1
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Deng H, Han Y, Liu L, Zhang H, Liu D, Wen J, Huang M, Zhao L. Targeting Myeloid Leukemia-1 in Cancer Therapy: Advances and Directions. J Med Chem 2024; 67:5963-5998. [PMID: 38597264 DOI: 10.1021/acs.jmedchem.3c01998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
As a tripartite cell death switch, B-cell lymphoma protein 2 (Bcl-2) family members precisely regulate the endogenous apoptosis pathway in response to various cell signal stresses through protein-protein interactions. Myeloid leukemia-1 (Mcl-1), a key anti-apoptotic Bcl-2 family member, is positioned downstream in the endogenous apoptotic pathway and plays a central role in regulating mitochondrial function. Mcl-1 is highly expressed in a variety of hematological malignancies and solid tumors, contributing to tumorigenesis, poor prognosis, and chemoresistance, making it an attractive target for cancer treatment. This Perspective aims to discuss the mechanism by which Mcl-1 regulates apoptosis and non-apoptotic functions in cancer cells and to outline the discovery and optimization process of potent Mcl-1 modulators. In addition, we summarize the structural characteristics of potent inhibitors that bind to Mcl-1 through multiple co-crystal structures and analyze the cardiotoxicity caused by current Mcl-1 inhibitors, providing prospects for rational targeting of Mcl-1.
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Affiliation(s)
- Hongguang Deng
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yu Han
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Liang Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hong Zhang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Dan Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiachen Wen
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Min Huang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Linxiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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2
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Faraji N, Daly NL, Arab SS, Khosroushahi AY. In silico design of potential Mcl-1 peptide-based inhibitors. J Mol Model 2024; 30:108. [PMID: 38499818 DOI: 10.1007/s00894-024-05901-8] [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: 12/09/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
CONTEXT BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods. MM-PBSA results showed that the mutations of A4fE and A2eE in analogue 5 demonstrate a preference towards binding with Mcl-1. As evidenced by Circular dichroism results, the helicity increases from 18 to 34%, these findings could enhance the potential of analogue 5 as an anti-cancer agent targeting Mcl-1. The applied strategies in this research could shed light on the in silico peptide design. Moreover, analogue 5 as a drug candidate can be evaluated in vitro and in vivo studies. METHODS The sequence of the lead peptide was determined using the ApInAPDB database and PRALINE program. Contact finder and PDBsum web server softwares were used to determine the contact involved amino acids in complex with Mcl-1. All identified salt bridge contributing residues were unaltered to preserve the binding affinity. After proposing novel analogues, their secondary structures were predicted by Cham finder web server software and GOR, Neural Network, and Chou-Fasman algorithms. Finally, molecular dynamics simulations run for 100 ns were done using the GROMACS, version 5.0.7, with the CHARMM36 force field. MM-PBSA was used to assess binding affinity specificity in targeting Mcl-1 and Bcl-xL (B-cell lymphoma extra-large).
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Affiliation(s)
- Naser Faraji
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4870, Australia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Yari Khosroushahi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Wolf E, Lento C, Pu J, Dickinson BC, Wilson DJ. Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2. Biochemistry 2023; 62:1619-1630. [PMID: 37192192 PMCID: PMC10249625 DOI: 10.1021/acs.biochem.2c00709] [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: 12/20/2022] [Revised: 05/02/2023] [Indexed: 05/18/2023]
Abstract
The structurally conserved B-cell lymphoma 2 (Bcl-2) family of protein function to promote or inhibit apoptosis through an exceedingly complex web of specific, intrafamilial protein-protein interactions. The critical role of these proteins in lymphomas and other cancers has motivated a widespread interest in understanding the molecular mechanisms that drive specificity in Bcl-2 family interactions. However, the high degree of structural similarity among Bcl-2 homologues has made it difficult to rationalize the highly specific (and often divergent) binding behavior exhibited by these proteins using conventional structural arguments. In this work, we use time-resolved hydrogen deuterium exchange mass spectrometry to explore shifts in conformational dynamics associated with binding partner engagement in the Bcl-2 family proteins Bcl-2 and Mcl-1. Using this approach combined with homology modeling, we reveal that Mcl-1 binding is driven by a large-scale shift in conformational dynamics, while Bcl-2 complexation occurs primarily through a classical charge compensation mechanism. This work has implications for understanding the evolution of internally regulated biological systems composed of structurally similar proteins and for the development of drugs targeting Bcl-2 family proteins for promotion of apoptosis in cancer.
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Affiliation(s)
- Esther Wolf
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Cristina Lento
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jinyue Pu
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Derek J. Wilson
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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4
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Sancho M, Leiva D, Lucendo E, Orzáez M. Understanding MCL1: from cellular function and regulation to pharmacological inhibition. FEBS J 2022; 289:6209-6234. [PMID: 34310025 PMCID: PMC9787394 DOI: 10.1111/febs.16136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 12/30/2022]
Abstract
Myeloid cell leukemia-1 (MCL1), an antiapoptotic member of the BCL2 family characterized by a short half-life, functions as a rapid sensor that regulates cell death and other relevant processes that include cell cycle progression and mitochondrial homeostasis. In cancer, MCL1 overexpression contributes to cell survival and resistance to diverse chemotherapeutic agents; for this reason, several MCL1 inhibitors are currently under preclinical and clinical development for cancer treatment. However, the nonapoptotic functions of MCL1 may influence their therapeutic potential. Overall, the complexity of MCL1 regulation and function represent challenges to the clinical application of MCL1 inhibitors. We now summarize the current knowledge regarding MCL1 structure, regulation, and function that could impact the clinical success of MCL1 inhibitors.
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Affiliation(s)
- Mónica Sancho
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
| | - Diego Leiva
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
| | - Estefanía Lucendo
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
| | - Mar Orzáez
- Targeted Therapies on Cancer and Inflammation LaboratoryCentro de Investigación Príncipe FelipeValenciaSpain
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5
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Deng H, Huang M, Liu H, Zhang H, Liu L, Gao B, Li X, Li J, Niu Q, Zhang Z, Luan S, Zhang J, Jing Y, Liu D, Zhao L. Development of a series of novel Mcl-1 inhibitors bearing an indole carboxylic acid moiety. Bioorg Chem 2022; 127:106018. [PMID: 35901526 DOI: 10.1016/j.bioorg.2022.106018] [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: 03/30/2022] [Revised: 06/03/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022]
Abstract
The B cell lymphoma protein 2 (Bcl-2) family proteins regulate cell apoptosis by participating in the endogenous apoptosis pathway. As an important anti-apoptotic protein, Myeloid cell leukemia 1 (Mcl-1) is overexpressed in a variety of tumor cells, and targeting this protein has been a promising strategy for cancer therapy. Herein, based on the 1H-indole-5-carboxylic acid structure previously discovered, we have developed a series of novel compounds with increased affinities and selectivity toward Mcl-1 through structure-based drug design. Among those compounds, 26 exerted relatively better affinity and selectivity for Mcl-1 with moderate inhibition in HL-60 cells. Mechanism studies showed that compound 26 could induce cancer cells apoptosis in an Mcl-1-dependent manner. It also exhibited good microsomal and plasma stability with acceptable pharmacokinetics profiles. Furthermore, treatment with target compound in a 4T1 xenograft mouse model significantly suppressed the tumor growth. Overall, the small molecule described herein represents a promising Mcl-1 inhibitor for further study.
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Affiliation(s)
- Hongguang Deng
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Min Huang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hui Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China; Liaoning Key Laboratory of Targeting Drugs for Hematological Malignancies, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hong Zhang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Liang Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bensheng Gao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xianlu Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jinbo Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Qun Niu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhenwei Zhang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shenglin Luan
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jingyi Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China; Liaoning Key Laboratory of Targeting Drugs for Hematological Malignancies, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yongkui Jing
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China; Liaoning Key Laboratory of Targeting Drugs for Hematological Malignancies, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Dan Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Linxiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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6
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Xi J, Yao L, Zhang R, Chen K, Li M, Zhang D, Cui M, Nie H, Wang P, Li X, Jiang R. 2-oxy-3-phenylacrylic acid derivatives as potent Mcl-1 inhibitors for treatment of cancer. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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7
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Wang H, Guo M, Wei H, Chen Y. Targeting MCL-1 in cancer: current status and perspectives. J Hematol Oncol 2021; 14:67. [PMID: 33883020 PMCID: PMC8061042 DOI: 10.1186/s13045-021-01079-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Myeloid leukemia 1 (MCL-1) is an antiapoptotic protein of the BCL-2 family that prevents apoptosis by binding to the pro-apoptotic BCL-2 proteins. Overexpression of MCL-1 is frequently observed in many tumor types and is closely associated with tumorigenesis, poor prognosis and drug resistance. The central role of MCL-1 in regulating the mitochondrial apoptotic pathway makes it an attractive target for cancer therapy. Significant progress has been made with regard to MCL-1 inhibitors, some of which have entered clinical trials. Here, we discuss the mechanism by which MCL-1 regulates cancer cell apoptosis and review the progress related to MCL-1 small molecule inhibitors and their role in cancer therapy.
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Affiliation(s)
- Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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8
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Ibarra AA, Bartlett GJ, Hegedüs Z, Dutt S, Hobor F, Horner KA, Hetherington K, Spence K, Nelson A, Edwards TA, Woolfson DN, Sessions RB, Wilson AJ. Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces. ACS Chem Biol 2019; 14:2252-2263. [PMID: 31525028 PMCID: PMC6804253 DOI: 10.1021/acschembio.9b00560] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Protein–protein
interactions (PPIs) are vital to all biological
processes. These interactions are often dynamic, sometimes transient,
typically occur over large topographically shallow protein surfaces,
and can exhibit a broad range of affinities. Considerable progress
has been made in determining PPI structures. However, given the above
properties, understanding the key determinants of their thermodynamic
stability remains a challenge in chemical biology. An improved ability
to identify and engineer PPIs would advance understanding of biological
mechanisms and mutant phenotypes and also provide a firmer foundation
for inhibitor design. In silico prediction of PPI
hot-spot amino acids using computational alanine scanning (CAS) offers
a rapid approach for predicting key residues that drive protein–protein
association. This can be applied to all known PPI structures; however
there is a trade-off between throughput and accuracy. Here we describe
a comparative analysis of multiple CAS methods, which highlights effective
approaches to improve the accuracy of predicting hot-spot residues.
Alongside this, we introduce a new method, BUDE Alanine Scanning,
which can be applied to single structures from crystallography and
to structural ensembles from NMR or molecular dynamics data. The comparative
analyses facilitate accurate prediction of hot-spots that we validate
experimentally with three diverse targets: NOXA-B/MCL-1 (an α-helix-mediated
PPI), SIMS/SUMO, and GKAP/SHANK-PDZ (both β-strand-mediated
interactions). Finally, the approach is applied to the accurate prediction
of hot-spot residues at a topographically novel Affimer/BCL-xL protein–protein interface.
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Affiliation(s)
- Amaurys A. Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Zsöfia Hegedüs
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Som Dutt
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Katherine A. Horner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Kristina Hetherington
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Kirstin Spence
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Adam Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Derek N. Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Richard B. Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
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9
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Denis C, Sopková-de Oliveira Santos J, Bureau R, Voisin-Chiret AS. Hot-Spots of Mcl-1 Protein. J Med Chem 2019; 63:928-943. [DOI: 10.1021/acs.jmedchem.9b00983] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Camille Denis
- Normandie Univiversité, UNICAEN, CERMN, 14000 Caen, France
| | | | - Ronan Bureau
- Normandie Univiversité, UNICAEN, CERMN, 14000 Caen, France
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10
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Investigating the Molecular Basis of N-Substituted 1-Hydroxy-4-Sulfamoyl-2-Naphthoate Compounds Binding to Mcl1. Processes (Basel) 2019. [DOI: 10.3390/pr7040224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Myeloid cell leukemia-1 (Mcl1) is an anti–apoptotic protein that has gained considerable attention due to its overexpression activity prevents cell death. Therefore, a potential inhibitor that specifically targets Mcl1 with higher binding affinity is necessary. Recently, a series of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoate compounds was reported that targets Mcl1, but its binding mechanism remains unexplored. Here, we attempted to explore the molecular mechanism of binding to Mcl1 using advanced computational approaches: pharmacophore-based 3D-QSAR, docking, and MD simulation. The selected pharmacophore—NNRRR—yielded a statistically significant 3D-QSAR model containing high confidence scores (R2 = 0.9209, Q2 = 0.8459, and RMSE = 0.3473). The contour maps—comprising hydrogen bond donor, hydrophobic, negative ionic and electron withdrawal effects—from our 3D-QSAR model identified the favorable regions crucial for maximum activity. Furthermore, the external validation of the selected model using enrichment and decoys analysis reveals a high predictive power. Also, the screening capacity of the selected model had scores of 0.94, 0.90, and 8.26 from ROC, AUC, and RIE analysis, respectively. The molecular docking of the highly active compound—C40; 4-(N-benzyl-N-(4-(4-chloro-3,5-dimethylphenoxy) phenyl) sulfamoyl)-1-hydroxy-2-naphthoate—predicted the low-energy conformational pose, and the MD simulation revealed crucial details responsible for the molecular mechanism of binding with Mcl1.
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11
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Marimuthu P, Singaravelu K. Unraveling the molecular mechanism of benzothiophene and benzofuran scaffold-merged compounds binding to anti-apoptotic Myeloid cell leukemia 1. J Biomol Struct Dyn 2018; 37:1992-2003. [DOI: 10.1080/07391102.2018.1474805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Parthiban Marimuthu
- Faculty of Science and Engineering, Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, Turku, Finland
| | - Kalaimathy Singaravelu
- Department of Information Technology, Turku Centre for Biotechnology, University of Turku, Turku, Finland
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12
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Hedir S, De Giorgi M, Fogha J, De Pascale M, Weiswald LB, Brotin E, Marekha B, Denoyelle C, Denis C, Suzanne P, Gautier F, Juin P, Ligat L, Lopez F, Carlier L, Legay R, Bureau R, Rault S, Poulain L, Oliveira Santos JSD, Voisin-Chiret AS. Structure-guided design of pyridoclax derivatives based on Noxa / Mcl-1 interaction mode. Eur J Med Chem 2018; 159:357-380. [PMID: 30308410 DOI: 10.1016/j.ejmech.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022]
Abstract
Protein-protein interactions are attractive targets because they control numerous cellular processes. In oncology, apoptosis regulating Bcl-2 family proteins are of particular interest. Apoptotic cell death is controlled via PPIs between the anti-apoptotic proteins hydrophobic groove and the pro-apoptotic proteins BH3 domain. In ovarian carcinoma, it has been previously demonstrated that Bcl-xL and Mcl-1 cooperate to protect tumor cells against apoptosis. Moreover, Mcl-1 is a key regulator of cancer cell survival and is a known resistance factor to Bcl-2/Bcl-xL pharmacological inhibitors making it an attractive therapeutic target. Here, using a structure-guided design from the oligopyridine lead Pyridoclax based on Noxa/Mcl-1 interaction we identified a new derivative, active at lower concentration as compared to Pyridoclax. This new derivative selectively binds to the Mcl-1 hydrophobic groove and releases Bak and Bim from Mcl-1 to induce cell death and sensitize cancer cells to Bcl-2/Bcl-xL targeting strategies.
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Affiliation(s)
- Siham Hedir
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Marcella De Giorgi
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Jade Fogha
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Martina De Pascale
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Louis-Bastien Weiswald
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Emilie Brotin
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Bogdan Marekha
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Christophe Denoyelle
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Camille Denis
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Peggy Suzanne
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Fabien Gautier
- Team 8 "Stress adaptation and tumor escape", CRCINA, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, Nantes, France; ICO site René Gauducheau, Boulevard Jacques Monod, Saint Herblain, 44805, France
| | - Philippe Juin
- Team 8 "Stress adaptation and tumor escape", CRCINA, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, Nantes, France; ICO site René Gauducheau, Boulevard Jacques Monod, Saint Herblain, 44805, France
| | - Laetitia Ligat
- INSERM UMR1037-Plateforme Protéomique-Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, 2 avenue Hubert Curien, 31100 Toulouse, France; Université Toulouse III-Paul Sabatier, UMR1037 CRCT, 31000 Toulouse, France
| | - Frédéric Lopez
- INSERM UMR1037-Plateforme Protéomique-Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, 2 avenue Hubert Curien, 31100 Toulouse, France; Université Toulouse III-Paul Sabatier, UMR1037 CRCT, 31000 Toulouse, France
| | - Ludovic Carlier
- Sorbonne Université, Ecole normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Rémi Legay
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Ronan Bureau
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Sylvain Rault
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Laurent Poulain
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France.
| | - Jana Sopková-de Oliveira Santos
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France.
| | - Anne Sophie Voisin-Chiret
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France.
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