1
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Raines SLM, Falcinelli SD, Peterson JJ, Van Gulck E, Allard B, Kirchherr J, Vega J, Najera I, Boden D, Archin NM, Margolis DM. Nanoparticle delivery of Tat synergizes with classical latency reversal agents to express HIV antigen targets. Antimicrob Agents Chemother 2024:e0020124. [PMID: 38829049 DOI: 10.1128/aac.00201-24] [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: 02/05/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Limited cellular levels of the HIV transcriptional activator Tat are one contributor to proviral latency that might be targeted in HIV cure strategies. We recently demonstrated that lipid nanoparticles containing HIV tat mRNA induce HIV expression in primary CD4 T cells. Here, we sought to further characterize tat mRNA in the context of several benchmark latency reversal agents (LRAs), including inhibitor of apoptosis protein antagonists (IAPi), bromodomain and extra-Terminal motif inhibitors (BETi), and histone deacetylase inhibitors (HDACi). tat mRNA reversed latency across several different cell line models of HIV latency, an effect dependent on the TAR hairpin loop. Synergistic enhancement of tat mRNA activity was observed with IAPi, HDACi, and BETi, albeit to variable degrees. In primary CD4 T cells from durably suppressed people with HIV, tat mRNA profoundly increased the frequencies of elongated, multiply-spliced, and polyadenylated HIV transcripts, while having a lesser impact on TAR transcript frequencies. tat mRNAs alone resulted in variable HIV p24 protein induction across donors. However, tat mRNA in combination with IAPi, BETi, or HDACi markedly enhanced HIV RNA and protein expression without overt cytotoxicity or cellular activation. Notably, combination regimens approached or in some cases exceeded the latency reversal activity of maximal mitogenic T cell stimulation. Higher levels of tat mRNA-driven HIV p24 induction were observed in donors with larger mitogen-inducible HIV reservoirs, and expression increased with prolonged exposure time. Combination LRA strategies employing both small molecule inhibitors and Tat delivered to CD4 T cells are a promising approach to effectively target the HIV reservoir.
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Affiliation(s)
- Samuel L M Raines
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shane D Falcinelli
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jackson J Peterson
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ellen Van Gulck
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Brigitte Allard
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jerel Vega
- Arcturus Therapeutics, Science Center Drive, San Diego, California, USA
| | - Isabel Najera
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Daniel Boden
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Nancie M Archin
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M Margolis
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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2
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Liu R, Chen X, Li J, Liu X, Shu M. Discovery of novel bromodomain-containing protein 4 (BRD4-BD1) inhibitors combined with 3d-QSAR, molecular docking and molecular dynamics in silico. J Biomol Struct Dyn 2024:1-18. [PMID: 38425011 DOI: 10.1080/07391102.2024.2321249] [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: 09/28/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Bromine-containing domain protein 4 (BRD4) plays a crucial role in regulating transcription and genome stability. Selective inhibitors of BRD4-BD1 can specifically target specific bromine domains to affect cell proliferation, apoptosis, and differentiation. In this work, 43 selective benzoazepinone BRD4-BD1 inhibitors were studied using molecular simulations and three-dimensional quantitative conformation relationships (3D-QSAR). A reliable 3D-QSAR model was established based on COMFA (Q2 = 0.532, R2 = 0.981) and COMSIA (S + E + H (Q2 = 0.536, R2 = 0.979) two different analysis methods. Through 3D-QSAR model prediction and quantum chemical analysis, 15 small molecules with stronger inhibitory activity than the template compounds were constructed, and 5 new compounds with higher predictive activity and binding affinity were screened by molecular docking and ADMET methods. According to the molecular dynamics simulation, the key residues that can interact with BRD4-BD1 protein and molecular docking results are consistent, including ASN140, MET132, GLN85, MET105, ASN135 and TYR97. From the MD trajectory, we calculated and analyzed RMSD, RMSF, free binding energy, FECM, DCCM and PCA, the loop region formed by amino acids VAL45∼PRO62 showed α-helix, β-folding and clustering towards the active center with the extension of simulation time. Further optimization of the structure of active candidate compounds A6, A11, A14, and A15 will provide the necessary theoretical basis for the synthesis and activity evaluation of novel BRD4-BD1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rong Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Xiaodie Chen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Jiali Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Xingyun Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
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3
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Zhu R, Li J, Dong R, Hu Q, Chen Z, Chen X, Zhong Z, Xiang Q, Huang C, Lin B, Wu X, Zhang Y, Zhao L, Xu Y. Optimization of the synthesis of BET BD2 selective inhibitor XY153. Chem Biodivers 2024; 21:e202301584. [PMID: 38163253 DOI: 10.1002/cbdv.202301584] [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: 10/08/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
XY153 is a promising BET BD2 inhibitor with an IC50 value of 0.79 nM against BRD4 BD2. It shows 354-fold selectivity over BRD4-BD1 and 6-fold selectivity over other BET BD2 domains. However, the reported synthesis route of XY153 and its derivatives are extremely poor-yielding. After the synthesis of three key fragments, XY153 can only be obtained with a yield of 1.3 % in the original four-step reaction. In this study, we reported a three-step alternative route in the synthesis process of XY153. The reaction conditions for this route were thoroughly investigated and optimized, resulting in a significantly improved yield of 61.5 %. This efficient synthesis route establishes a robust chemical foundation for the rapid synthesis of XY153 derivatives as BET BD2 inhibitors in the near future.
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Affiliation(s)
- Run Zhu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Junhua Li
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Ruibo Dong
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, 130021, China
| | - Qingqing Hu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Zhiming Chen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoshan Chen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixin Zhong
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuping Xiang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Cen Huang
- Jiangsu S&T Exchange Center with Foreign Countries, No. 175 Longpan Road, Nanjing, 210042, China
| | - Bin Lin
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, P. R. China
| | - Xishan Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Yan Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Linxiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yong Xu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
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4
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Jiang W, Hou Q, Xu H, Yang K, Wang X, Zhang K, Zeng Y, Li W, Wang B, Luo G, Zhao X, Shen H, Xu Y, Wu X. Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia. J Med Chem 2024; 67:1513-1532. [PMID: 38175809 DOI: 10.1021/acs.jmedchem.3c02104] [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: 01/06/2024]
Abstract
Bromodomain-selective BET inhibition has emerged as a promising strategy to improve the safety profiles of pan-BET inhibitors. Herein, we report the discovery of potent phenoxyaryl pyridones as highly BD2-selective BET inhibitors. Compound 23 (IC50 = 2.9 nM) exhibited a comparable BRD4 BD2 inhibitory activity relative to 10 (IC50 = 1.0 nM) and remarkably improved selectivity over BRD4 BD1 (23: 2583-fold; 10: 344-fold). This lead compound significantly inhibited the proliferation of acute myeloid leukemia (AML) cell lines through induction of G0/G1 arrest and apoptosis in vitro. Excellent in vivo antitumor efficacy with 23 was achieved in an MV;411 mouse xenograft model. Pleasingly, compound 23 (hERG IC50 > 30 μM) mitigated the inhibition of the human ether-à-go-go-related gene (hERG) ion channel compared with 10 (hERG IC50 = 2.8 μM). This work provides a promising BD2-selective lead for the development of more effective and safe BET inhibitors as anticancer agents.
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Affiliation(s)
- Wenhua Jiang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Qiangqiang Hou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Kexin Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaohui Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Kuojun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Zeng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Wenqiang Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Bingrui Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Guangmei Luo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaofan Zhao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hui Shen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yong Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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5
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Yu S, Zhang Y, Yang J, Xu H, Lan S, Zhao B, Luo M, Ma X, Zhang H, Wang S, Shen H, Zhang Y, Xu Y, Li R. Discovery of (R)-4-(8-methoxy-2-methyl-1-(1-phenylethy)-1H-imidazo[4,5-c]quinnolin-7-yl)-3,5-dimethylisoxazole as a potent and selective BET inhibitor for treatment of acute myeloid leukemia (AML) guided by FEP calculation. Eur J Med Chem 2024; 263:115924. [PMID: 37992518 DOI: 10.1016/j.ejmech.2023.115924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023]
Abstract
The functions of the bromodomain and extra terminal (BET) family of proteins have been proved to be involved in various diseases, particularly the acute myeloid leukemia (AML). In this work, guided by free energy perturbation (FEP) calculation, a methyl group was selected to be attached to the 1H-imidazo[4,5-c]quinoline skeleton, and a series of congeneric compounds were synthesized. Among them, compound 10 demonstrated outstanding activity against BRD4 BD1 with an IC50 value of 1.9 nM and exhibited remarkable antiproliferative effects against MV4-11 cells. The X-ray cocrystal structure proved that 10 occupied the acetylated lysine (KAc) binding cavity and the WPF shelf of BRD4 BD1. Additionally, 10 displayed high selectivity towards BET family members, effectively inhibiting the growth of AML cells, promoting apoptosis, and arresting the cell cycle at the G0/G1 phase. Further mechanistic studies demonstrated that compound 10 could suppress the expression of c-Myc and CDK6 while enhancing the expression of P21, PARP, and cleaved PARP. Moreover, 10 exhibited remarkable pharmacokinetic properties and significant antitumor efficacy in vivo. Therefore, compound 10 may represent a new, potent and selective BET bromodomain inhibitor for the development of therapeutics to treat AML.
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Affiliation(s)
- Su Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Zhang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Suke Lan
- College of Chemistry & Environment Protection Engineering, Southwest Minzu University, Chengdu, 610041, China
| | - Binyan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meng Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Ma
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongjia Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shirui Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hui Shen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Yan Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China
| | - Yong Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou, 510530, China.
| | - Rui Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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6
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Gajjela BK, Zhou MM. Bromodomain inhibitors and therapeutic applications. Curr Opin Chem Biol 2023; 75:102323. [PMID: 37207401 PMCID: PMC10524616 DOI: 10.1016/j.cbpa.2023.102323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023]
Abstract
The bromodomain acts to recognize acetylated lysine in histones and transcription proteins and plays a fundamental role in chromatin-based cellular processes including gene transcription and chromatin remodeling. Many bromodomain proteins, particularly the bromodomain and extra terminal domain (BET) protein BRD4 have been implicated in cancers and inflammatory disorders and recognized as attractive drug targets. Although clinical studies of many BET bromodomain inhibitors have made substantial progress toward harnessing the therapeutic potential of targeting the bromodomain proteins, the development of this new class of epigenetic drugs is met with challenges, especially on-target dose-limiting toxicity. In this review, we highlight the current development of new-generation small molecule inhibitors for the BET and non-BET bromodomain proteins and discuss the research strategies used to target different bromodomain proteins for a wide array of human diseases including cancers and inflammatory disorders.
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Affiliation(s)
- Bharath Kumar Gajjela
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States.
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7
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Feng C, Zhang L, Chang X, Qin D, Zhang T. Regulation of post-translational modification of PD-L1 and advances in tumor immunotherapy. Front Immunol 2023; 14:1230135. [PMID: 37554324 PMCID: PMC10405826 DOI: 10.3389/fimmu.2023.1230135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
The immune checkpoint molecules programmed cell death receptor 1 (PD-1) and programmed death ligand 1 (PD-L1) are one of the most promising targets for tumor immunotherapy. PD-L1 is overexpressed on the surface of tumor cells and inhibits T cell activation upon binding to PD⁃1 on the surface of T cells, resulting in tumor immune escape. The therapeutic strategy of targeting PD-1/PD-L1 involves blocking this binding and restoring the tumor-killing effect of immune cells. However, in clinical settings, a relatively low proportion of cancer patients have responded well to PD-1/PD-L1 blockade, and clinical outcomes have reached a bottleneck and no substantial progress has been made. In recent years, PD-L1 post-translation modifications (PTMs) have gradually become a hot topic in the field of PD-L1 research, which will provide new insights to improve the efficacy of current anti-PD-1/PD-L1 therapies. Here, we summarized and discussed multiple PTMs of PD-L1, including glycosylation, ubiquitination, phosphorylation, acetylation and palmitoylation, with a major emphasis on mechanism-based therapeutic strategies (including relevant enzymes and targets that are already in clinical use and that may become drugs in the future). We also summarized the latest research progress of PTMs of PD-L1/PD-1 in regulating immunotherapy. The review provided novel strategies and directions for tumor immunotherapy research based on the PTMs of PD-L1/PD-1.
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Affiliation(s)
- Chong Feng
- Thoracic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Lening Zhang
- Thoracic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Xin Chang
- Ophthalmology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Dongliang Qin
- Thoracic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Tao Zhang
- Gastrointestinal and Colorectal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
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Abstract
An analysis of 156 published clinical candidates from the Journal of Medicinal Chemistry between 2018 and 2021 was conducted to identify lead generation strategies most frequently employed leading to drug candidates. As in a previous publication, the most frequent lead generation strategies resulting in clinical candidates were from known compounds (59%) followed by random screening approaches (21%). The remainder of the approaches included directed screening, fragment screening, DNA-encoded library screening (DEL), and virtual screening. An analysis of similarity was also conducted based on Tanimoto-MCS and revealed most clinical candidates were distant from their original hits; however, most shared a key pharmacophore that translated from hit-to-clinical candidate. An examination of frequency of oxygen, nitrogen, fluorine, chlorine, and sulfur incorporation in clinical candidates was also conducted. The three most similar and least similar hit-to-clinical pairs from random screening were examined to provide perspective on changes that occur that lead to successful clinical candidates.
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Affiliation(s)
- Dean G Brown
- Jnana Therapeutics, One Design Center Pl Suite 19-400, Boston, Massachusetts 02210, United States
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9
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Pan Z, Zhao Y, Wang X, Xie X, Liu M, Zhang K, Wang L, Bai D, Foster LJ, Shu R, He G. Targeting bromodomain-containing proteins: research advances of drug discovery. MOLECULAR BIOMEDICINE 2023; 4:13. [PMID: 37142850 PMCID: PMC10159834 DOI: 10.1186/s43556-023-00127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/02/2023] [Indexed: 05/06/2023] Open
Abstract
Bromodomain (BD) is an evolutionarily conserved protein module found in 46 different BD-containing proteins (BCPs). BD acts as a specific reader for acetylated lysine residues (KAc) and serves an essential role in transcriptional regulation, chromatin remodeling, DNA damage repair, and cell proliferation. On the other hand, BCPs have been shown to be involved in the pathogenesis of a variety of diseases, including cancers, inflammation, cardiovascular diseases, and viral infections. Over the past decade, researchers have brought new therapeutic strategies to relevant diseases by inhibiting the activity or downregulating the expression of BCPs to interfere with the transcription of pathogenic genes. An increasing number of potent inhibitors and degraders of BCPs have been developed, some of which are already in clinical trials. In this paper, we provide a comprehensive review of recent advances in the study of drugs that inhibit or down-regulate BCPs, focusing on the development history, molecular structure, biological activity, interaction with BCPs and therapeutic potentials of these drugs. In addition, we discuss current challenges, issues to be addressed and future research directions for the development of BCPs inhibitors. Lessons learned from the successful or unsuccessful development experiences of these inhibitors or degraders will facilitate the further development of efficient, selective and less toxic inhibitors of BCPs and eventually achieve drug application in the clinic.
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Affiliation(s)
- Zhaoping Pan
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuxi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Xie
- College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Mingxia Liu
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyao Zhang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lian Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Rui Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Gu He
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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10
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Chauhan J, Yoshioka M, Pogash S, Strovel JW, Fletcher S. Discovery and anti-tumor activity of 4-(benzylamino)-6-(3,5-dimethylisoxazol-4-yl)quinoline-2(1H)-one (CG13250), a potent, selective and orally bioavailable BET bromodomain inhibitor. Bioorg Med Chem Lett 2023; 86:129220. [PMID: 36905966 DOI: 10.1016/j.bmcl.2023.129220] [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: 01/14/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
The bromodomain and extra-terminal domain (BET) proteins are epigenetic readers involved in the regulation of gene transcription. Inhibitors of the BET proteins, in particular BRD4, have demonstrated anti-tumour activities and efficacies in clinical trials. Herein, we describe the discovery of potent and selective inhibitors of BRD4, and demonstrate that the lead compound CG13250 is orally bioavailable and efficacious in a mouse xenograft model of leukemia.
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Affiliation(s)
- Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA
| | - Makoto Yoshioka
- ConverGene LLC, 4800 Montgomery Lane, c/o Dreyfuss 10th Floor, Bethesda, MD 20814, USA
| | - Sarah Pogash
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA
| | - Jeffrey W Strovel
- ConverGene LLC, 4800 Montgomery Lane, c/o Dreyfuss 10th Floor, Bethesda, MD 20814, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N Pine Street, Baltimore, MD 21201, USA; University of Maryland Greenebaum Cancer Center, Baltimore, MD 21201, USA.
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11
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Humphreys PG, Anderson NA, Bamborough P, Baxter A, Chung CW, Cookson R, Craggs PD, Dalton T, Fournier JCL, Gordon LJ, Gray HF, Gray MW, Gregory R, Hirst DJ, Jamieson C, Jones KL, Kessedjian H, Lugo D, McGonagle G, Patel VK, Patten C, Poole DL, Prinjha RK, Ramirez-Molina C, Rioja I, Seal G, Stafford KAJ, Shah RR, Tape D, Theodoulou NH, Tomlinson L, Ukuser S, Wall ID, Wellaway N, White G. Identification and Optimization of a Ligand-Efficient Benzoazepinone Bromodomain and Extra Terminal (BET) Family Acetyl-Lysine Mimetic into the Oral Candidate Quality Molecule I-BET432. J Med Chem 2022; 65:15174-15207. [DOI: 10.1021/acs.jmedchem.2c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Niall A. Anderson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Bamborough
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew Baxter
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Chun-wa Chung
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rosa Cookson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Peter D. Craggs
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Toryn Dalton
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laurie J. Gordon
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Heather F. Gray
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew W. Gray
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Richard Gregory
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David J. Hirst
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Craig Jamieson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | | | | | - David Lugo
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Grant McGonagle
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | - Darren L. Poole
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rab K. Prinjha
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Inmaculada Rioja
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gail Seal
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Rishi R. Shah
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Daniel Tape
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laura Tomlinson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sabri Ukuser
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D. Wall
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Natalie Wellaway
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gemma White
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
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12
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Biol 2022; 17:2673-2678. [PMID: 36268572 DOI: 10.1021/acschembio.2c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Pharmacol Transl Sci 2022; 5:829-834. [PMID: 36268124 PMCID: PMC9578134 DOI: 10.1021/acsptsci.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/28/2022]
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14
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Infect Dis 2022; 8:1975-1980. [PMID: 36073808 DOI: 10.1021/acsinfecdis.2c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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15
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Med Chem Lett 2022; 13:1524-1529. [PMID: 36262399 PMCID: PMC9575161 DOI: 10.1021/acsmedchemlett.2c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/30/2022] Open
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16
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. J Med Chem 2022; 65:11894-11899. [PMID: 36073827 DOI: 10.1021/acs.jmedchem.2c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Neurosci 2022. [PMID: 36067366 DOI: 10.1021/acschemneuro.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Chen X, Meng F, Zhang J, Zhang Z, Ye X, Zhang W, Tong Y, Ji X, Xu R, Xu XL, You QD, Jiang ZY. Discovery of 2-((2-methylbenzyl)thio)-6-oxo-4-(3,4,5-trimethoxyphenyl)-1,6-dihydropyrimidine-5-carbonitrile as a novel and effective bromodomain and extra-terminal (BET) inhibitor for the treatment of sepsis. Eur J Med Chem 2022; 238:114423. [DOI: 10.1016/j.ejmech.2022.114423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
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19
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Schwalm MP, Knapp S. BET bromodomain inhibitors. Curr Opin Chem Biol 2022; 68:102148. [DOI: 10.1016/j.cbpa.2022.102148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/28/2022]
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20
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Guest E, Cervantes LF, Pickett SD, Brooks CL, Hirst JD. Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. J Chem Inf Model 2022; 62:1458-1470. [PMID: 35258972 PMCID: PMC9098113 DOI: 10.1021/acs.jcim.1c01229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Accurate and rapid predictions of the binding affinity of a compound to a target are one of the ultimate goals of computer aided drug design. Alchemical approaches to free energy estimations follow the path from an initial state of the system to the final state through alchemical changes of the energy function during a molecular dynamics simulation. Herein, we explore the accuracy and efficiency of two such techniques: relative free energy perturbation (FEP) and multisite lambda dynamics (MSλD). These are applied to a series of inhibitors for the bromodomain-containing protein 4 (BRD4). We demonstrate a procedure for obtaining accurate relative binding free energies using MSλD when dealing with a change in the net charge of the ligand. This resulted in an impressive comparison with experiment, with an average difference of 0.4 ± 0.4 kcal mol-1. In a benchmarking study for the relative FEP calculations, we found that using 20 lambda windows with 0.5 ns of equilibration and 1 ns of data collection for each window gave the optimal compromise between accuracy and speed. Overall, relative FEP and MSλD predicted binding free energies with comparable accuracy, an average of 0.6 kcal mol-1 for each method. However, MSλD makes predictions for a larger molecular space over a much shorter time scale than relative FEP, with MSλD requiring a factor of 18 times less simulation time for the entire molecule space.
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Affiliation(s)
- Ellen
E. Guest
- School
of Chemistry, University of Nottingham,
University Park, Nottingham NG7 2RD, U.K.
| | - Luis F. Cervantes
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen D. Pickett
- Computational
Chemistry, GlaxoSmithKline RD Pharmaceuticals, Stevenage SG1 2NY, U.K.
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jonathan D. Hirst
- School
of Chemistry, University of Nottingham,
University Park, Nottingham NG7 2RD, U.K.,
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21
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Li J, Zhang C, Xu H, Wang C, Dong R, Shen H, Zhuang X, Chen X, Li Q, Lu J, Zhang M, Wu X, Loomes KM, Zhou Y, Zhang Y, Liu J, Xu Y. Structure-Based Discovery and Optimization of Furo[3,2- c]pyridin-4(5 H)-one Derivatives as Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (BET) Inhibitors. J Med Chem 2022; 65:5760-5799. [PMID: 35333526 DOI: 10.1021/acs.jmedchem.2c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pan-bromodomain and extra terminal (Pan-BET) inhibitors show profound efficacy but exhibit pharmacology-driven toxicities in clinical trials. The development of domain-selective BET inhibitors to separate efficacy and toxicity is urgently needed. Herein, we report a series of furo[3,2-c]pyridin-4(5H)-one derivatives as novel BD2-selective BET inhibitors. The representative compound 8l (XY153) potently bound to BRD4 BD2 with an half-maximum inhibitory concentration (IC50) value of 0.79 nM and displayed 354-fold selectivity over BRD4 BD1. Besides, 8l exhibited 6-fold BRD4 BD2 domain selectivity over other BET BD2 domains. Compound 8l displayed potent antiproliferative activity against multiple tumor cell lines, especially MV4-11 (IC50 = 0.55 nM), while showing weak cytotoxicity against the normal lung fibroblast cell line. It highlights the safety profile of this series of BD2 inhibitors. 8l also demonstrated good metabolic stability in vitro. These data indicate that 8l may serve as a new and valuable lead compound for the development of potential therapeutics against acute myeloid leukemia (AML).
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Affiliation(s)
- Junhua Li
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Cheng Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chao Wang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Ruibo Dong
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Hui Shen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Xiaoxi Zhuang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Xiaoshan Chen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Qiu Li
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Jibu Lu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Maofeng Zhang
- College of Pharmacy, Taizhou Polytechnic College, Taizhou 225300, China
| | - Xishan Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Kerry M Loomes
- School of Biological Sciences & Maurice Wilkins Centre, University of Auckland, Auckland 1010, New Zealand
| | - Yulai Zhou
- School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Yan Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Jinsong Liu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yong Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.,Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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22
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Chen J, Tang P, Wang Y, Wang J, Yang C, Li Y, Yang G, Wu F, Zhang J, Ouyang L. Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and Development. J Med Chem 2022; 65:5184-5211. [PMID: 35324195 DOI: 10.1021/acs.jmedchem.1c01835] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Blocking the interactions between bromodomain and extraterminal (BET) proteins and acetylated lysines of histones by small molecules has important implications for the treatment of cancers and other diseases. Many pan-BET inhibitors have shown satisfactory results in clinical trials, but their potential for poor tolerability and toxicity persist. However, recently reported studies illustrate that some BET bromodomain (BET-BD1 or BET-BD2)-selective inhibitors have advantage over pan-inhibitors, including reduced toxicity concerns. Furthermore, some selective BET inhibitors have similar or even better therapeutic efficacy in inflammatory diseases or cancers. Therefore, the development of selective BET inhibitors has become a hot spot for medicinal chemists. Here, we summarize the known selective BET-BD1 and BET-BD2 inhibitors and review the methods for enhancing the selectivity and potency of these inhibitors based on their different modes of interactions with BET-BD1 or BET-BD2. Finally, we discuss prospective strategies that selectively target the bromodomains of BET proteins.
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Affiliation(s)
- Juncheng Chen
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Pan Tang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxi Wang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chengcan Yang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yang Li
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Gaoxia Yang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fengbo Wu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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23
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Kaitoh K, Yamanishi Y. Scaffold-Retained Structure Generator to Exhaustively Create Molecules in an Arbitrary Chemical Space. J Chem Inf Model 2022; 62:2212-2225. [DOI: 10.1021/acs.jcim.1c01130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
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24
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Humphreys PG, Atkinson SJ, Bamborough P, Bit RA, Chung CW, Craggs PD, Cutler L, Davis R, Ferrie A, Gong G, Gordon LJ, Gray M, Harrison LA, Hayhow TG, Haynes A, Henley N, Hirst DJ, Holyer ID, Lindon MJ, Lovatt C, Lugo D, McCleary S, Molnar J, Osmani Q, Patten C, Preston A, Rioja I, Seal JT, Smithers N, Sun F, Tang D, Taylor S, Theodoulou NH, Thomas C, Watson RJ, Wellaway CR, Zhu L, Tomkinson NCO, Prinjha RK. Design, Synthesis, and Characterization of I-BET567, a Pan-Bromodomain and Extra Terminal (BET) Bromodomain Oral Candidate. J Med Chem 2022; 65:2262-2287. [PMID: 34995458 DOI: 10.1021/acs.jmedchem.1c01747] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Through regulation of the epigenome, the bromodomain and extra terminal (BET) family of proteins represent important therapeutic targets for the treatment of human disease. Through mimicking the endogenous N-acetyl-lysine group and disrupting the protein-protein interaction between histone tails and the bromodomain, several small molecule pan-BET inhibitors have progressed to oncology clinical trials. This work describes the medicinal chemistry strategy and execution to deliver an orally bioavailable tetrahydroquinoline (THQ) pan-BET candidate. Critical to the success of this endeavor was a potency agnostic analysis of a data set of 1999 THQ BET inhibitors within the GSK collection which enabled identification of appropriate lipophilicity space to deliver compounds with a higher probability of desired oral candidate quality properties. SAR knowledge was leveraged via Free-Wilson analysis within this design space to identify a small group of targets which ultimately delivered I-BET567 (27), a pan-BET candidate inhibitor that demonstrated efficacy in mouse models of oncology and inflammation.
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Affiliation(s)
| | | | - Paul Bamborough
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Rino A Bit
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter D Craggs
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Leanne Cutler
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Rob Davis
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Alan Ferrie
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - GangLi Gong
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Laurie J Gordon
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Matthew Gray
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Lee A Harrison
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Thomas G Hayhow
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Andrea Haynes
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Nick Henley
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David J Hirst
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Ian D Holyer
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Matthew J Lindon
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Cerys Lovatt
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David Lugo
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Scott McCleary
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Judit Molnar
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Qendresa Osmani
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chris Patten
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Alex Preston
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Inmaculada Rioja
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Jonathan T Seal
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Nicholas Smithers
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Fenglai Sun
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Dalin Tang
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Simon Taylor
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Natalie H Theodoulou
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom.,WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Clare Thomas
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Robert J Watson
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | | | - Linrong Zhu
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Rab K Prinjha
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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