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Carpenter KA, Altman RB. Databases of ligand-binding pockets and protein-ligand interactions. Comput Struct Biotechnol J 2024; 23:1320-1338. [PMID: 38585646 PMCID: PMC10997877 DOI: 10.1016/j.csbj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
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Affiliation(s)
- Kristy A. Carpenter
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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2
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Runa F, Ortiz-Soto G, de Barros NR, Kelber JA. Targeting SMAD-Dependent Signaling: Considerations in Epithelial and Mesenchymal Solid Tumors. Pharmaceuticals (Basel) 2024; 17:326. [PMID: 38543112 PMCID: PMC10975212 DOI: 10.3390/ph17030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 04/01/2024] Open
Abstract
SMADs are the canonical intracellular effector proteins of the TGF-β (transforming growth factor-β). SMADs translocate from plasma membrane receptors to the nucleus regulated by many SMAD-interacting proteins through phosphorylation and other post-translational modifications that govern their nucleocytoplasmic shuttling and subsequent transcriptional activity. The signaling pathway of TGF-β/SMAD exhibits both tumor-suppressing and tumor-promoting phenotypes in epithelial-derived solid tumors. Collectively, the pleiotropic nature of TGF-β/SMAD signaling presents significant challenges for the development of effective cancer therapies. Here, we review preclinical studies that evaluate the efficacy of inhibitors targeting major SMAD-regulating and/or -interacting proteins, particularly enzymes that may play important roles in epithelial or mesenchymal compartments within solid tumors.
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Affiliation(s)
- Farhana Runa
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
| | | | | | - Jonathan A Kelber
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
- Department of Biology, Baylor University, Waco, TX 76706, USA
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3
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Han W, Yang Y, Yu F, Li Q, Liu A, Xu W, Li J, Xue X. Design, synthesis and anticancer activity evaluation of 4-(3-1H-indazolyl)amino quinazoline derivatives as PAK4 inhibitors. Bioorg Med Chem 2023; 95:117501. [PMID: 37864885 DOI: 10.1016/j.bmc.2023.117501] [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: 08/21/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
A novel series of 4-(3-1H-indazolyl)amino quinazoline derivatives were developed as PAK4 inhibitors based on a scaffold hopping strategy. Compounds 27e, 27g, 27i and 27j were found to exhibit potent inhibitory activity against PAK4 (IC50 = 10, 13, 11 and 9 nM, respectively). Subsequent cellular assay demonstrated that compound 27e possessed the strongest antiproliferative activity against A549 cells with an IC50 value of 0.61 μM, a little bit better than PF-3758309. Further anticancer mechanistic investigation revealed that compound 27e significantly induced apoptosis of A549 cells in a concentration-dependent manner and blocked the cell cycle at phase G0/G1. A docking model between compound 27e and PAK4 was proposed to elucidate its possible binding modes. As a promising PAK4 inhibitor, compound 27e may serve as a candidate for the development of novel PAK4-targeted anticancer drug.
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Affiliation(s)
- Wei Han
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yusang Yang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Fan Yu
- The Engineering Research Center of Synthetic Polypeptide Drug Discovery and Evaluation, China Pharmaceutical University, Nanjing 211198, China
| | - Qianqian Li
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Anyao Liu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenbo Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabin Li
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaowen Xue
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China.
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4
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Sun B, Liu W, Wang Q, Liu Y, Yu S, Liu M, Han J. Design, Synthesis, and Activity Evaluation of Novel Dual-Target Inhibitors with Antifungal and Immunoregulatory Properties. J Med Chem 2023; 66:13007-13027. [PMID: 37705322 DOI: 10.1021/acs.jmedchem.3c00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Dual-target (CYP51/PD-L1) plays an important role in the process of fungal proliferation and immune suppression. A series of novel quinazoline compounds with dual-target inhibition function was constructed using the skeleton growth method, and their structures were synthesized, characterized, and evaluated. Among them, the perfected compounds (L11, L20, L21) were selected for further study, which exhibited remarkable biological activity against different fungal strains (MIC50, 0.25-2.0 μg/mL) in vitro. On the one hand, these compounds inhibited CYP51 activity, induced ROS aggregation, and mitochondrial damage; this ultimately caused fungal lysis and death. On the other hand, they also effectively activated the body's immune ability by blocking the interaction between PD-L1 and PD-1, slowed down the inflammatory reaction, and accelerated the recovery process of fungal infections.
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Affiliation(s)
- Bin Sun
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
| | - Wenxia Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
| | - Qingpeng Wang
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
| | - Yating Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
| | - Shuai Yu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
| | - Min Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
| | - Jun Han
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng 252000, PR China
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5
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Somanath PR, Chernoff J, Cummings BS, Prasad SM, Homan HD. Targeting P21-Activated Kinase-1 for Metastatic Prostate Cancer. Cancers (Basel) 2023; 15:cancers15082236. [PMID: 37190165 DOI: 10.3390/cancers15082236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 05/17/2023] Open
Abstract
Metastatic prostate cancer (mPCa) has limited therapeutic options and a high mortality rate. The p21-activated kinase (PAK) family of proteins is important in cell survival, proliferation, and motility in physiology, and pathologies such as infectious, inflammatory, vascular, and neurological diseases as well as cancers. Group-I PAKs (PAK1, PAK2, and PAK3) are involved in the regulation of actin dynamics and thus are integral for cell morphology, adhesion to the extracellular matrix, and cell motility. They also play prominent roles in cell survival and proliferation. These properties make group-I PAKs a potentially important target for cancer therapy. In contrast to normal prostate and prostatic epithelial cells, group-I PAKs are highly expressed in mPCA and PCa tissue. Importantly, the expression of group-I PAKs is proportional to the Gleason score of the patients. While several compounds have been identified that target group-I PAKs and these are active in cells and mice, and while some inhibitors have entered human trials, as of yet, none have been FDA-approved. Probable reasons for this lack of translation include issues related to selectivity, specificity, stability, and efficacy resulting in side effects and/or lack of efficacy. In the current review, we describe the pathophysiology and current treatment guidelines of PCa, present group-I PAKs as a potential druggable target to treat mPCa patients, and discuss the various ATP-competitive and allosteric inhibitors of PAKs. We also discuss the development and testing of a nanotechnology-based therapeutic formulation of group-I PAK inhibitors and its significant potential advantages as a novel, selective, stable, and efficacious mPCa therapeutic over other PCa therapeutics in the pipeline.
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Affiliation(s)
- Payaningal R Somanath
- Department of Clinical & Administrative Pharmacy, College of Pharmacy, University of Georgia, Augusta, GA 30912, USA
- MetasTx LLC, Basking Ridge, NJ 07920, USA
| | - Jonathan Chernoff
- MetasTx LLC, Basking Ridge, NJ 07920, USA
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Brian S Cummings
- MetasTx LLC, Basking Ridge, NJ 07920, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sandip M Prasad
- Morristown Medical Center, Atlantic Health System, Morristown, NJ 07960, USA
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Hao C, Li X, Wang Z, Liu L, He F, Pan Z. Optically activated MEK1/2 inhibitors (Opti-MEKi) as potential antimelanoma agents. Eur J Med Chem 2023; 251:115236. [PMID: 36924668 DOI: 10.1016/j.ejmech.2023.115236] [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: 10/22/2022] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023]
Abstract
Mitogen-activated protein kinase kinases 1/2 (MEK1/2) play critical roles in the canonical RAS/RAF/MEK/ERK pathway. Highly selective and potent non-ATP-competitive allosteric MEK1/2 inhibitors have been developed, and three of them were clinically approved for the treatment of BRAFV600 -mutant melanoma. However, the accompanying side effects of the systemically administered MEK1/2 drugs largely constrain their tolerable doses and efficacy. In this study, a series of mirdametinib-based optically activatable MEK1/2 inhibitors (opti-MEKi) were designed and synthesized. A structural-based design led to the discovery of photocaged compounds with dramatically diminished efficacy in vitro, whose activities can be spatiotemporally induced by short durations of irradiation of ultraviolet (365 nm) light. We demonstrated the robust photoactivation of MEK1/2 inhibition and antimelanoma activity in cultured human cells, as well as in a xenograft zebrafish model. Taken together, the modular approach presented herein provides a method for the optical control of MEK1/2 inhibitor activity, and these data support the further development of optically activatable agents for light-mediated antimelanoma phototherapy.
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Affiliation(s)
- Chenzhou Hao
- State Key Laboratory of Chemical Oncogenomics, Provincial Key Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xiaofeng Li
- State Key Laboratory of Chemical Oncogenomics, Provincial Key Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Zhunchao Wang
- State Key Laboratory of Chemical Oncogenomics, Provincial Key Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Lihong Liu
- State Key Laboratory of Chemical Oncogenomics, Provincial Key Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Fengli He
- State Key Laboratory of Chemical Oncogenomics, Provincial Key Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Zhengying Pan
- State Key Laboratory of Chemical Oncogenomics, Provincial Key Laboratory of Chemical Genomics, Engineering Laboratory for Chiral Drug Synthesis, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
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7
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Parshuram Satpute D, Shirwadkar U, Kumar Tharalla A, Dattatray Shinde S, Nikhil Vaidya G, Joshi S, Patel Vatsa P, Jain A, Singh AA, Garg R, Mandoli A, Kumar D. Discovery of fluorinated 2‑Styryl 4(3H)-quinazolinone as potential therapeutic hit for oral cancer. Bioorg Med Chem 2023; 81:117193. [PMID: 36796126 DOI: 10.1016/j.bmc.2023.117193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignant epithelial neoplasm, affects the mouth and throat, and accounts for 90 % of oral cancers. Considering the associated morbidity with neck dissections and the limitation of existing therapeutic agents, the discovery and development of new anticancer drugs/drug candidates for oral cancer treatment are of the utmost need. In this context, reported here is the identification of fluorinated 2‑styryl 4(3H)-quinazolinone as a promising hit for oral cancer. Preliminary studies indicate that the compound blocks the transition of G1 to S phase, thereby leading to arrest in the G1/S phase. Subsequent RNA-seq analysis revealed that the compound induces the activation of molecular pathways involved in apoptosis (such as TNF signalling through NF-κB, p53 pathways) and cell differentiation and suppresses the pathways of cellular growth and development (such as KRAS signaling) in CAL-27 cancer cells. It is noted that identified hit complies with a favorable range of ADME properties as per the computational analysis.
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Affiliation(s)
- Dinesh Parshuram Satpute
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Urjita Shirwadkar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Anil Kumar Tharalla
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Sangita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Gargi Nikhil Vaidya
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Swarali Joshi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Priyanka Patel Vatsa
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India
| | - Alok Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India; Department of Bio-engineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Abhishek A Singh
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Rachana Garg
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India; Division of Neurosurgery, Department of Surgery, City of Hope National Medical Center, Duarte, CA 91010, USA.
| | - Amit Mandoli
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India.
| | - Dinesh Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmadabad, Palaj, Gandhinagar-382355, Gujarat, India.
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8
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Sun Y, Xue Y, Liu H, Mu S, Sun P, Sun Y, Wang L, Wang H, Wang J, Wu T, Yin W, Qin Q, Sun Y, Yang H, Zhao D, Cheng M. Discovery of CZS-241: A Potent, Selective, and Orally Available Polo-Like Kinase 4 Inhibitor for the Treatment of Chronic Myeloid Leukemia. J Med Chem 2023; 66:2396-2421. [PMID: 36734825 DOI: 10.1021/acs.jmedchem.2c02124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent studies demonstrate that PLK4 has emerged as a therapeutic target for the treatment of multiple cancers owing to its indispensable role in cell division. Herein, starting from previously identified effective compound CZS-034, based on rational drug design strategies, tyrosine kinase receptor A (TRKA) selectivity- and metabolic stability-guided structure-activity relationship (SAR) exploration were carried out to discover a highly potent (IC50 = 2.6 nM) and selective (SF = 1054.4 over TRKA) PLK4 inhibitor B43 (CZS-241) with acceptable human liver microsome stability (t1/2 = 31.5 min). Moreover, compound B43 effectively inhibited leukemia cells in 29 tested cell lines, especially chronic myeloid leukemia (CML) cell lines K562 and KU-812. Pharmacokinetic characteristics revealed that compound B43 possessed over 4 h of half-life and 70.8% bioavailability in mice. In the K562 cells xenograft mouse model, a 20 mg/kg/day dosage treatment obviously suppressed tumor progression. As a potential and novel PLK4-targeted candidate drug for CML, compound B43 is undergoing extensive preclinical safety evaluation.
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Affiliation(s)
- Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Yanli Xue
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Hongbing Liu
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Shuyi Mu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Pengkun Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Yu Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Lin Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Jingkai Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Huali Yang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, P. R. China
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9
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Liu N, Wang X, Fu Q, Qin Q, Wu T, Lv R, Zhao D, Cheng M. Design, synthesis and biological evaluation of pyrazolo[3,4- b]pyridine derivatives as TRK inhibitors. RSC Med Chem 2023; 14:85-102. [PMID: 36760745 PMCID: PMC9890667 DOI: 10.1039/d2md00334a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Tropomyosin receptor kinases (TRKs) are associated with the proliferation and differentiation of cells, and thus their continuous activation and overexpression cause cancer. Herein, based on scaffold hopping and computer-aid drug design, 38 pyrazolo[3,4-b]pyridine derivatives were synthesised. Further, we evaluated their activities to inhibit TRKA. Among them, compound C03 showed acceptable activity with an IC50 value of 56 nM and it inhibited the proliferation of the Km-12 cell line with an IC50 value of 0.304 μM together with obvious selectivity for the MCF-7 cell line and HUVEC cell line. Furthermore, compound C03 possessed good plasma stability and low inhibitory activity to a panel of cytochrome P450 isoforms except CYP2C9. Overall, C03 has potential for further exploration.
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Affiliation(s)
- Nian Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Xin Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Qinglin Fu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Ruicheng Lv
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District Shenyang 110016 PR China
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10
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The Inhibitory Mechanism of 7 H-Pyrrolo[2,3-d]pyrimidine Derivatives as Inhibitors of P21-Activated Kinase 4 through Molecular Dynamics Simulation. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010413. [PMID: 36615619 PMCID: PMC9823812 DOI: 10.3390/molecules28010413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]
Abstract
The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7H-pyrrolo[2,3-d]pyrimidine competitive inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations and binding free energy calculations. The results show that the inhibitors had strong interactions with the hinge region, the β-sheets, and the residues with charged side chains around the 4-substituent. The terminal amino group of the inhibitor 5n was different from the other three, which could cause the enhancement of hydrogen bonds or electrostatic interactions formed with the surrounding residues. Thus, inhibitor 5n had the strongest inhibition capacity. The different halogen atoms on the 2-substituents of the inhibitors 5h, 5g, and 5e caused differences in the positions of the 2-benzene rings and affected the interactions of the hinge region. It also affected to some extent the orientations of the 4-imino groups and consequently their affinities for the surrounding charged residues. The combined results lead to the weakest inhibitory capacity of inhibitor 5e.
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11
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Mao Y, Lee E, Yang X, Bae EJ, Jeon R, Park BH. Targeting p21-activated kinase 4 (PAK4) with pyrazolo[3,4- d]pyrimidine derivative SPA7012 attenuates hepatic ischaemia-reperfusion injury in mice. J Enzyme Inhib Med Chem 2022; 37:2133-2146. [PMID: 35920284 PMCID: PMC9354638 DOI: 10.1080/14756366.2022.2106478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
p21-Activated kinase 4 (PAK4), one of the serine/threonine kinases activated by Rho-family GTPases, has been widely studied as an oncogenic protein that is overexpressed in many types of cancers. In our recent study, PAK4 upregulation was observed in mice exhibiting hepatic ischaemia-reperfusion (I/R) and in liver transplantation patients. Liver I/R injury was also attenuated in Pak4 KO mice. Herein, we report a novel series of pyrazolo[3,4-d]pyrimidine derivatives of type I ½ PAK4 inhibitors. The most potent compound SPA7012 was evaluated to determine the pharmacological potential of PAK4 inhibitor in I/R injury in mice. Mice with I/R injury showed typical patterns of liver damage, as demonstrated by increases in serum levels of aminotransferases and proinflammatory cytokines, hepatocellular necrosis and apoptosis, and inflammatory cell infiltration, relative to sham mice. Conversely, intraperitoneal administration of SPA7012 dramatically attenuated biochemical and histopathologic changes. Mechanistically, stabilisation of nuclear factor-erythroid 2-related factor 2 (Nrf2), a master regulator of anti-oxidative response, was observed following SPA7012 treatment. SPA7012 treatment in primary hepatocytes also attenuated hypoxia-reoxygenation-induced apoptotic cell death and inflammation. Together, these results provide experimental evidence supporting the use of PAK4 inhibitors for alleviation of I/R-induced liver damage.
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Affiliation(s)
- Yuancheng Mao
- Department of Biochemistry and Research Institute for Endocrine Sciences, Jeonbuk National University Medical School, Jeonju, Republic of Korea
| | - Eun Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Xiaohui Yang
- School of Pharmacy, Jeonbuk National University, Jeonju, Republic of Korea
| | - Eun Ju Bae
- School of Pharmacy, Jeonbuk National University, Jeonju, Republic of Korea
| | - Raok Jeon
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Byung-Hyun Park
- Department of Biochemistry and Research Institute for Endocrine Sciences, Jeonbuk National University Medical School, Jeonju, Republic of Korea
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12
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Structure-based discovery of 1-(3-fluoro-5-(5-(3-(methylsulfonyl)phenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)phenyl)-3-(pyrimidin-5-yl)urea as a potent and selective nanomolar type-II PLK4 inhibitor. Eur J Med Chem 2022; 243:114714. [DOI: 10.1016/j.ejmech.2022.114714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 02/08/2023]
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13
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Li Y, Lu Q, Xie C, Yu Y, Zhang A. Recent advances on development of p21-activated kinase 4 inhibitors as anti-tumor agents. Front Pharmacol 2022; 13:956220. [PMID: 36105226 PMCID: PMC9465411 DOI: 10.3389/fphar.2022.956220] [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: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022] Open
Abstract
The p21-activated kinase 4 (PAK4) is a member of the PAKs family. It is overexpressed in multiple tumor tissues. Pharmacological inhibition of PAK4 attenuates proliferation, migration, and invasion of cancer cells. Recent studies revealed that inhibition of PAK4 sensitizes immunotherapy which has been extensively exploited as a new strategy to treat cancer. In the past few years, a large number of PAK4 inhibitors have been reported. Of note, the allosteric inhibitor KPT-9274 has been tested in phase Ⅰ clinic trials. Herein, we provide an update on recent research progress on the PAK4 mediated signaling pathway and highlight the development of the PAK4 small molecular inhibitors in recent 5 years. Meanwhile, challenges, limitations, and future developmental directions will be discussed as well.
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Affiliation(s)
- Yang Li
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Lu
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Chenghu Xie
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yiming Yu
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ao Zhang
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Ao Zhang,
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14
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Liu L, Sun Y, Gao Z, Yin W, Jiang H, Wu T, Sun Y, Qin Q, Zhao D, Cheng M. Design, synthesis, and evaluation of novel 3,4-isoxazolediamide derivatives for the combination treatment of azole-resistant candidiasis. Arch Pharm (Weinheim) 2022; 355:e2200266. [PMID: 36029272 DOI: 10.1002/ardp.202200266] [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: 05/20/2022] [Revised: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022]
Abstract
Invasive fungal infections are emerging as serious infectious diseases worldwide. Due to the frequent emergence of resistance, the cure for invasive fungal infections is often unachievable. The molecular chaperone Hsp90 provides a promising target because it supports survival, virulence, and drug resistance in a variety of pathogens. Herein, we report on the structural optimization and structure-activity relationship studies of 3,4-isoxazolediamide analogs. As a new class of fungal Hsp90 inhibitor, compound B25 was found to have good synergistic effects with fluconazole and to avoid potential mammalian toxicity. It also showed remarkable metabolic stability in vitro. Collectively, B25 could be a promising lead compound for drug discovery targeting fungal Hsp90 and deserves further investigation.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Zixuan Gao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Hong Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
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15
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Sun Y, Sun Y, Wang L, Wu T, Yin W, Wang J, Xue Y, Qin Q, Sun Y, Yang H, Zhao D, Cheng M. Design, synthesis, and biological evaluation of novel pyrazolo [3,4-d]pyrimidine derivatives as potent PLK4 inhibitors for the treatment of TRIM37-amplified breast cancer. Eur J Med Chem 2022; 238:114424. [DOI: 10.1016/j.ejmech.2022.114424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/11/2022]
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16
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Yuan Y, Zhang H, Li D, Li Y, Lin F, Wang Y, Song H, Liu X, Li F, Zhang J. PAK4 in cancer development: Emerging player and therapeutic opportunities. Cancer Lett 2022; 545:215813. [DOI: 10.1016/j.canlet.2022.215813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/02/2022]
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17
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Wu T, Qin Q, Lv R, Liu N, Yin W, Hao C, Sun Y, Zhang C, Sun Y, Zhao D, Cheng M. Discovery of quinazoline derivatives CZw-124 as a pan-TRK inhibitor with potent anticancer effects in vitro and in vivo. Eur J Med Chem 2022; 238:114451. [PMID: 35617855 DOI: 10.1016/j.ejmech.2022.114451] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/28/2022]
Abstract
Herein, we report the discovery process and antitumor activity of the TRK inhibitor CZw-124 (8o), which is a quinazoline derivative. Starting from a PAK4 inhibitor, we used various drug design strategies, including pharmacophore feature supplementation, F-scanning, and blocking metabolic sites, and finally found a TRK inhibitor CZw-124 that is effective in vitro and in vivo. Docking studies and molecular dynamics simulations revealed a possible mode of binding of CZw-124 to TRKA. Biological activity evaluation showed that CZw-124 belongs to a class of pan-TRK inhibitors with moderate kinase selectivity. It inhibited the proliferation and induced the apoptosis of Km-12 cells in vitro by interfering with the phosphorylation of TRKA. Pharmacodynamic evaluation in vivo showed that CZw-124 had a tumor inhibition rate comparable to that of larotrectinib after oral administration of 40 mg/kg/d (tumor growth inhibiton = 71%).
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Affiliation(s)
- Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Ruicheng Lv
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Nian Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Chenzhou Hao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Chu Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
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18
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Wang C, Xia J, Lei Y, Lu R, Zhang M, Lv H, Hong Q, Lu T, Chen Y, Li H. Synthesis and biological evaluation of 7H-pyrrolo [2,3-d] pyrimidine derivatives as potential p21-activated kinase 4 (PAK4) inhibitors. Bioorg Med Chem 2022; 60:116700. [PMID: 35272236 DOI: 10.1016/j.bmc.2022.116700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 11/02/2022]
Abstract
PAK4 has been validated as a crucial effector of various signal pathways and play an important role in driving tumor progression. Here, we developed a series of 7H-pyrrolo [2,3-d] pyrimidine derivatives as PAK4 inhibitors. Compounds 5n and 5o showed higher enzymatic inhibitory activities (IC50 = 2.7 and 20.2 nM, respectively) and potent activity (IC50 = 7.8 and 38.3 nM, respectively) against MV4-11 cell line. Further flow cytometry assay revealed that the compound 5n can arrest MV4-11 cells at G0/G1 phase and induce cell apoptosis. Molecular mechanism study indicated that compound 5n regulated the phosphorylation of PAK4 in vitro. The docking study supported that compound 5n binds to PAK4 through various hydrogen bonding interactions and hydrophobic interactions. Thus, compound 5n represents a promising lead for the discovery of PAK4 directed therapeutic agents and may be considered for further drug development.
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Affiliation(s)
- Cong Wang
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - Jiawei Xia
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - Yan Lei
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - Rui Lu
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - Mingliang Zhang
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - He Lv
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - Qianqian Hong
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Hongmei Li
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, PR China.
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19
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Chen Y, Wang ZZ, Hao GF, Song BA. Web support for the more efficient discovery of kinase inhibitors. Drug Discov Today 2022; 27:2216-2225. [DOI: 10.1016/j.drudis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/16/2022] [Accepted: 04/01/2022] [Indexed: 11/24/2022]
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20
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Yin W, Wu T, Liu L, Jiang H, Zhang Y, Cui H, Sun Y, Qin Q, Sun Y, Gao Z, Zhao L, Su X, Zhao D, Cheng M. Species-Selective Targeting of Fungal Hsp90: Design, Synthesis, and Evaluation of Novel 4,5-Diarylisoxazole Derivatives for the Combination Treatment of Azole-Resistant Candidiasis. J Med Chem 2022; 65:5539-5564. [PMID: 35298171 DOI: 10.1021/acs.jmedchem.1c01991] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Invasive fungal infections are emerging as serious infectious diseases worldwide. Because of the development of antifungal drug resistance, the limited efficacy of the existing drugs has led to high mortality in patients. The use of the essential eukaryotic chaperone Hsp90, which plays a multifaceted role in drug resistance across diverse pathogenic fungal species, is considered to be a new strategy to mitigate the resistance and counter the threat posed by drug-resistant fungi. Thus, a series of 4,5-diarylisoxazole analogues as fungal Hsp90 inhibitors were designed and synthesized that had potent synergistic effects with fluconazole in vitro and in vivo. In particular, compound A17 could avoid the potential mammalian toxicity of Hsp90 inhibitors based on key reside differences between humans and fungi. These data support the feasibility of targeting fungal Hsp90 as a promising antifungal strategy and further development of compound A17 as a valuable research probe for the investigation of fungal Hsp90.
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Affiliation(s)
- Wenbo Yin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Lei Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Hong Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yuxin Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Hengxian Cui
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Zixuan Gao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Liyu Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xin Su
- The School of Life Science and Biopharmaceutical, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
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21
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Song P, Zhao F, Li D, Qu J, Yao M, Su Y, Wang H, Zhou M, Wang Y, Gao Y, Li F, Zhao D, Zhang F, Rao Y, Xia M, Li H, Wang J, Cheng M. Synthesis of selective PAK4 inhibitors for lung metastasis of lung cancer and melanoma cells. Acta Pharm Sin B 2022; 12:2905-2922. [PMID: 35755272 PMCID: PMC9214071 DOI: 10.1016/j.apsb.2022.02.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The p21 activated kinase 4 (PAK4) is serine/threonine protein kinase that is critical for cancer progression. Guided by X-ray crystallography and structure-based optimization, we report a novel subseries of C-3-substituted 6-ethynyl-1H-indole derivatives that display high potential and specificity towards group II PAKs. Among these inhibitors, compound 55 exhibited excellent inhibitory activity and kinase selectivity, displayed superior anti-migratory and anti-invasive properties against the lung cancer cell line A549 and the melanoma cell line B16. Compound 55 exhibited potent in vivo antitumor metastatic efficacy, with over 80% and 90% inhibition of lung metastasis in A549 or B16-BL6 lung metastasis models, respectively. Further mechanistic studies demonstrated that compound 55 mitigated TGF-β1-induced epithelial-mesenchymal transition (EMT).
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22
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Biswal J, Jayaprakash P, Rayala SK, Venkatraman G, Rangaswamy R, Jeyaraman J. WaterMap and Molecular Dynamic Simulation-Guided Discovery of Potential PAK1 Inhibitors Using Repurposing Approaches. ACS OMEGA 2021; 6:26829-26845. [PMID: 34693105 PMCID: PMC8529594 DOI: 10.1021/acsomega.1c02032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 06/13/2023]
Abstract
p21-Activated kinase 1 (PAK1) is positioned at the nexus of several oncogenic signaling pathways. Currently, there are no approved inhibitors for disabling the transfer of phosphate in the active site directly, as they are limited by lower affinity, and poor kinase selectivity. In this work, a repurposing study utilizing FDA-approved drugs from the DrugBank database was pursued with an initial selection of 27 molecules out of ∼2162 drug molecules, based on their docking energies and molecular interaction patterns. From the molecules that were considered for WaterMap analysis, seven molecules, namely, Mitoxantrone, Labetalol, Acalabrutinib, Sacubitril, Flubendazole, Trazodone, and Niraparib, ascertained the ability to overlap with high-energy hydration sites. Considering many other displaced unfavorable water molecules, only Acalabrutinib, Flubendazole, and Trazodone molecules highlighted their prominence in terms of binding affinity gains through ΔΔG that ranges between 6.44 and 2.59 kcal/mol. Even if Mitoxantrone exhibited the highest docking score and greater interaction strength, it did not comply with the WaterMap and molecular dynamics simulation results. Moreover, detailed MD simulation trajectory analyses suggested that the drug molecules Flubendazole, Niraparib, and Acalabrutinib were highly stable, observed from their RMSD values and consistent interaction pattern with Glu315, Glu345, Leu347, and Asp407 including the hydrophobic interactions maintained in the three replicates. However, the drug molecule Trazodone displayed a loss of crucial interaction with Leu347, which was essential to inhibit the kinase activity of PAK1. The molecular orbital and electrostatic potential analyses elucidated the reactivity and strong complementarity potentials of the drug molecules in the binding pocket of PAK1. Therefore, the CADD-based reposition efforts, reported in this work, helped in the successful identification of new PAK1 inhibitors that requires further investigation by in vitro analysis.
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Affiliation(s)
- Jayashree Biswal
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Prajisha Jayaprakash
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Suresh Kumar Rayala
- Department
of Biotechnology, Indian Institute of Technology
Madras, Room No. BT 306, Chennai 600 036, Tamil Nadu, India
| | - Ganesh Venkatraman
- Department
of Human Genetics, College of Biomedical Sciences, Sri Ramachandra University, Porur, Chennai 600 116, Tamil Nadu, India
| | - Raghu Rangaswamy
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
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23
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Kalogirou AS, East MP, Laitinen T, Torrice CD, Maffuid KA, Drewry DH, Koutentis PA, Johnson GL, Crona DJ, Asquith CRM. Synthesis and Evaluation of Novel 1,2,6-Thiadiazinone Kinase Inhibitors as Potent Inhibitors of Solid Tumors. Molecules 2021; 26:molecules26195911. [PMID: 34641454 PMCID: PMC8513058 DOI: 10.3390/molecules26195911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
A focused series of substituted 4H-1,2,6-thiadiazin-4-ones was designed and synthesized to probe the anti-cancer properties of this scaffold. Insights from previous kinase inhibitor programs were used to carefully select several different substitution patterns. Compounds were tested on bladder, prostate, pancreatic, breast, chordoma, and lung cancer cell lines with an additional skin fibroblast cell line as a toxicity control. This resulted in the identification of several low single digit micro molar compounds with promising therapeutic windows, particularly for bladder and prostate cancer. A number of key structural features of the 4H-1,2,6-thiadiazin-4-one scaffold are discussed that show promising scope for future improvement.
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Affiliation(s)
- Andreas S. Kalogirou
- Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenis Str., Engomi, P.O. Box 22006, Nicosia 1516, Cyprus
- Department of Chemistry, University of Cyprus, P.O. Box 20537, Nicosia 1678, Cyprus;
- Correspondence: (A.S.K.); (C.R.M.A.); Tel.: +357-22-559655 (A.S.K.); +1-919-491-3177 (C.R.M.A.)
| | - Michael P. East
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (M.P.E.); (G.L.J.)
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland;
| | - Chad D. Torrice
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.D.T.); (K.A.M.); (D.J.C.)
| | - Kaitlyn A. Maffuid
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.D.T.); (K.A.M.); (D.J.C.)
| | - David H. Drewry
- Structural Genomics Consortium, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA;
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Gary L. Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (M.P.E.); (G.L.J.)
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel J. Crona
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; (C.D.T.); (K.A.M.); (D.J.C.)
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christopher R. M. Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (M.P.E.); (G.L.J.)
- Correspondence: (A.S.K.); (C.R.M.A.); Tel.: +357-22-559655 (A.S.K.); +1-919-491-3177 (C.R.M.A.)
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24
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Wang H, Song P, Gao Y, Shen L, Xu H, Wang J, Cheng M. Drug discovery targeting p21-activated kinase 4 (PAK4): a patent review. Expert Opin Ther Pat 2021; 31:977-987. [PMID: 34369844 DOI: 10.1080/13543776.2021.1944100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: The Ser/Thr protein kinase PAK4 is a downstream regulator of Cdc42, mediating cytoskeleton remodeling, and cell motility, and inhibiting apoptosis and transcriptional regulation. Nowadays, efforts in PAK4 inhibitor development are focusing on improving inhibitory selectivity, cellular potency, and in vivo pharmacokinetic properties, and identifying the feasibility of immunotherapy combination in oncology therapy.Areas covered: This review summarized the development of PAK4 inhibitors that reported on patents in the past two decades. According to their binding features, these inhibitors were classified into type I, type I 1/2, and PAMs. Their designing ideas and SAR were elucidated in this review. Moreover, synergistic therapy of PAK4 inhibitors with PD-1/PD-L1 or CAR-T were also summarized .Expert opinion: In the past years, preclinical and clinical studies of PAK4 inhibitors ended in failure due to poor selectivity, cellular activity, or pharmacokinetic issues. There are researchers questioning the reliability of PAK4 as a drug target, particularly PAK4-related therapy is concerned with the distinguishment of the non-kinase functions and catalytic functions triggered by PAK4 phosphorylation. Meanwhile, synergistic effects of PAK4 inhibitors with PD-1/PD-L1 and CAR-T immunotherapy shed light for the development of PAK4 inhibitors.
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Affiliation(s)
- Hanxun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Peilu Song
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yinli Gao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Lanlan Shen
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Hanqin Xu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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Zhu R, Nasu K, Hijiya N, Yoshihashi M, Hirakawa T, Aoyagi Y, Narahara H. hsa-miR-199a-3p Inhibits Motility, Invasiveness, and Contractility of Ovarian Endometriotic Stromal Cells. REPRODUCTIVE SCIENCES (THOUSAND OAKS, CALIF.) 2021; 28:3498-3507. [PMID: 33987822 DOI: 10.1007/s43032-021-00604-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023]
Abstract
It is suggested that aberrantly expressed microRNAs are involved in the pathogenesis of endometriosis. Our previous study demonstrated that expression of the microRNA hsa-miR-199a-3p is attenuated in human endometriotic cyst stromal cells (ECSCs). The current study aimed to define the roles of hsa-miR-199a-3p in the development of endometriosis. ECSCs and normal endometrial stromal cells (NESCs) were isolated from ovarian endometrioma and normal endometrial tissues, respectively. We evaluated the effect of transfected hsa-miR-199a-3p on the migration, invasion, and contractility of ECSCs using Transwell migration assays, in vitro wound healing assays, Transwell invasion assays, and collagen gel contraction assays. We also examined the downstream target of hsa-miR-199a-3p with an online public database search and luciferase reporter assay. Expression of hsa-miR-199a-3p in ECSCs was significantly lower than that in NESCs, whereas the expression of p21-activated kinase 4 (PAK4) mRNA was significantly higher. Transfection of hsa-miR-199a-3p inhibited the migration, invasion, and contractility of ECSCs via inhibition of PAK4 mRNA expression. PAK4 was confirmed to be the direct target of hsa-miR-199a-3p. Transfection of PAK4 small interfering RNA and the PAK4 inhibitor PF-3758309 also inhibited ECSC migration, invasion, and contractility. These findings suggest that hsa-miR-199a-3p may act as a tumor suppressor in endometriosis development. Attenuation of hsa-miR-199a-3p expression was favorable for ECSCs to acquire the highly invasive, motile, and contractile characteristics of endometriotic cells and is involved in the development of endometriosis. Accordingly, PAK4 inhibitors may be promising for the treatment of endometriosis.
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Affiliation(s)
- Ruofei Zhu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Idaigaoka 1-1, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan
| | - Kaei Nasu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Idaigaoka 1-1, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan.
- Division of Obstetrics and Gynecology, Support System for Community Medicine, Faculty of Medicine, Oita University, Oita, Yufu-shi, Japan.
| | - Naoki Hijiya
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Yufu-shi, Japan
| | - Masato Yoshihashi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Idaigaoka 1-1, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan
| | - Tomoko Hirakawa
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Idaigaoka 1-1, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan
| | - Yoko Aoyagi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Idaigaoka 1-1, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan
| | - Hisashi Narahara
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Idaigaoka 1-1, Hasama-machi, Yufu-shi, Oita, 879-5593, Japan
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Bauer MR, Di Fruscia P, Lucas SCC, Michaelides IN, Nelson JE, Storer RI, Whitehurst BC. Put a ring on it: application of small aliphatic rings in medicinal chemistry. RSC Med Chem 2021; 12:448-471. [PMID: 33937776 PMCID: PMC8083977 DOI: 10.1039/d0md00370k] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
Aliphatic three- and four-membered rings including cyclopropanes, cyclobutanes, oxetanes, azetidines and bicyclo[1.1.1]pentanes have been increasingly exploited in medicinal chemistry for their beneficial physicochemical properties and applications as functional group bioisosteres. This review provides a historical perspective and comparative up to date overview of commonly applied small rings, exemplifying key principles with recent literature examples. In addition to describing the merits and advantages of each ring system, potential hazards and liabilities are also illustrated and explained, including any significant chemical or metabolic stability and toxicity risks.
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Affiliation(s)
- Matthias R Bauer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Paolo Di Fruscia
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Simon C C Lucas
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | | | - Jennifer E Nelson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - R Ian Storer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
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Kanev GK, de Graaf C, Westerman BA, de Esch IJP, Kooistra AJ. KLIFS: an overhaul after the first 5 years of supporting kinase research. Nucleic Acids Res 2021; 49:D562-D569. [PMID: 33084889 PMCID: PMC7778968 DOI: 10.1093/nar/gkaa895] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Kinases are a prime target of drug development efforts with >60 drug approvals in the past two decades. Due to the research into this protein family, a wealth of data has been accumulated that keeps on growing. KLIFS-Kinase-Ligand Interaction Fingerprints and Structures-is a structural database focusing on how kinase inhibitors interact with their targets. The aim of KLIFS is to support (structure-based) kinase research through the systematic collection, annotation, and processing of kinase structures. Now, 5 years after releasing the initial KLIFS website, the database has undergone a complete overhaul with a new website, new logo, and new functionalities. In this article, we start by looking back at how KLIFS has been used by the research community, followed by a description of the renewed KLIFS, and conclude with showcasing the functionalities of KLIFS. Major changes include the integration of approved drugs and inhibitors in clinical trials, extension of the coverage to atypical kinases, and a RESTful API for programmatic access. KLIFS is available at the new domain https://klifs.net.
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Affiliation(s)
- Georgi K Kanev
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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Zhang M, Fang X, Wang C, Hua Y, Huang C, Wang M, Zhu L, Wang Z, Gao Y, Zhang T, Liu H, Zhang Y, Lu S, Lu T, Chen Y, Li H. Design and synthesis of 1H-indazole-3-carboxamide derivatives as potent and selective PAK1 inhibitors with anti-tumour migration and invasion activities. Eur J Med Chem 2020; 203:112517. [DOI: 10.1016/j.ejmech.2020.112517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/15/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
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Yao D, Li C, Rajoka MSR, He Z, Huang J, Wang J, Zhang J. P21-Activated Kinase 1: Emerging biological functions and potential therapeutic targets in Cancer. Am J Cancer Res 2020; 10:9741-9766. [PMID: 32863957 PMCID: PMC7449905 DOI: 10.7150/thno.46913] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
The p21-Activated kinase 1 (PAK1), a member of serine-threonine kinases family, was initially identified as an interactor of the Rho GTPases RAC1 and CDC42, which affect a wide range of processes associated with cell motility, survival, metabolism, cell cycle, proliferation, transformation, stress, inflammation, and gene expression. Recently, the PAK1 has emerged as a potential therapeutic target in cancer due to its role in many oncogenic signaling pathways. Many PAK1 inhibitors have been developed as potential preclinical agents for cancer therapy. Here, we provide an overview of essential roles that PAK1 plays in cancer, including its structure and autoactivation mechanism, its crucial function from onset to progression to metastasis, metabolism, immune escape and even drug resistance in cancer; endogenous regulators; and cancer-related pathways. We also summarize the reported PAK1 small-molecule inhibitors based on their structure types and their potential application in cancer. In addition, we provide overviews on current progress and future challenges of PAK1 in cancer, hoping to provide new ideas for the diagnosis and treatment of cancer.
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Qin Q, Wu T, Yin W, Sun Y, Zhang X, Wang R, Guo J, Zhao D, Cheng M. Discovery of 2,4-diaminopyrimidine derivatives targeting p21-activated kinase 4: Biological evaluation and docking studies. Arch Pharm (Weinheim) 2020; 353:e2000097. [PMID: 32627873 DOI: 10.1002/ardp.202000097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/05/2023]
Abstract
In this study, novel 2,4-diaminopyrimidine derivatives targeting p21-activated kinase 4 (PAK4) were discovered and evaluated for their biological activity against PAK4. Among the derivatives studied, promising compounds A2, B6, and B8 displayed the highest inhibitory activities against PAK4 (IC50 = 18.4, 5.9, and 20.4 nM, respectively). From the cellular assay, compound B6 exhibited the highest potency with an IC50 value of 2.533 μM against A549 cells. Some compounds were selected for computational ADME (absorption, distribution, metabolism, and elimination) properties and molecular docking studies against PAK4. The detailed structure-activity relationship based on the biochemical activities and molecular docking studies were explored. According to the docking studies, compound B6 had the lowest docking score (docking energy: -7.593 kcal/mol). The molecular docking simulation indicated the binding mode between compound B6 and PAK4. All these results suggest compound B6 as a useful candidate for the development of a PAK4 inhibitor.
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Affiliation(s)
- Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jing Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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31
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Synthesis of (R) and (S)-3-Chloro-5-(2,4-dimethylpiperazin-1-yl)-4H-1,2,6-thiadiazin-4-ones. MOLBANK 2020. [DOI: 10.3390/m1139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The reaction of 3,5-dichloro-4H-1,2,6-thiadiazin-4-one with (R) and (S)-1,3-dimethylpiperazines (1 equiv), in THF, at ca. 20 °C gives (R) and (S)-3-chloro-5-(2,4-dimethylpiperazin-1-yl)-4H-1,2,6-thiadiazin-4-ones in 70% and 68% yields, respectively. The new compounds were fully characterized.
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Chacón Simon S, Wang F, Thomas LR, Phan J, Zhao B, Olejniczak ET, Macdonald JD, Shaw JG, Schlund C, Payne W, Creighton J, Stauffer SR, Waterson AG, Tansey WP, Fesik SW. Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2020; 63:4315-4333. [PMID: 32223236 DOI: 10.1021/acs.jmedchem.0c00224] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The frequent deregulation of MYC and its elevated expression via multiple mechanisms drives cells to a tumorigenic state. Indeed, MYC is overexpressed in up to ∼50% of human cancers and is considered a highly validated anticancer target. Recently, we discovered that WD repeat-containing protein 5 (WDR5) binds to MYC and is a critical cofactor required for the recruitment of MYC to its target genes and reported the first small molecule inhibitors of the WDR5-MYC interaction using structure-based design. These compounds display high binding affinity, but have poor physicochemical properties and are hence not suitable for in vivo studies. Herein, we conducted an NMR-based fragment screening to identify additional chemical matter and, using a structure-based approach, we merged a fragment hit with the previously reported sulfonamide series. Compounds in this series can disrupt the WDR5-MYC interaction in cells, and as a consequence, we observed a reduction of MYC localization to chromatin.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Shaun R Stauffer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Alex G Waterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | | | - Stephen W Fesik
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
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Wang R, Chen Y, Yang B, Yu S, Zhao X, Zhang C, Hao C, Zhao D, Cheng M. Design, synthesis, biological evaluation and molecular modeling of novel 1H-pyrrolo[2,3-b]pyridine derivatives as potential anti-tumor agents. Bioorg Chem 2019; 94:103474. [PMID: 31859010 DOI: 10.1016/j.bioorg.2019.103474] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 11/19/2019] [Accepted: 11/24/2019] [Indexed: 02/06/2023]
Abstract
A class of 3-substituted 1H-pyrrolo[2,3-b]pyridine derivatives were designed, synthesized and evaluated for their in vitro biological activities against maternal embryonic leucine zipper kinase (MELK). Among these derivatives, the optimized compound 16h exhibited potent enzyme inhibition (IC50 = 32 nM) and excellent anti-proliferative effect with IC50 values from 0.109 μM to 0.245 μM on A549, MDA-MB-231 and MCF-7 cell lines. The results of flow cytometry indicated that 16h promoted apoptosis of A549 cells in a dose-dependent manner and effectively arrested A549 cells in the G0/G1 phase. Further investigation indicated that compound 16h potently suppressed the migration of A549 cells, had moderate stability in rat liver microsomes and showed moderate inhibitory activity against various subtypes of human cytochrome P450. However, compound 16h is a multi-target kinase inhibitor and recently several studies reported MELK expression is not required for cancer growth, suggesting that compound 16h suppressed the proliferation and migration of cancer cells should through an off-target mechanism. Collectively, compound 16h has the potential to serve as a new lead compound for further anticancer drug discovery.
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Affiliation(s)
- Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yixuan Chen
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Bowen Yang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Sijia Yu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xiangxin Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Cai Zhang
- The School of Life Science and Biopharmaceutical, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Chenzhou Hao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
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Guo J, Wang T, Wu T, Zhang K, Yin W, Zhu M, Pang Y, Hao C, He Z, Cheng M, Liu Y, Zheng J, Gu J, Zhao D. Synthesis, bioconversion, pharmacokinetic and pharmacodynamic evaluation of N-isopropyl-oxy-carbonyloxymethyl prodrugs of CZh-226, a potent and selective PAK4 inhibitor. Eur J Med Chem 2019; 186:111878. [PMID: 31757524 DOI: 10.1016/j.ejmech.2019.111878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
We have previously disclosed compound 3 (CZh-226), a potent and selective PAK4 inhibitor, but its development was delayed due to poor oral pharmacokinetics. In an attempt to improve this issue, we synthesised a series of prodrugs by masking its terminal nitrogen of the piperazine moiety. Most synthesised prodrugs of 3 have low or no inhibition of PAK4 activity. The stability of synthetic prodrugs was evaluated in PBS, SGF, SIF, rat plasma and liver S9 fraction. Of these, prodrug 19 was not only stable under both acidic and neutral conditions but also could be quickly converted to parent drug 3 in rat plasma and liver S9 fraction. Such effective conversion into parent drug 3 was observed in rats, providing higher exposure of 3 compared to its direct administration. When given via oral route at daily doses of 25 and 50 mg/kg, the prodrug 19 was effective and well tolerated in mouse model of HCT-116 and B16F10.
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Affiliation(s)
- Jing Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Tingting Wang
- Research Institute of Translational Medicine, The First Bethune Hospital of Jilin University, Changchun, 130061, China; Research Center for Drug Metabolism, College of Life Science, Jilin University, Changchun, 130012, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Kehan Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Mingyue Zhu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yu Pang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Chenzhou Hao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Zhonggui He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiang Zheng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Jingkai Gu
- Research Institute of Translational Medicine, The First Bethune Hospital of Jilin University, Changchun, 130061, China; Research Center for Drug Metabolism, College of Life Science, Jilin University, Changchun, 130012, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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Wang H, Gao Z, Song P, Hu B, Wang J, Cheng M. Molecular dynamics simulation and QM/MM calculation reveal the selectivity mechanism of type I 1/2 kinase inhibitors: the effect of intramolecular H-bonds and conformational restriction for improved selectivity. Phys Chem Chem Phys 2019; 21:24147-24164. [PMID: 31657381 DOI: 10.1039/c9cp04353e] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the selectivity mechanisms of inhibitors towards highly similar proteins is extremely important work on the way to a new drug. Here, we aim to reveal the selectivity mechanisms of type I 1/2 kinase inhibitors towards p21-activated kinase (PAK4) and mitogen-activated protein kinase kinase kinase 14 (MAP3K14, NIK). PAK4, belonging to the serine/threonine protein kinases, is involved in cell signaling pathways and controls cellular functions and has received attention as an attractive drug target. The high sequence identity between PAK4 and NIK makes it challenging to design selective PAK4 inhibitors. In this work, computational methods including protein comparison, molecular docking, QM/MM, molecular dynamics simulations, and density functional theory (DFT) calculation were employed to explore the binding mechanisms of selective inhibitors against NIK and PAK4. The simulation results revealed the crucial factors accounting for selective inhibition of PAK4 over NIK, including different protein-ligand interactions, the positions and conformations of key residues, and the ligands flexibilities. This study will shed light on understanding the selectivity mechanisms of PAK4 and NIK inhibitors.
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Affiliation(s)
- Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
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Gao Y, Wang H, Wang J, Cheng M. In silico studies on p21-activated kinase 4 inhibitors: comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations, and MM-GBSA calculation. J Biomol Struct Dyn 2019; 38:4119-4133. [PMID: 31556340 DOI: 10.1080/07391102.2019.1673823] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
P21-activated kinase 4 (PAK4) is a serine/threonine protein kinase, which is associated with many cancer diseases, and thus being considered as a potential drug target. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations were performed to explore the structure-activity relationship of a series of pyrropyrazole PAK4 inhibitors. The statistical parameters of comparative molecular field analysis (CoMFA, Q 2 = 0.837, R 2 = 0.990, and R 2 pred = 0.967) and comparative molecular similarity indices analysis (CoMSIA, Q 2 = 0.720, R 2 = 0.972, and R 2 pred = 0.946) were obtained from 3D-QSAR model, which exhibited good predictive ability and significant statistical reliability. The binding mode of PAK4 with its inhibitors was obtained through molecular docking study, which indicated that the residues of GLU396, LEU398, LYS350, and ASP458 were important for activity. Molecular mechanics generalized born surface area (MM-GBSA) method was performed to calculate the binding free energy, which indicated that the coulomb, lipophilic and van der Waals (vdW) interactions made major contributions to the binding affinity. Furthermore, through 100 ns MD simulations, we obtained the key amino acid residues and the types of interactions they participated in. Based on the constructed 3D-QSAR model, some novel pyrropyrazole derivatives targeting PAK4 were designed with improved predicted activities. Pharmacokinetic and toxicity predictions of the designed PAK4 inhibitors were obtained by the pkCSM, indicating these compounds had better absorption, distribution, metabolism, excretion and toxicity (ADMET) properties. Above research provided a valuable insight for developing novel and effective pyrropyrazole compounds targeting PAK4.
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Affiliation(s)
- Yinli Gao
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
| | - Jian Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang Liaoning Province, People's Republic of China
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Song PL, Wang G, Su Y, Wang HX, Wang J, Li F, Cheng MS. Strategy and validation of a structure-based method for the discovery of selective inhibitors of PAK isoforms and the evaluation of their anti-cancer activity. Bioorg Chem 2019; 91:103168. [DOI: 10.1016/j.bioorg.2019.103168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023]
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Wang H, Gao Y, Wang J, Cheng M. Computational Strategy Revealing the Structural Determinant of Ligand Selectivity towards Highly Similar Protein Targets. Curr Drug Targets 2019; 21:76-88. [PMID: 31556854 DOI: 10.2174/1389450120666190926113524] [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: 04/27/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Poor selectivity of drug candidates may lead to toxicity and side effects accounting for as high as 60% failure rate, thus, the selectivity is consistently significant and challenging for drug discovery. OBJECTIVE To find highly specific small molecules towards very similar protein targets, multiple strategies are always employed, including (1) To make use of the diverse shape of binding pocket to avoid steric bump; (2) To increase binding affinities for favorite residues; (3) To achieve selectivity through allosteric regulation of target; (4) To stabalize the inactive conformation of protein target and (5) To occupy dual binding pockets of single target. CONCLUSION In this review, we summarize computational strategies along with examples of their successful applications in designing selective ligands, with the aim to provide insights into everdiversifying drug development practice and inspire medicinal chemists to utilize computational strategies to avoid potential side effects due to low selectivity of ligands.
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Affiliation(s)
- Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Yinli Gao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
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Su Y, Song P, Wang H, Hu B, Wang J, Cheng MS. Precise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation. J Biomol Struct Dyn 2019; 38:3825-3837. [DOI: 10.1080/07391102.2019.1664330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuan Su
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Peilu Song
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Mao-Sheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
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Demakova MY, Islamova RM, Suslonov VV. Palladium-Catalyzed Synthesis of 4-Aminoquinazolines from Amide Oxime Ethers and 2-Iodobenzonitrile. RUSS J GEN CHEM+ 2019. [DOI: 10.1134/s1070363219040054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Recent advancements of 4-aminoquinazoline derivatives as kinase inhibitors and their applications in medicinal chemistry. Eur J Med Chem 2019; 170:55-72. [DOI: 10.1016/j.ejmech.2019.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/21/2019] [Accepted: 03/01/2019] [Indexed: 12/30/2022]
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Design, synthesis, structure-activity relationships study and X-ray crystallography of 3-substituted-indolin-2-one-5-carboxamide derivatives as PAK4 inhibitors. Eur J Med Chem 2018; 155:197-209. [DOI: 10.1016/j.ejmech.2018.05.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
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