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Liu M, Zhang K, Li Q, Pang H, Pan Z, Huang X, Wang L, Wu F, He G. Recent Advances on Small-Molecule Bromodomain-Containing Histone Acetyltransferase Inhibitors. J Med Chem 2023; 66:1678-1699. [PMID: 36695774 DOI: 10.1021/acs.jmedchem.2c01638] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In recent years, substantial research has been conducted on molecular mechanisms and inhibitors targeting bromodomains (BRDs) and extra-terminal (BET) family proteins. On this basis, non-BET BRD is gradually becoming a research hot spot. BRDs are abundant in histone acetyltransferase (HAT)-associated activating transcription factors, and BRD-containing HATs have been linked to cancer, inflammation, and viral replication. Therefore, the development of BRD-containing HATs as chemical probes is useful for understanding the specific biological roles of BRDs in diseases and drug discovery. Several types of BRD-containing HATs, including CBP/P300, PCAF/GCN5, and TAF1, are discussed in this context in terms of their structures, functions, and small-molecule inhibitors. Additionally, progress in BRD inhibitors/chemical probes and proteolysis targeting chimeras in terms of drug design, biological activity, and disease application are summarized. These findings provide insights into the development of BRD inhibitors as potential drug candidates for various diseases.
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Affiliation(s)
- Mingxia Liu
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Kaiyao Zhang
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qinjue Li
- West China School of Public Health, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Haiying Pang
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhaoping Pan
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Xiaowei Huang
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Lian Wang
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Fengbo Wu
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Gu He
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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2
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Zhou S, Zou H, Wang Y, Lo GV, Yuan S. Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6667-6678. [PMID: 35993568 DOI: 10.1021/acs.jcim.2c00447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The dissociation of the transthyretin (TTR) tetramer into a monomer is closely related to various TTR amyloidoses in humans. While the tetramer dissociation has been reported to be the rate-limiting step for TTR aggregation, few details are known about the mechanism. Here, molecular dynamics (MD) simulations were performed by combining conventional MD and biased metadynamics to investigate the mechanism for the wild-type (WT) and mutant (T119M) structures. Both were found to have a great deal in common. Conventional MD simulations reveal that interfacial hydrophobic interactions contribute significantly to stabilize the tetramer. Interfacial residues including L17, V20, L110, and V121 with close contacts form a hydrophobic channel. Metadynamics simulations indicate that the mouth opening of the hydrophobic channel is the first and the most difficult step for dissociation. Interactions of V20 between opposing dimers lock four monomers into the tetramer, and disruption of the interactions is found to be involved in the final step. During the dissociation, an increasing extent of solvation was observed by calculating the radial distribution functions of water around interfacial hydrophobic residues, suggesting that water plays a role in driving the tetramer dissociation. Moreover, compared to T119, residue M119 has a longer side chain that extends into the hydrophobic channel, making solvation more difficult, consistent with a higher energy barrier for dissociation of the T119M tetramer. This result provides a good explanation for the protective role of the T119M mutation. Overall, this study can provide atomic-level insights to better understand the pathogenesis of TTR amyloidosis and guide rational drug design in the future.
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Affiliation(s)
- Shuangyan Zhou
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Huizhen Zou
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yu Wang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Glenn V Lo
- Department of Chemistry and Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, Louisiana 70310, United States
| | - Shuai Yuan
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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Zhou X, Shi M, Wang X, Xu D. Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ Protein via Well-Tempered Metadynamics. Front Chem 2022; 10:921695. [PMID: 35646830 PMCID: PMC9133541 DOI: 10.3389/fchem.2022.921695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Using supramolecules for protein function regulation is an effective strategy in chemical biology and drug discovery. However, due to the presence of multiple binding sites on protein surfaces, protein function regulation via selective binding of supramolecules is challenging. Recently, the functions of 14-3-3 proteins, which play an important role in regulating intracellular signaling pathways via protein–protein interactions, have been modulated using a supramolecular tweezer, CLR01. However, the binding mechanisms of the tweezer molecule to 14-3-3 proteins are still unclear, which has hindered the development of novel supramolecules targeting the 14-3-3 proteins. Herein, the binding mechanisms of the tweezer to the lysine residues on 14-3-3σ (an isoform in 14-3-3 protein family) were explored by well-tempered metadynamics. The results indicated that the inclusion complex formed between the protein and supramolecule is affected by both kinetic and thermodynamic factors. In particular, simulations confirmed that K214 could form a strong binding complex with the tweezer; the binding free energy was calculated to be −10.5 kcal·mol−1 with an association barrier height of 3.7 kcal·mol−1. In addition, several other lysine residues on 14-3-3σ were identified as being well-recognized by the tweezer, which agrees with experimental results, although only K214/tweezer was co-crystallized. Additionally, the binding mechanisms of the tweezer to all lysine residues were analyzed by exploring the representative conformations during the formation of the inclusion complex. This could be helpful for the development of new inhibitors based on tweezers with more functions against 14-3-3 proteins via modifications of CLR01. We also believe that the proposed computational strategies can be extended to understand the binding mechanism of multi-binding sites proteins with supramolecules and will, thus, be useful toward drug design.
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Affiliation(s)
- Xin Zhou
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
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4
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Wang X, Zhang B, Li X, Liu X, Wang S, Xie Y, Pi J, Yang Z, Li J, Jia Q, Zhang Y. Mechanisms Underlying Gastrodin Alleviating Vincristine-Induced Peripheral Neuropathic Pain. Front Pharmacol 2022; 12:744663. [PMID: 34975470 PMCID: PMC8716817 DOI: 10.3389/fphar.2021.744663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022] Open
Abstract
Gastrodin (GAS) is the main bioactive ingredient of Gastrodia, a famous Chinese herbal medicine widely used as an analgesic, but the underlying analgesic mechanism is still unclear. In this study, we first observed the effects of GAS on the vincristine-induced peripheral neuropathic pain by alleviating the mechanical and thermal hyperalgesia. Further studies showed that GAS could inhibit the current density of NaV1.7 and NaV1.8 channels and accelerate the inactivation process of NaV1.7 and NaV1.8 channel, thereby inhibiting the hyperexcitability of neurons. Additionally, GAS could significantly reduce the over-expression of NaV1.7 and NaV1.8 on DRG neurons from vincristine-treated rats according to the analysis of Western blot and immunofluorescence results. Moreover, based on the molecular docking and molecular dynamic simulation, the binding free energies of the constructed systems were calculated, and the binding sites of GAS on the sodium channels (NaV1.7 and NaV1.8) were preliminarily determined. This study has shown that modulation of NaV1.7 and NaV1.8 sodium channels by GAS contributing to the alleviation of vincristine-induced peripheral neuropathic pain, thus expanding the understanding of complex action of GAS as a neuromodulator.
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Affiliation(s)
- Xiangyu Wang
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Boxuan Zhang
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Xuedong Li
- School of Pharmacy, Hebei Medical University, Shijiazhuang, China.,Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, China
| | - Xingang Liu
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Songsong Wang
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Yuan Xie
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Jialing Pi
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Zhiyuan Yang
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Jincan Li
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Qingzhong Jia
- Departments of Pharmacology, Hebei Medical University, Shijiazhuang, China.,School of Pharmacy, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Innovative Drug Research and Evaluation of Hebei Province, Shijiazhuang, China.,Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, China
| | - Yang Zhang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, China.,Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, China
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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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6
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Chen Y, Shao X, Zhao X, Ji Y, Liu X, Li P, Zhang M, Wang Q. Targeting protein arginine methyltransferase 5 in cancers: Roles, inhibitors and mechanisms. Biomed Pharmacother 2021; 144:112252. [PMID: 34619493 DOI: 10.1016/j.biopha.2021.112252] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 12/31/2022] Open
Abstract
The protein arginine methyltransferase 5 (PRMT5) as the major type II arginine methyltransferase catalyzes the mono- and symmetric dimethylation of arginine residues in both histone and non-histone proteins. Recently, increasing evidence has demonstrated that PRMT5 plays an indispensable role in the occurrence and development of various human cancers by promoting the cell proliferation, invasion, and migration. It has become a promising and valuable target in the cancer epigenetic therapy. This review is to summarize the clinical significance of PRMT5 in the cancers such as lung cancer, breast cancer and colorectal cancer, and the drug discovery targeting PRMT5. Importantly, the existing PRMT5 inhibitors representing different molecular mechanisms, and their pharmacological effect, mechanism of action and biological affinity are analyzed. Clinical status, current problems and future perspective of PRMT5 inhibitors for the treatment of cancers are also discussed, all of which provides crucial help for the future discovery of PRMT5 targeted drugs for cancer treatment.
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Affiliation(s)
- Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Xiangge Zhao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Yuan Ji
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Xiaorong Liu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Peixuan Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Mingyu Zhang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China
| | - Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China; Engineering Technology Research Center for the Utilization of Functional Components of Organic Natural Products, Dalian University, Dalian 116622, China.
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7
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Wang Q, Zhang Q, Leung ELH, Chen Y, Yao X. Exploring the thermodynamic, kinetic and inhibitory mechanisms of 5-iTU targeting mitotic kinase haspin by integrated molecular dynamics. Phys Chem Chem Phys 2021; 23:18404-18413. [PMID: 34612381 DOI: 10.1039/d1cp02783b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
As a human mitotic kinase, haspin is considered as a promising target for various diseases including cancers. However, no inhibitors targeting haspin have entered clinical trials presently. 5-iTU (5-iodotubercidin) is a useful and classical chemical probe for the investigation of haspin activity, but its inhibitory mechanism remains unclear. In this study, integrated molecular dynamics (MD) of conventional MD, extended adaptive biasing force (eABF), random acceleration MD and well-tempered metadynamics were applied to investigate the thermodynamic and kinetic features of 5-iTU and three derivatives targeting haspin. To emphasize the importance of gatekeeper Phe605, two haspin mutants (F605Y and F605T) were also built. The results showed that the binding affinity of 5-iTU and haspin was highest in all wild type (WT) systems, relying on the strong halogen aromatic π interaction between 5-iTU and gatekeeper Phe605. Gatekeeper mutations, because of damage to this interaction, led to the rearrangement of water distributions at the binding site and the decrease of 5-iTU residence times. Additionally, compared with the smaller 5-fTU, 5-iTU dissociated from WT haspin with more difficulty through distinct unbinding pathways. These findings will provide crucial guidance for the design and development of novel haspin inhibitors and the rational modification of existing inhibitors.
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Affiliation(s)
- Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China.
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8
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Wang Q, Shao X, Leung ELH, Chen Y, Yao X. Selectively targeting individual bromodomain: Drug discovery and molecular mechanisms. Pharmacol Res 2021; 172:105804. [PMID: 34450309 DOI: 10.1016/j.phrs.2021.105804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Bromodomain-containing proteins include bromodomain and extra-terminal (BET) and non-BET families. Due to the conserved bromodomain (BD) module between BD-containing proteins, and especially BETs with each member having two BDs (BD1 and BD2), the high degree of structural similarity makes BD-selective inhibitors much difficult to be designed. However, increasing evidences emphasized that individual BDs had distinct functions and different cellular phenotypes after pharmacological inhibition, and selectively targeting one of the BDs could result in a different efficacy and tolerability profile. This review is to summarize the pioneering progress of BD-selective inhibitors targeting BET and non-BET proteins, focusing on their structural features, biological activity, therapeutic application and experimental/theoretical mechanisms. The present proteolysis targeting chimeras (PROTAC) degraders targeting BDs, and clinical status of BD-selective inhibitors were also analyzed, providing a new insight into future direction of bromodomain-selective drug discovery.
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Affiliation(s)
- Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Elaine Lai Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China
| | - Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China.
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China.
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Wu S, Wang L, Zhang L, Xu X, Zhao J. Molecular dynamics insights into binding selectivity of inhibitors toward BRD4 and CBP. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Wu SL, Zhao J, Sun HB, Li HY, Yin YY, Zhang LL. Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:221-246. [PMID: 33661069 DOI: 10.1080/1062936x.2021.1887351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
CREB binding protein (CBP) and its paralog E1A binding protein (p300) are related to the development of inflammatory diseases, cancers and other diseases, and have been potential targets for the treatment of human diseases. In this work, interaction mechanism of three small molecules E3T, E3H, and E3B with CBP was investigated by employing molecular dynamics (MD) simulations, principal component analysis (PCA), and molecular mechanics/generalized born surface area (MM-GBSA) method. The results indicate that inhibitor bindings cause the changes of movement modes and structural flexibility of CBP, and van der Waals interactions mostly drive associations of inhibitors with CBP. In the meantime, the results based on inhibitor-residue interactions not only show that eight residues of CBP can strongly interact with E3T, E3H and E3B but also verify that the CH-CH, CH-π, and π-π interactions are responsible for vital contributions in associations of E3T, E3H and E3B with CBP. In addition, the H-O radial distribution functions (RDFs) were computed to assess the stability of hydrogen bonding interactions between inhibitors and CBP, and the obtained information identifies several key hydrogen bonds playing key roles in bindings of E3T, E3H and E3B to CBP. Potential new inhibitors have been proposed.
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Affiliation(s)
- S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H Y Li
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
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11
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Bi X, Chen Y, Sun Z, Lu W, Xu P, Lu T, Ding H, Zhang N, Jiang H, Chen K, Zhou B, Luo C. Structure-based drug optimization and biological evaluation of tetrahydroquinolin derivatives as selective and potent CBP bromodomain inhibitors. Bioorg Med Chem Lett 2020; 30:127480. [PMID: 32882416 DOI: 10.1016/j.bmcl.2020.127480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/22/2020] [Accepted: 08/06/2020] [Indexed: 11/26/2022]
Abstract
CBP bromodomain could recognize acetylated lysine and function as transcription coactivator to regulate transcription and downstream gene expression. Furthermore, CBP has been shown to be related to many human malignancies including acute myeloid leukemia. Herein, we identified DC-CPin734 as a potent CBP bromodomain inhibitor with a TR-FRET IC50 value of 19.5 ± 1.1 nM and over 400-fold of selectivity against BRD4 bromodomains through structure based rational drug design guided iterative chemical modification endeavoring to discover optimal tail-substituted tetrahydroquinolin derivatives. Moreover, DC-CPin734 showed potent inhibitory activity to AML cell line MV4-11 with an IC50 value of 0.55 ± 0.04 μM, and its cellular on-target effects were further evidenced by c-Myc downregulation results. In summary, DC-CPin734 showing good potency, selectivity and anti AML activity could serve as a potent and selective in vitro and in vivo probe of CBP bromodomain and a promising lead compound for future drug development.
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Affiliation(s)
- Xiaoyang Bi
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yu Chen
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhongya Sun
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Life and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Wenchao Lu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Pan Xu
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Tian Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Hong Ding
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
| | - Bing Zhou
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.
| | - Cheng Luo
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
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12
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Chen Y, Bi X, Zhang F, Sun Z, Xu P, Jiang H, Lu W, Lu T, Ding H, Zhang N, Jiang H, Chen K, Zhou B, Luo C. Design, synthesis, and biological evaluation of tetrahydroquinolin derivatives as potent inhibitors of CBP bromodomain. Bioorg Chem 2020; 101:103991. [PMID: 32559581 DOI: 10.1016/j.bioorg.2020.103991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
CREB-binding protein (CBP) is a large multi-domain protein containing a HAT domain catalyzing transacetylation and a bromodomain responsible for acetylated lysine recognition. CBPs could act as transcription co-activators to regulate gene expression and have been shown to play a significant role in the development and progression of many cancers. Herein, through in silico screening two hit compounds with tetrahydroquinolin methyl carbamate scaffold were discovered, among which DC-CPin7 showed an in vitro inhibitory activity with the TR-FRET IC50 value of 2.5 ± 0.3 μM. We obtained a high-resolution co-crystal structure of the CBP bromodomain in complex with DC-CPin7 to guide following structure-based rational drug design, which yielded over ten DC-CPin7 derivatives with much higher potency, among which DC-CPin711 showed approximately 40-fold potency compared with hit compound DC-CPin7 with an in vitro TR-FRET IC50 value of 63.3 ± 4.0 nM. Notably, DC-CPin711 showed over 150-fold selectivity against BRD4 bromodomains. Moreover, DC-CPin711 showed micromolar level of anti-leukemia proliferation through G1 phase cell cycle arrest and cell apoptosis. In summary, through a combination of computational and crystal-based structure optimization, DC-CPin711 showed potent in vitro inhibitory activities to CBP bromodomain with a decent selectivity towards BRD4 bromodomains and good cellular activity to leukemia cells, which could further be applied to related biological and translational studies as well as serve as a lead compound for future development of potent and selective CBP bromodomain inhibitors.
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Affiliation(s)
- Yu Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaoyang Bi
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Fengcai Zhang
- School of Pharmacy, Nanchang University, Nanchang 330006, China
| | - Zhongya Sun
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Life and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Pan Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Hao Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wenchao Lu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tian Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Hong Ding
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
| | - Bing Zhou
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.
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13
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Shadrack DM, Swai HS. Solvent effects on molecular encapsulation of Toussantine-A by chitosan nanoparticle: A metadynamics study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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14
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Chen J, Pang L, Wang W, Wang L, Zhang JZH, Zhu T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2019; 38:985-996. [PMID: 30843759 DOI: 10.1080/07391102.2019.1591304] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CDK2 can be used as an attractive target for development of efficient inhibitors curing multiple disease relating with CDK2. In this work, molecular dynamics (MD) simulations and binding free energy calculations were coupled to probe conformational changes of CDK2 due to inhibitor associations and binding mechanisms of inhibitors PM1, FMD and X64 to CDK2. The results suggest that the binding strength of FMD and X64 to CDK2 is stronger than that of PM1. Principal component (PC) analysis and cross-correlation map calculations based on the equilibrated MD trajectories demonstrate that the structural difference in inhibitors exerts important impact on motion modes and dynamics behavior of CDK2. Residue-based free energy decomposition method was adopted to estimate the inhibitor-residue spectrum. The results not only efficiently identify the hot interaction spot of inhibitors with CDK2 but also show that the hydrophobic rings R1, R2 and R3 as well as polar groups of three inhibitors play key roles in favorably binding of inhibitors to CDK2. This work is expected to contribute energetic basis and dynamics information to development of promising inhibitors toward CDK2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Lifei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
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15
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Tian S, Zeng J, Liu X, Chen J, Zhang JZH, Zhu T. Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Phys Chem Chem Phys 2019; 21:22103-22112. [DOI: 10.1039/c9cp03598b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations and binding free energy calculations are combined to investigate the selectivity of inhibitors toward type III phosphatidylinositol 4 kinases.
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Affiliation(s)
- Shuaizhen Tian
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Jinzhe Zeng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Xiao Liu
- School of Mathematics, Physics and Statistics
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan 250357
- China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
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