1
|
Mayol GF, Defelipe LA, Arcon JP, Turjanski AG, Marti MA. Solvent Sites Improve Docking Performance of Protein–Protein Complexes and Protein–Protein Interface-Targeted Drugs. J Chem Inf Model 2022; 62:3577-3588. [DOI: 10.1021/acs.jcim.2c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gonzalo F. Mayol
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Lucas A. Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, Hamburg 22607, Germany
| | - Juan Pablo Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
- The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Adrian G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| |
Collapse
|
2
|
Single and dual target inhibitors based on Bcl-2: Promising anti-tumor agents for cancer therapy. Eur J Med Chem 2020; 201:112446. [PMID: 32563811 DOI: 10.1016/j.ejmech.2020.112446] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023]
Abstract
B-cell lymphoma-2 (Bcl-2) proteins family is an essential checkpoint in apoptosis. Extensive evidences suggested that overexpression of anti-apoptotic Bcl-2 proteins can be observed in multiple cancer cell lines and primary tumor biopsy samples, which is an important reason for tumor cells to evade apoptosis and further acquire drug resistance for chemotherapy. Hence, down-regulation of anti-apoptotic Bcl-2 proteins is effective for the treatment of cancers. In view that Bcl-2 inhibitors and some other anti-tumor agents, such as HDAC inhibitors and Mdm2 inhibitors, exert synergy effects in tumor cells, it is pointed out that dual-targeting therapies based on these targets are regarded as rational strategies to enhance the effectiveness of single target agents for cancer treatment. This review briefly introduces the apoptosis, the structure of Bcl-2 family proteins, and focuses on the current status and recent advances of Bcl-2 inhibitors and the corresponding SARs of them. Moreover, we discuss the synergisms between Bcl-2 and other anti-tumor targets, and summarize the current dual-target agents.
Collapse
|
3
|
Roscoe I, Parker M, Dong D, Li X, Li Z. Human Serum Albumin and the p53-Derived Peptide Fusion Protein Promotes Cytotoxicity Irrespective of p53 Status in Cancer Cells. Mol Pharm 2018; 15:5046-5057. [PMID: 30226785 DOI: 10.1021/acs.molpharmaceut.8b00647] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | - Xun Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji’nan, Shandong, P. R. China
| | | |
Collapse
|
4
|
Wang Z, Song T, Feng Y, Guo Z, Fan Y, Xu W, Liu L, Wang A, Zhang Z. Bcl-2/MDM2 Dual Inhibitors Based on Universal Pyramid-Like α-Helical Mimetics. J Med Chem 2016; 59:3152-62. [PMID: 26982372 DOI: 10.1021/acs.jmedchem.5b01913] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
No α-helical mimetic that exhibits Bcl-2/MDM2 dual inhibition has been rationally designed due to the different helicities of the α-helixes at their binding interfaces. Herein, we extracted a one-turn α-helix-mimicking ortho-triarene unit from o-phenylene foldamers. Linking benzamide substrates with a rotatable C-N bond, we constructed a novel semirigid pyramid-like scaffold that could support its two-turn α-helix mimicry without aromatic stacking interactions and could adopt the different dihedral angles of the key residues of p53 and BH3-only peptides. On the basis of this universal scaffold, a series of substituent groups were installed to capture the key residues of both p53TAD and BimBH3 and balance the differences of the bulks between them. Identified by FP, ITC, and NMR spectroscopy, a compound 6e (zq-1) that directly binds to Mcl-1, Bcl-2, and MDM2 with balanced submicromolar affinities was obtained. Cell-based experiments demonstrated its antitumor ability through Bcl-2/MDM2 dual inhibition simultaneously.
Collapse
Affiliation(s)
- Ziqian Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Ting Song
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Yingang Feng
- Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101, People's Republic of China
| | - Zongwei Guo
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Yudan Fan
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Wenjie Xu
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Lu Liu
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Anhui Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| |
Collapse
|
5
|
Goldar S, Khaniani MS, Derakhshan SM, Baradaran B. Molecular mechanisms of apoptosis and roles in cancer development and treatment. Asian Pac J Cancer Prev 2016; 16:2129-44. [PMID: 25824729 DOI: 10.7314/apjcp.2015.16.6.2129] [Citation(s) in RCA: 365] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Programmed cell death (PCD) or apoptosis is a mechanism which is crucial for all multicellular organisms to control cell proliferation and maintain tissue homeostasis as well as eliminate harmful or unnecessary cells from an organism. Defects in the physiological mechanisms of apoptosis may contribute to different human diseases like cancer. Identification of the mechanisms of apoptosis and its effector proteins as well as the genes responsible for apoptosis has provided a new opportunity to discover and develop novel agents that can increase the sensitivity of cancer cells to undergo apoptosis or reset their apoptotic threshold. These novel targeted therapies include those targeting anti-apoptotic Bcl-2 family members, p53, the extrinsic pathway, FLICE-inhibitory protein (c-FLIP), inhibitor of apoptosis (IAP) proteins, and the caspases. In recent years a number of these novel agents have been assessed in preclinical and clinical trials. In this review, we introduce some of the key regulatory molecules that control the apoptotic pathways, extrinsic and intrinsic death receptors, discuss how defects in apoptotic pathways contribute to cancer, and list several agents being developed to target apoptosis.
Collapse
Affiliation(s)
- Samira Goldar
- Department of Biochemistry and Clinical Labratorary, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran E-mail :
| | | | | | | |
Collapse
|
6
|
Chi SW. Structural insights into the transcription-independent apoptotic pathway of p53. BMB Rep 2014; 47:167-72. [PMID: 24499665 PMCID: PMC4163879 DOI: 10.5483/bmbrep.2014.47.3.261] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/16/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022] Open
Abstract
Reactivating the p53 pathway in tumors is an important strategy for anticancer therapy. In response to diverse cellular stresses, the tumor suppressor p53 mediates apoptosis in a transcriptionindependent and transcription-dependent manner. Although extensive studies have focused on the transcription-dependent apoptotic pathway of p53, the transcription-independent apoptotic pathway of p53 has only recently been discovered. Molecular interactions between p53 and Bcl-2 family proteins in the mitochondria play an essential role in the transcriptionindependent apoptosis of p53. This review describes the structural basis for the transcription-independent apoptotic pathway of p53 and discusses its potential application to anticancer therapy. [BMB Reports 2014; 47(3): 167-172]
Collapse
Affiliation(s)
- Seung-Wook Chi
- Medical Proteomics Research Center, KRIBB, Daejeon 305-806; Department of Bio-Analytical Science, University of Science and Technology, Daejeon 305-350, Korea
| |
Collapse
|
7
|
Lee DH, Ha JH, Kim Y, Jang M, Park SJ, Yoon HS, Kim EH, Bae KH, Park BC, Park SG, Yi GS, Chi SW. A conserved mechanism for binding of p53 DNA-binding domain and anti-apoptotic Bcl-2 family proteins. Mol Cells 2014; 37:264-9. [PMID: 24646834 PMCID: PMC3969048 DOI: 10.14348/molcells.2014.0001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 01/14/2014] [Indexed: 01/12/2023] Open
Abstract
The molecular interaction between tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins plays an essential role in the transcription-independent apoptotic pathway of p53. In this study, we investigated the binding of p53 DNA-binding domain (p53DBD) with the anti-apoptotic Bcl-2 family proteins, Bcl-w, Mcl-1, and Bcl-2, using GST pull-down assay and NMR spectroscopy. The GST pull-down assays and NMR experiments demonstrated the direct binding of the p53DBD with Bcl-w, Mcl-1, and Bcl-2. Further, NMR chemical shift perturbation data showed that Bcl-w and Mcl-1 bind to the positively charged DNA-binding surface of p53DBD. Noticeably, the refined structural models of the complexes between p53DBD and Bcl-w, Mcl-1, and Bcl-2 showed that the binding mode of p53DBD is highly conserved among the anti-apoptotic Bcl-2 family proteins. Furthermore, the chemical shift perturbations on Bcl-w, Mcl-1, and Bcl-2 induced by p53DBD binding occurred not only at the p53DBD-binding acidic region but also at the BH3 peptide-binding pocket, which suggests an allosteric conformational change similar to that observed in Bcl-XL. Taken altogether, our results revealed a structural basis for a conserved binding mechanism between p53DBD and the anti-apoptotic Bcl-2 family proteins, which shed light on to the molecular understanding of the transcription-independent apoptosis pathway of p53.
Collapse
Affiliation(s)
- Dong-Hwa Lee
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Ji-Hyang Ha
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Yul Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute for Science and Technology, Daejeon 305-701,
Korea
| | - Mi Jang
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Sung Jean Park
- College of Pharmacy, Gachon University, Incheon 406-799,
Korea
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637511,
Singapore
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Cheongwon 363-883,
Korea
| | - Kwang-Hee Bae
- Research Center for Integrated Cellulomics, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Byoung Chul Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Sung Goo Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, Korea Advanced Institute for Science and Technology, Daejeon 305-701,
Korea
| | - Seung-Wook Chi
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| |
Collapse
|
8
|
Structural basis for the conserved binding mechanism of MDM2-inhibiting peptides and anti-apoptotic Bcl-2 family proteins. Biochem Biophys Res Commun 2014; 445:120-5. [PMID: 24491548 DOI: 10.1016/j.bbrc.2014.01.130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/25/2014] [Indexed: 02/04/2023]
Abstract
The interaction between tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins serves a critical role in the transcription-independent apoptosis mechanism of p53. Our previous studies showed that an MDM2-inhibiting motif (residues 15-29) in the p53 transactivation domain (p53TAD) mediates the interaction with anti-apoptotic Bcl-2 family proteins. In this study, we provided structural models of the complexes between the MDM2-inhibiting p53TAD peptide and Mcl-1, Bcl-w, and Kaposi sarcoma-associated herpes virus (KSHV) Bcl-2 using NMR chemical shift perturbation data. The binding mode of the MDM2-inhibiting p53TAD peptide is highly conserved among the anti-apoptotic Bcl-2 family proteins despite their distinct specificities for pro-apoptotic Bcl-2 family proteins. We also identified the binding of a phage-display-derived MDM2-inhibiting peptide 12-1 to anti-apoptotic Bcl-XL protein by using NMR spectroscopy. The structural model of the Bcl-XL/12-1 peptide complex revealed that the conserved residues Phe4, Trp8, and Leu11 in the MDM2-inhibiting peptide fit into a hydrophobic cleft of Bcl-XL in a manner similar to that of pro-apoptotic Bcl-2 homology 3 (BH3) peptides. Our results shed light on the mechanism underlying dual-targeting of the FxxxWxxL-based α-helical motif to MDM2 and anti-apoptotic Bcl-2 family proteins for anticancer therapy.
Collapse
|