: 10.1021/acsmedchemlett.1c00670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
The development of KRAS-PDEδ protein-protein interaction (PPI) inhibitors is generally hampered by limited antitumor activity. Herein, the first hydrophobic tagging (HyT)-based PDEδ degraders were designed. Compound 17c efficiently bound to PDEδ and induced degradation of PDEδ in SW480 colon cancer cells. As compared with PDEδ inhibitor deltazinone, HyT-based degrader 17c exhibited improved antitumor activity toward KRAS mutant cancer cells. This study highlighted the potential of HyT as a valuable chemical tool for tumorigenic PDEδ knockdown, which could be developed into a promising strategy for antitumor drug discovery.
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Affiliation(s)
- Menglu Guo
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Shipeng He
- Institute
of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Junfei Cheng
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Yu Li
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Guoqiang Dong
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China,
| | - Chunquan Sheng
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China,
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29
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Yin G, Lv G, Zhang J, Jiang H, Lai T, Yang Y, Ren Y, Wang J, Yi C, Chen H, Huang Y, Xiao C. Early-stage structure-based drug discovery for small GTPases by NMR spectroscopy. Pharmacol Ther 2022; 236:108110. [PMID: 35007659 DOI: 10.1016/j.pharmthera.2022.108110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Small GTPase or Ras superfamily, including Ras, Rho, Rab, Ran and Arf, are fundamental in regulating a wide range of cellular processes such as growth, differentiation, migration and apoptosis. They share structural and functional similarities for binding guanine nucleotides and hydrolyzing GTP. Dysregulations of Ras proteins are involved in the pathophysiology of multiple human diseases, however there is still a stringent need for effective treatments targeting these proteins. For decades, small GTPases were recognized as 'undruggable' targets due to their complex regulatory mechanisms and lack of deep pockets for ligand binding. NMR has been critical in deciphering the structural and dynamic properties of the switch regions that are underpinning molecular switch functions of small GTPases, which pave the way for developing new effective inhibitors. The recent progress of drug or lead molecule development made for small GTPases profoundly delineated how modern NMR techniques reshape the field of drug discovery. In this review, we will summarize the progress of structural and dynamic studies of small GTPases, the NMR techniques developed for structure-based drug screening and their applications in early-stage drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guohua Lv
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Jerry Zhang
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Tianqi Lai
- Division of Histology & Embryology, Medical College, Jinan University, Guangzhou 511486, Guangdong, China
| | - Yushan Yang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Yong Ren
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Chenju Yi
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China; Research Institute of Xi'an Jiaotong University, Zhejiang, Hangzhou, Zhejiang Province 311215, PR China
| | - Yun Huang
- Howard Hughes Medical Institute, Chevy Chase 20815, MD, USA; Department of Physiology & Biophysics, Weill Cornell Medicine, New York 10065, NY, USA.
| | - Chaoni Xiao
- College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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30
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Chen J, Zeng Q, Wang W, Hu Q, Bao H. Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes. RSC Adv 2022; 12:1742-1757. [PMID: 35425180 PMCID: PMC8978876 DOI: 10.1039/d1ra07936k] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode the effect of Q61A, Q61H and Q61L on the activity of KRAS. Dynamics analyses based on MR-GaMD trajectory reveal that motion modes and dynamics behavior of the switch domain in KRAS are heavily affected by the three Q61 mutants. Information of free energy landscapes (FELs) shows that Q61A, Q61H and Q61L induce structural disorder of the switch domain and disturb the activity of KRAS. Analysis of the interaction network uncovers that the decrease in the stability of hydrogen bonding interactions (HBIs) of GTP with residues V29 and D30 induced by Q61A, Q61H and Q61L is responsible for the structural disorder of the switch-I and that in the occupancy of the hydrogen bond between GTP and residue G60 leads to the structural disorder of the switch-II. Thus, the high disorder of the switch domain caused by three current Q61 mutants produces a significant effect on binding of KRAS to its effectors. This work is expected to provide useful information for further understanding function and target roles of KRAS in anti-cancer drug development.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Qingkai Zeng
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Wei Wang
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Qingquan Hu
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine Jinan 250355 China
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31
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Selvarajoo N, Stanslas J, Islam MK, Sagineedu SR, Lian HK, Lim JCW. Pharmacological Modulation of Apoptosis and Autophagy in Pancreatic Cancer Treatment. Mini Rev Med Chem 2022; 22:2581-2595. [PMID: 35331093 DOI: 10.2174/1389557522666220324123605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/02/2022] [Accepted: 01/21/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pancreatic cancer is a fatal malignant neoplasm with infrequent signs and symptoms until a progressive stage. In 2020, GLOBOCAN reported that pancreatic cancer accounts for 4.7% of all cancer deaths. Despite the availability of standard chemotherapy regimens for treatment, the survival benefits are not guaranteed because tumor cells become chemoresistant even due to the development of chemoresistance in tumor cells even with a short treatment course, where apoptosis and autophagy play critical roles. OBJECTIVE This review compiled essential information on the regulatory mechanisms and roles of apoptosis and autophagy in pancreatic cancer, as well as drug-like molecules that target different pathways in pancreatic cancer eradication, with an aim to provide ideas to the scientific communities in discovering novel and specific drugs to treat pancreatic cancer, specifically PDAC. METHOD Electronic databases that were searched for research articles for this review were Scopus, Science Direct, PubMed, Springer Link, and Google Scholar. The published studies were identified and retrieved using selected keywords. DISCUSSION/CONCLUSION Many small-molecule anticancer agents have been developed to regulate autophagy and apoptosis associated with pancreatic cancer treatment, where most of them target apoptosis directly through EGFR/Ras/Raf/MAPK and PI3K/Akt/mTOR pathways. The cancer drugs that regulate autophagy in treating cancer can be categorized into three groups: i) direct autophagy inducers (e.g., rapamycin), ii) indirect autophagy inducers (e.g., resveratrol), and iii) autophagy inhibitors. Resveratrol persuades both apoptosis and autophagy with a cytoprotective effect, while autophagy inhibitors (e.g., 3-methyladenine, chloroquine) can turn off the protective autophagic effect for therapeutic benefits. Several studies showed that autophagy inhibition resulted in a synergistic effect with chemotherapy (e.g., a combination of metformin with gemcitabine/ 5FU). Such drugs possess a unique clinical value in treating pancreatic cancer as well as other autophagy-dependent carcinomas.
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Affiliation(s)
- Nityaa Selvarajoo
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Johnson Stanslas
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohammad Kaisarul Islam
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sreenivasa Rao Sagineedu
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - Ho Kok Lian
- Department of Pathology, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Jonathan Chee Woei Lim
- Pharmacotherapeutics Unit, Department of Medicine, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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32
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Abstract
Proteolysis-targeting chimeras are a new modality of chemical tools and potential therapeutics involving the induction of protein degradation. Cyclin-dependent kinase (CDK) protein, which is involved in cycles and transcription cycles, participates in regulation of the cell cycle, transcription and splicing. Proteolysis-targeting chimeras targeting CDKs show several advantages over traditional CDK small-molecule inhibitors in potency, selectivity and drug resistance. In addition, the discovery of molecule glues promotes the development of CDK degraders. Herein, the authors describe the existing CDK degraders and focus on the discussion of the structural characteristics and design of these degraders.
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Yin X, Li W, Zhang J, Zhao W, Cai H, Zhang C, Liu Z, Guo Y, Wang J. AMPK-Mediated Metabolic Switching Is High Effective for Phytochemical Levo-Tetrahydropalmatine (l-THP) to Reduce Hepatocellular Carcinoma Tumor Growth. Metabolites 2021; 11:metabo11120811. [PMID: 34940569 PMCID: PMC8703446 DOI: 10.3390/metabo11120811] [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: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022] Open
Abstract
Targeting cancer cell metabolism has been an attractive approach for cancer treatment. However, the role of metabolic alternation in cancer is still unknown whether it functions as a tumor promoter or suppressor. Applying the cancer gene-metabolism integrative network model, we predict adenosine monophosphate-activated protein kinase (AMPK) to function as a central hub of metabolic landscape switching in specific liver cancer subtypes. For the first time, we demonstrate that the phytochemical levo-tetrahydropalmatine (l-THP), a Corydalis yanhusuo-derived clinical drug, as an AMPK activator via autophagy-mediated metabolic switching could kill the hepatocellular carcinoma HepG2 cells. Mechanistically, l-THP promotes the autophagic response by activating the AMPK-mTOR-ULK1 and the ROS-JNK-ATG cascades and impairing the ERK/AKT signaling. All these processes ultimately synergize to induce the decreased mitochondrial oxidative phosphorylation (OXPHOS) and mitochondrial damage. Notably, silencing AMPK significantly inhibits the autophagic flux and recovers the decreased OXPHOS metabolism, which results in HepG2 resistance to l-THP treatment. More importantly, l-THP potently reduces the growth of xenograft HepG2 tumor in nude mice without affecting other organs. From this perspective, our findings support the conclusion that metabolic change is an alternative approach to influence the development of HCC.
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Affiliation(s)
- Xunzhe Yin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; (X.Y.); (H.C.); (C.Z.)
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; (W.L.); (J.Z.); (W.Z.)
| | - Wenbo Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; (W.L.); (J.Z.); (W.Z.)
| | - Jiaxin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; (W.L.); (J.Z.); (W.Z.)
| | - Wenjing Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; (W.L.); (J.Z.); (W.Z.)
| | - Huaxing Cai
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; (X.Y.); (H.C.); (C.Z.)
| | - Chi Zhang
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; (X.Y.); (H.C.); (C.Z.)
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; (W.L.); (J.Z.); (W.Z.)
- Correspondence: (Z.L.); (Y.G.)
| | - Yan Guo
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China; (X.Y.); (H.C.); (C.Z.)
- Correspondence: (Z.L.); (Y.G.)
| | - Jin Wang
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY 11794-3400, USA;
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Huang XM, Huang JJ, Du JJ, Zhang N, Long Z, Yang Y, Zhong FF, Zheng BW, Shen YF, Huang Z, Qin X, Chen JH, Lin QY, Lin WJ, Ma WZ. Autophagy inhibitors increase the susceptibility of KRAS-mutant human colorectal cancer cells to a combined treatment of 2-deoxy-D-glucose and lovastatin. Acta Pharmacol Sin 2021; 42:1875-1887. [PMID: 33608672 PMCID: PMC8564510 DOI: 10.1038/s41401-021-00612-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/09/2021] [Indexed: 12/17/2022] Open
Abstract
RAS-driven colorectal cancer relies on glucose metabolism to support uncontrolled growth. However, monotherapy with glycolysis inhibitors like 2-deoxy-D-glucose causes limited effectiveness. Recent studies suggest that anti-tumor effects of glycolysis inhibition could be improved by combination treatment with inhibitors of oxidative phosphorylation. In this study we investigated the effect of a combination of 2-deoxy-D-glucose with lovastatin (a known inhibitor of mevalonate pathway and oxidative phosphorylation) on growth of KRAS-mutant human colorectal cancer cell lines HCT116 and LoVo. A combination of lovastatin (>3.75 μM) and 2-deoxy-D-glucose (>1.25 mM) synergistically reduced cell viability, arrested cells in the G2/M phase, and induced apoptosis. The combined treatment also reduced cellular oxygen consumption and extracellular acidification rate, resulting in decreased production of ATP and lower steady-state ATP levels. Energy depletion markedly activated AMPK, inhibited mTOR and RAS signaling pathways, eventually inducing autophagy, the cellular pro-survival process under metabolic stress, whereas inhibition of autophagy by chloroquine (6.25 μM) enhanced the cytotoxic effect of the combination of lovastatin and 2-deoxy-D-glucose. These in vitro experiment results were reproduced in a nude mouse xenograft model of HCT116 cells. Our findings suggest that concurrently targeting glycolysis, oxidative phosphorylation, and autophagy may be a promising regimen for the management of RAS-driven colorectal cancers.
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Affiliation(s)
- Xiao-Ming Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jia-Jun Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jing-Jing Du
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Na Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ze Long
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - You Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Fang-Fang Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Bo-Wen Zheng
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yun-Fu Shen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Zhe Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Xiang Qin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jun-He Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qian-Yu Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wan-Jun Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wen-Zhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
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Pomplun S, Jbara M, Schissel CK, Wilson Hawken S, Boija A, Li C, Klein I, Pentelute BL. Parallel Automated Flow Synthesis of Covalent Protein Complexes That Can Inhibit MYC-Driven Transcription. ACS CENTRAL SCIENCE 2021; 7:1408-1418. [PMID: 34471684 PMCID: PMC8393199 DOI: 10.1021/acscentsci.1c00663] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 06/11/2023]
Abstract
Dysregulation of the transcription factor MYC is involved in many human cancers. The dimeric transcription factor complexes of MYC/MAX and MAX/MAX activate or inhibit, respectively, gene transcription upon binding to the same enhancer box DNA. Targeting these complexes in cancer is a long-standing challenge. Inspired by the inhibitory activity of the MAX/MAX dimer, we engineered covalently linked, synthetic homo- and heterodimeric protein complexes to attenuate oncogenic MYC-driven transcription. We prepared the covalent protein complexes (∼20 kDa, 167-231 residues) in a single shot via parallel automated flow synthesis in hours. The stabilized covalent dimers display DNA binding activity, are intrinsically cell-penetrant, and inhibit cancer cell proliferation in different cell lines. RNA sequencing and gene set enrichment analysis in A549 cancer cells confirmed that the synthetic dimers interfere with MYC-driven transcription. Our results demonstrate the potential of automated flow technology to rapidly deliver engineered synthetic protein complex mimetics that can serve as a starting point in developing inhibitors of MYC-driven cancer cell growth.
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Affiliation(s)
- Sebastian Pomplun
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Muhammad Jbara
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carly K. Schissel
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Susana Wilson Hawken
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ann Boija
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Charles Li
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Isaac Klein
- Whitehead
Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute
of MIT and Harvard, 415
Main Street, Cambridge, Massachusetts 02142, United States
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37
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Wang X, Gorfe AA, Putkey JA. Antipsychotic phenothiazine drugs bind to KRAS in vitro. JOURNAL OF BIOMOLECULAR NMR 2021; 75:233-244. [PMID: 34176062 DOI: 10.1007/s10858-021-00371-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
We used NMR to show that the antipsychotic phenothiazine drugs promazine and promethazine bind to GDP-KRAS. Promazine also binds to oncogenic GDP-KRAS(G12D), and to wild type GppNHp-KRAS. A panel of additional phenothiazines bind to GDP-KRAS but with lower affinity than promazine or promethazine. Binding is most dependent on substitutions at C-2 of the tricyclic phenothiazine ring. Promazine was used to generate an NMR-driven HADDOCK model of the drug/GDP-KRAS complex. The structural model shows the tricyclic phenothiazine ring of promazine associates with the hydrophobic pocket p1 that is bordered by the central β sheet and Switch II in KRAS. Binding appears to stabilize helix 2 in a conformation that is similar to that seen in KRAS bound to other small molecules. Association of phenothiazines with KRAS may affect normal KRAS signaling that could contribute to multiple biological activities of these antipsychotic drugs. Moreover, the phenothiazine ring represents a new core scaffold on which to design modulators of KRAS activity.
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Affiliation(s)
- Xu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX, 77030, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX, 77030, USA
| | - John A Putkey
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX, 77030, USA.
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38
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LaPlante G, Zhang W. Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors. Cancers (Basel) 2021; 13:3079. [PMID: 34203106 PMCID: PMC8235664 DOI: 10.3390/cancers13123079] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is a critical regulator of cellular protein levels and activity. It is, therefore, not surprising that its dysregulation is implicated in numerous human diseases, including many types of cancer. Moreover, since cancer cells exhibit increased rates of protein turnover, their heightened dependence on the UPS makes it an attractive target for inhibition via targeted therapeutics. Indeed, the clinical application of proteasome inhibitors in treatment of multiple myeloma has been very successful, stimulating the development of small-molecule inhibitors targeting other UPS components. On the other hand, while the discovery of potent and selective chemical compounds can be both challenging and time consuming, the area of targeted protein degradation through utilization of the UPS machinery has seen promising developments in recent years. The repertoire of proteolysis-targeting chimeras (PROTACs), which employ E3 ligases for the degradation of cancer-related proteins via the proteasome, continues to grow. In this review, we will provide a thorough overview of small-molecule UPS inhibitors and highlight advancements in the development of targeted protein degradation strategies for cancer therapeutics.
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Affiliation(s)
- Gabriel LaPlante
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada;
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada;
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, ON M5G1M1, Canada
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Chen J, Zhang S, Wang W, Pang L, Zhang Q, Liu X. Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis. J Chem Inf Model 2021; 61:1954-1969. [PMID: 33739090 DOI: 10.1021/acs.jcim.0c01470] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard to mutation-mediated tuning on the activity of K-Ras, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations followed by analysis of free energy landscapes (FELs) are performed on the GDP- and GTP-bound wild-type (WT), G12V, and D33E K-Ras. The results suggest that G12V and D33E not only evidently change the flexibility of SW1 and SW2 but also greatly affect correlated motions of SW1 and SW2 separately relative to the P-loop and SW1, which exerts a certain tuning on the activity of K-Ras. The information stemming from the analyses of FELs reveals that the conformations of SW1 and SW2 are in high disorders in the GDP- and GTP-associated WT and mutated K-Ras, possibly producing significant effect on binding of guanine nucleotide exchange factors or effectors to K-Ras. The interaction networks of GDP and GTP with K-Ras are identified and the results uncover that the instability in hydrogen-bonding interactions of SW1 with GDP and GTP is mostly responsible for conformational disorder of SW1 and SW2 as well as tunes the activity of oncogenic K-Ras.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
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40
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Wang P, van der Hoeven D, Ye N, Chen H, Liu Z, Ma X, Montufar-Solis D, Rehl KM, Cho KJ, Thapa S, Chen W, van der Hoeven R, Frost JA, Hancock JF, Zhou J. Scaffold repurposing of fendiline: Identification of potent KRAS plasma membrane localization inhibitors. Eur J Med Chem 2021; 217:113381. [PMID: 33756124 DOI: 10.1016/j.ejmech.2021.113381] [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] [Received: 12/08/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023]
Abstract
KRAS plays an essential role in regulating cell proliferation, differentiation, migration and survival. Mutated KRAS is a major driver of malignant transformation in multiple human cancers. We showed previously that fendiline (6) is an effective inhibitor of KRAS plasma membrane (PM) localization and function. In this study, we designed, synthesized and evaluated a series of new fendiline analogs to optimize its drug properties. Systemic structure-activity relationship studies by scaffold repurposing led to the discovery of several more active KRAS PM localization inhibitors such as compounds 12f (NY0244), 12h (NY0331) and 22 (NY0335) which exhibit nanomolar potencies. These compounds inhibited oncogenic KRAS-driven cancer cell proliferation at single-digit micromolar concentrations in vitro. In vivo studies in a xenograft model of pancreatic cancer revealed that 12h and 22 suppressed oncogenic KRAS-expressing MiaPaCa-2 tumor growth at a low dose range of 1-5 mg/kg with no vasodilatory effects, indicating their potential as chemical probes and anticancer therapeutics.
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Affiliation(s)
- Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Na Ye
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Zhiqing Liu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Xiaoping Ma
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Dina Montufar-Solis
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Kristen M Rehl
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, USA
| | - Sabita Thapa
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Wei Chen
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ransome van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Jeffrey A Frost
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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Van QN, Prakash P, Shrestha R, Balius TE, Turbyville TJ, Stephen AG. RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention. Biomolecules 2021; 11:377. [PMID: 33802474 PMCID: PMC8000715 DOI: 10.3390/biom11030377] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/18/2023] Open
Abstract
RAS proteins are mutated in approximately 20% of all cancers and are generally associated with poor clinical outcomes. RAS proteins are localized to the plasma membrane and function as molecular switches, turned on by partners that receive extracellular mitogenic signals. In the on-state, they activate intracellular signal transduction cascades. Membrane-bound RAS molecules segregate into multimers, known as nanoclusters. These nanoclusters, held together through weak protein-protein and protein-lipid associations, are highly dynamic and respond to cellular input signals and fluctuations in the local lipid environment. Disruption of RAS nanoclusters results in downregulation of RAS-mediated mitogenic signaling. In this review, we discuss the propensity of RAS proteins to display clustering behavior and the interfaces that are associated with these assemblies. Strategies to therapeutically disrupt nanocluster formation or the stabilization of signaling incompetent RAS complexes are discussed.
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Affiliation(s)
| | | | | | | | | | - Andrew G. Stephen
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, National Cancer Institute RAS Initiative, Inc., Frederick, MD 21702, USA; (Q.N.V.); (P.P.); (R.S.); (T.E.B.); (T.J.T.)
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42
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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43
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Rosenqvist P, Sabt A, Dyunyasheva V, Abankwa D, Virta P, Ora M. Stability of the Phosphotriester PDE6D Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202004426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry University of Turku FI- 20014 Turku Finland
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department National Research Centre Dokki 12622 Giza Egypt
| | | | - Daniel Abankwa
- Department of Life Sciences and Medicine University of Luxembourg 4362 Esch-sur-Alzette Luxembourg
| | - Pasi Virta
- Department of Chemistry University of Turku FI- 20014 Turku Finland
| | - Mikko Ora
- Department of Chemistry University of Turku FI- 20014 Turku Finland
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44
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Chen J, Wang W, Pang L, Zhu W. Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics. Phys Chem Chem Phys 2021; 22:21238-21250. [PMID: 32930679 DOI: 10.1039/d0cp03766d] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Uncovering molecular basis with regard to the conformational change of two switches I and II in the GppNHp (GNP)-bound H-Ras is highly significant for the understanding of Ras signaling. For this purpose, accelerated molecular dynamics (aMD) simulations and principal component (PC) analysis are integrated to probe the effect of mutations G12V, T35S and Q61K on conformational transformation between two switches of the GNP-bound H-Ras. The RMSF and cross-correlation analyses suggest that three mutations exert a vital effect on the flexibility and internal dynamics of two switches in the GNP-bound H-Ras. The results stemming from PC analysis indicate that two switches in the GNP-bound WT H-Ras tend to form a closed state in most conformations, while those in the GNP-bound mutated H-Ras display transformation between different states. This conclusion is further supported by free energy landscapes constructed by using the distances of residues 12 away from 35 and 35 away from 61 as reaction coordinates and different experimental studies. Interaction scanning is performed on aMD trajectories and the information shows that conformational transformations of two switches I and II induced by mutations extremely affect the GNP-residue interactions. Meanwhile, the scanning results also signify that residues G15, A18, F28, K117, A146 and K147 form stable contacts with GNP, while residues D30, E31, Y32, D33, P34 and E62 in two switches I and II produce unstable contacts with GNP. This study not only reveals dynamic behavior changes of two switches in H-Ras induced by mutations, but also unveils general principles and mechanisms with regard to functional conformational changes of H-Ras.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| | - Weiliang Zhu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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45
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Fuchs O, Bokorova R. Preclinical Studies of PROTACs in Hematological Malignancies. Cardiovasc Hematol Disord Drug Targets 2021; 21:7-22. [PMID: 33687890 DOI: 10.2174/1871529x21666210308111546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Incorrectly expressed or mutated proteins associated with hematologic malignancies have been generally targeted by chemotherapy using small-molecule inhibitors or monoclonal antibodies. But the majority of these intracellular proteins are without active sites and antigens. PROTACs, proteolysis targeting chimeras, are bifunctional molecules designed to polyubiquitinate and degrade specific pathological proteins of interest (POIs) by hijacking the activity of E3-ubiquitin ligases for POI polyubiquitination and subsequent degradation by the proteasome. This strategy utilizes the ubiquitin-proteasome system for the degradation of specific proteins in the cell. In many cases, including hematologic malignancies, inducing protein degradation as a therapeutic strategy offers therapeutic benefits over classical enzyme inhibition connected with resistance to inhibitors. Limitations of small-molecule inhibitors are shown. PROTACs can polyubiquitinate and mark for degradation of "undruggable"proteins, e.g. transcription factor STAT3 and scaffold proteins. Today, this technology is used in preclinical studies in various hematologic malignancies, mainly for targeting drug-resistant bromodomain and extraterminal proteins and Bruton tyrosine kinase. Several mechanisms limiting selectivity and safety of PROTAC molecules function are also discussed.
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Affiliation(s)
- Ota Fuchs
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Radka Bokorova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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46
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Zhao J, Sun H, Wang W, Zhang L, Chen J. Theoretical insights into mutation-mediated conformational changes of the GNP-bound H-RAS. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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Marshall CB, KleinJan F, Gebregiworgis T, Lee KY, Fang Z, Eves BJ, Liu NF, Gasmi-Seabrook GMC, Enomoto M, Ikura M. NMR in integrated biophysical drug discovery for RAS: past, present, and future. JOURNAL OF BIOMOLECULAR NMR 2020; 74:531-554. [PMID: 32804298 DOI: 10.1007/s10858-020-00338-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Mutations in RAS oncogenes occur in ~ 30% of human cancers, with KRAS being the most frequently altered isoform. RAS proteins comprise a conserved GTPase domain and a C-terminal lipid-modified tail that is unique to each isoform. The GTPase domain is a 'switch' that regulates multiple signaling cascades that drive cell growth and proliferation when activated by binding GTP, and the signal is terminated by GTP hydrolysis. Oncogenic RAS mutations disrupt the GTPase cycle, leading to accumulation of the activated GTP-bound state and promoting proliferation. RAS is a key target in oncology, however it lacks classic druggable pockets and has been extremely challenging to target. RAS signaling has thus been targeted indirectly, by harnessing key downstream effectors as well as upstream regulators, or disrupting the proper membrane localization required for signaling, by inhibiting either lipid modification or 'carrier' proteins. As a small (20 kDa) protein with multiple conformers in dynamic equilibrium, RAS is an excellent candidate for NMR-driven characterization and screening for direct inhibitors. Several molecules have been discovered that bind RAS and stabilize shallow pockets through conformational selection, and recent compounds have achieved substantial improvements in affinity. NMR-derived insight into targeting the RAS-membrane interface has revealed a new strategy to enhance the potency of small molecules, while another approach has been development of peptidyl inhibitors that bind through large interfaces rather than deep pockets. Remarkable progress has been made with mutation-specific covalent inhibitors that target the thiol of a G12C mutant, and these are now in clinical trials. Here we review the history of RAS inhibitor development and highlight the utility of NMR and integrated biophysical approaches in RAS drug discovery.
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Affiliation(s)
- Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
| | - Fenneke KleinJan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Zhenhao Fang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ben J Eves
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Ningdi F Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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48
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Osumi H, Muroi A, Sakahara M, Kawachi H, Okamoto T, Natsume Y, Yamanaka H, Takano H, Kusama D, Shinozaki E, Ooki A, Yamaguchi K, Ueno M, Takeuchi K, Noda T, Nagayama S, Koshikawa N, Yao R. Evaluation of the RAS signaling network in response to MEK inhibition using organoids derived from a familial adenomatous polyposis patient. Sci Rep 2020; 10:17455. [PMID: 33060766 PMCID: PMC7567075 DOI: 10.1038/s41598-020-74530-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/30/2020] [Indexed: 01/07/2023] Open
Abstract
RAS signaling is a promising target for colorectal cancer (CRC) therapy, and a variety of selective inhibitors have been developed. However, their use has often failed to demonstrate a significant benefit in CRC patients. Here, we used patient-derived organoids (PDOs) derived from a familial adenomatous polyposis (FAP) patient to analyze the response to chemotherapeutic agents targeting EGFR, BRAF and MEK. We found that PDOs carrying KRAS mutations were resistant to MEK inhibition, while those harboring the BRAF class 3 mutation were hypersensitive. We used a systematic approach to examine the phosphorylation of RAS effectors using reverse-phase protein array (RPPA) and found increased phosphorylation of MEK induced by binimetinib. A high basal level of ERK phosphorylation and its rebound activation after MEK inhibition were detected in KRAS-mutant PDOs. Notably, the phosphorylation of EGFR and AKT was more closely correlated with that of MEK than that of ERK. Transcriptome analysis identified MYC-mediated transcription and IFN signaling as significantly correlated gene sets in MEK inhibition. Our experiments demonstrated that RPPA analysis of PDOs, in combination with the genome and transcriptome, is a useful preclinical research platform to understand RAS signaling and provides clues for the development of chemotherapeutic strategies.
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Affiliation(s)
- Hiroki Osumi
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.,Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.,Director's Office, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Atsushi Muroi
- Division of Cancer Cell Research, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Yokohama, Kanagawa, 241-8515, Japan
| | - Mizuho Sakahara
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hiroshi Kawachi
- Division of Pathology, Cancer Institute Hospital, Department of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hiroshi Takano
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Daisuke Kusama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Eiji Shinozaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Akira Ooki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Masashi Ueno
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute Hospital, Department of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Tetsuo Noda
- Director's Office, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Naohiko Koshikawa
- Division of Cancer Cell Research, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Yokohama, Kanagawa, 241-8515, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.
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49
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Meyer SM, Williams CC, Akahori Y, Tanaka T, Aikawa H, Tong Y, Childs-Disney JL, Disney MD. Small molecule recognition of disease-relevant RNA structures. Chem Soc Rev 2020; 49:7167-7199. [PMID: 32975549 PMCID: PMC7717589 DOI: 10.1039/d0cs00560f] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeting RNAs with small molecules represents a new frontier in drug discovery and development. The rich structural diversity of folded RNAs offers a nearly unlimited reservoir of targets for small molecules to bind, similar to small molecule occupancy of protein binding pockets, thus creating the potential to modulate human biology. Although the bacterial ribosome has historically been the most well exploited RNA target, advances in RNA sequencing technologies and a growing understanding of RNA structure have led to an explosion of interest in the direct targeting of human pathological RNAs. This review highlights recent advances in this area, with a focus on the design of small molecule probes that selectively engage structures within disease-causing RNAs, with micromolar to nanomolar affinity. Additionally, we explore emerging RNA-target strategies, such as bleomycin A5 conjugates and ribonuclease targeting chimeras (RIBOTACs), that allow for the targeted degradation of RNAs with impressive potency and selectivity. The compounds discussed in this review have proven efficacious in human cell lines, patient-derived cells, and pre-clinical animal models, with one compound currently undergoing a Phase II clinical trial and another that recently garnerd FDA-approval, indicating a bright future for targeted small molecule therapeutics that affect RNA function.
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Affiliation(s)
- Samantha M Meyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Christopher C Williams
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Yoshihiro Akahori
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Toru Tanaka
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Haruo Aikawa
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Yuquan Tong
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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50
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Marak BN, Dowarah J, Khiangte L, Singh VP. A comprehensive insight on the recent development of Cyclic Dependent Kinase inhibitors as anticancer agents. Eur J Med Chem 2020; 203:112571. [DOI: 10.1016/j.ejmech.2020.112571] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
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