1
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Qiao X, Wu X, Chen S, Niu MM, Hua H, Zhang Y. Discovery of novel and potent dual-targeting AXL/HDAC2 inhibitors for colorectal cancer treatment via structure-based pharmacophore modelling, virtual screening, and molecular docking, molecular dynamics simulation studies, and biological evaluation. J Enzyme Inhib Med Chem 2024; 39:2295241. [PMID: 38134358 PMCID: PMC10763849 DOI: 10.1080/14756366.2023.2295241] [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: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. Nowadays, owing to the complex mechanism of tumorigenesis, simultaneous inhibition of multiple targets is an important anticancer strategy. Recent studies have demonstrated receptor tyrosine kinase AXL (AXL) and histone deacetylase 2 (HDAC2) are closely associated with colorectal cancer. Herein, we identified five hit compounds concurrently targeting AXL and HDAC2 using virtual screening. Inhibitory experiments revealed these hit compounds potently inhibited AXL and HDAC2 in the nanomolar range. Among them, Hit-3 showed the strongest inhibitory effects which were better than that of the positive control groups. Additionally, MD assays showed that Hit-3 could bind stably to the AXL and HDAC2 active pockets. Further MTT assays demonstrated that Hit-3 showed potent anti-proliferative activity. Most importantly, Hit-3 exhibited significant in vivo antitumor efficacy in xenograft models. Collectively, this study is the first discovery of dual-targeting AXL/HDAC2 inhibitors for colorectal cancer treatment.
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Affiliation(s)
- Xiao Qiao
- Department of Gastroenterology, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Xiangyu Wu
- Department of Gastroenterology, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Shutong Chen
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Huilian Hua
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yan Zhang
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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2
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Jin X, Wang Y, Chen J, Niu M, Yang Y, Zhang Q, Bao G. Novel dual-targeting inhibitors of NSD2 and HDAC2 for the treatment of liver cancer: structure-based virtual screening, molecular dynamics simulation, and in vitro and in vivo biological activity evaluations. J Enzyme Inhib Med Chem 2024; 39:2289355. [PMID: 38059332 DOI: 10.1080/14756366.2023.2289355] [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: 07/19/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023] Open
Abstract
Liver cancer exhibits a high degree of heterogeneity and involves intricate mechanisms. Recent research has revealed the significant role of histone lysine methylation and acetylation in the epigenetic regulation of liver cancer development. In this study, five inhibitors capable of targeting both histone lysine methyltransferase nuclear receptor-binding SET domain 2 (NSD2) and histone deacetylase 2 (HDAC2) were identified using a structure-based virtual screening approach. Notably, DT-NH-1 displayed a potent inhibition of NSD2 (IC50 = 0.08 ± 0.03 μM) and HDAC2 (IC50 = 5.24 ± 0.87 nM). DT-NH-1 also demonstrated a strong anti-proliferative activity against various liver cancer cell lines, particularly HepG2 cells, and exhibited a high level of biological safety. In an experimental xenograft model involving HepG2 cells, DT-NH-1 showed a significant reduction in tumour growth. Consequently, these findings indicate that DT-NH-1 will be a promising lead compound for the treatment of liver cancer with epigenetic dual-target inhibitors.
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Affiliation(s)
- Xing Jin
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yuting Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jing Chen
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Miaomiao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yang Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Qiaoxuan Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guangyu Bao
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
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3
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Lu L, Li K, Pu J, Wang S, Liang T, Wang J. Dual-target inhibitors of colchicine binding site for cancer treatment. Eur J Med Chem 2024; 274:116543. [PMID: 38823265 DOI: 10.1016/j.ejmech.2024.116543] [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: 04/26/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
Colchicine binding site inhibitors (CBSIs) have attracted much attention due to their antitumor efficacies and the advantages of inhibiting angiogenesis and overcoming multidrug resistance. However, no CBSI has been currently approved for cancer treatment due to the insufficient efficacies, serious toxicities and poor pharmacokinetic properties. Design of dual-target inhibitors is becoming a potential strategy for cancer treatment to improve anticancer efficacy, decrease adverse events and overcome drug resistance. Therefore, we reviewed dual-target inhibitors of colchicine binding site (CBS), summarized the design strategies and the biological activities of these dual-target inhibitors, expecting to provide inspiration for developing novel dual inhibitors based on CBS.
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Affiliation(s)
- Lu Lu
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, Henan University, Kaifeng, Henan Province, 475004, China
| | - Keke Li
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, Henan University, Kaifeng, Henan Province, 475004, China
| | - Jiaxin Pu
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, Henan University, Kaifeng, Henan Province, 475004, China
| | - Shaochi Wang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, 450052, China
| | - Tingting Liang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, Henan University, Kaifeng, Henan Province, 475004, China; The Zhongzhou Laboratory for Integrative Biology, Henan University, Zhengzhou, Henan Province, 450000, China.
| | - Jianhong Wang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, Henan University, Kaifeng, Henan Province, 475004, China.
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4
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Zhang L, Guan L, Wang Y, Niu MM, Yan J. Discovery of a dual-target DYRK2 and HDAC8 inhibitor for the treatment of hepatocellular carcinoma. Biomed Pharmacother 2024; 177:116839. [PMID: 38889633 DOI: 10.1016/j.biopha.2024.116839] [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: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/26/2024] [Indexed: 06/20/2024] Open
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) and histone deacetylase 8 (HDAC8) have been shown to be associated with the development of several cancers. Here, we identified a dual-target DYRK2/HDAC8 inhibitor (DYC-1) through a combined virtual screening protocol. DYC-1 exhibited nanomolar inhibitory activity against both DYRK2 (IC50 = 5.27 ± 0.13 nM) and HDAC8 (IC50 = 8.06 ± 0.47 nM). Molecular dynamics simulations showed that DYC-1 had positive binding stability with DYRK2 and HDAC8. Importantly, the cytotoxicity assay indicated that DYC-1 exhibited superior antiproliferative activity against human liver cancer, especially SK-HEP-1 cells, and had no significant inhibition on normal liver cells. Moreover, DYC-1 showed a strong inhibitory effect on the growth of SK-HEP-1 xenograft tumors with no significant side effects. These data suggest that DYC-1 is a high-efficacy and low-toxic antitumor agent for the treatment of hepatocellular carcinoma.
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Affiliation(s)
- Li Zhang
- Department of Pharmacy, Changzhi People's Hospital, Changzhi Medical College, Changzhi 046000, China.
| | - Lixia Guan
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China
| | - Yuting Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China
| | - Jinhu Yan
- Department of Pain Treatment, Changzhi Hospital of Traditional Chinese Medicine, Changzhi 046000, China.
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5
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Mei S, Zou Y, Jiang S, Xue L, Wang Y, Jing H, Yang P, Niu MM, Li J, Yuan K, Zhang Y. Highly potent dual-targeting angiotensin-converting enzyme 2 (ACE2) and Neuropilin-1 (NRP1) peptides: A promising broad-spectrum therapeutic strategy against SARS-CoV-2 infection. Eur J Med Chem 2024; 263:115908. [PMID: 37981444 DOI: 10.1016/j.ejmech.2023.115908] [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: 05/22/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 11/21/2023]
Abstract
The efficacy of approved vaccines has been diminishing due to the increasing advent of SARS-CoV-2 variants with diverse mutations that favor sneak entry. Nonetheless, these variants recognize the conservative host receptors angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1) for entry, rendering the dual blockade of ACE2 and NRP1 an advantageous pan-inhibition strategy. Here, we identified a highly potent dual-targeting peptide AP-1 using structure-based virtual screening protocol. AP-1 had nanoscale binding affinities for ACE2 (Kd = 6.1 ± 0.2 nM) and NRP1 (Kd = 13.4 ± 1.2 nM) and approximately 102- and 8-fold stronger than positive inhibitors S471-503 and NMTP-5, respectively. Further evidence in pseudovirus cell infection and cytotoxicity assays demonstrated that AP-1 exhibited remarkable entry inhibition of variants of concern (VOCs) of SARS-CoV-2 without impairing host cell viability. Together, our findings suggest that AP-1 with dual-targeting ACE2/NRP1 efficacy could be a promising broad-spectrum agent for treating SARS-CoV-2 emerging VOCs.
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Affiliation(s)
- Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Su Jiang
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Yuting Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Han Jing
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Jiangsu Key Laboratory of Drug Design and Optimization, Ministry of Education, China Pharmaceutical University, Nanjing, 211198, China
| | - Jindong Li
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yan Zhang
- Department of Pharmacy, Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
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6
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Zheng L, Zou Y, Xie T, Wu X, Tan Y, Mei S, Geng Y, Chen S, Xu S, Niu MM. Discovery of a Dual Tubulin and Neuropilin-1 (NRP1) Inhibitor with Potent In Vivo Anti-Tumor Activity via Pharmacophore-based Docking Screening, Structure Optimization, and Biological Evaluation. J Med Chem 2023; 66:16187-16200. [PMID: 38093696 DOI: 10.1021/acs.jmedchem.3c01572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Dual inhibition of tubulin and neuropilin-1 (NRP1) may become an effective method for cancer treatment by simultaneously killing tumor cells and inhibiting tumor angiogenesis. Herein, we identified dual tubulin/NRP1-targeting inhibitor TN-2, which exhibited good inhibitory activity against both tubulin polymerization (IC50 = 0.71 ± 0.03 μM) and NRP1 (IC50 = 0.85 ± 0.04 μM). Importantly, it significantly inhibited the viability of several human prostate tumor cell lines. Further mechanism studies indicated that TN-2 could inhibit tubulin polymerization and cause G2/M arrest, thereby inducing cell apoptosis. It could also suppress cell tube formation, migration, and invasion. Moreover, TN-2 showed obvious antitumor effects on the PC-3 cell-derived xenograft model with negligible side effects and good pharmacokinetic profiles. These data demonstrate that TN-2 could be a promising dual-target chemotherapeutic agent for the treatment of prostate cancer.
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Affiliation(s)
- Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 211198, China
| | - Tianyuan Xie
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Xiuyuan Wu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yuchen Tan
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 211198, China
| | - Yifei Geng
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 211198, China
| | - Shutong Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 211198, China
| | - Shengtao Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 211198, China
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7
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Sharma S, Chandra K, Naik A, Sharma A, Sharma R, Thakur A, Grewal AS, Dhingra AK, Banerjee A, Liou JP, Guru SK, Nepali K. Flavone-based dual PARP-Tubulin inhibitor manifesting efficacy against endometrial cancer. J Enzyme Inhib Med Chem 2023; 38:2276665. [PMID: 37919954 PMCID: PMC10627047 DOI: 10.1080/14756366.2023.2276665] [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: 07/08/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
Structural tailoring of the flavone framework (position 7) via organopalladium-catalyzed C-C bond formation was attempted in this study. The impact of substituents with varied electronic effects (phenyl ring, position 2 of the benzopyran scaffold) on the antitumor properties was also assessed. Resultantly, the efforts yielded a furyl arm bearing benzopyran possessing a 4-fluoro phenyl ring (position 2) (14) that manifested a magnificent antitumor profile against the Ishikawa cell lines mediated through dual inhibition of PARP and tubulin [(IC50 (PARP1) = 74 nM, IC50 (PARP2) = 109 nM) and tubulin (IC50 = 1.4 µM)]. Further investigations confirmed the ability of 14 to induce apoptosis as well as autophagy and cause cell cycle arrest at the G2/M phase. Overall, the outcome of the study culminated in a tractable dual PARP-tubulin inhibitor endowed with an impressive activity profile against endometrial cancer.
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Affiliation(s)
- Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Kavya Chandra
- Department of Biological Sciences, BITS Pilani KK Birla Goa campus, Goa, India
| | - Aliva Naik
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Anamika Sharma
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | | | | | - Arnab Banerjee
- Department of Biological Sciences, BITS Pilani KK Birla Goa campus, Goa, India
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Santosh Kumar Guru
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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8
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Thakur A, Rana M, Ritika, Mathew J, Nepali S, Pan CH, Liou JP, Nepali K. Small molecule tractable PARP inhibitors: Scaffold construction approaches, mechanistic insights and structure activity relationship. Bioorg Chem 2023; 141:106893. [PMID: 37783100 DOI: 10.1016/j.bioorg.2023.106893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
Diverse drug design strategies viz. molecular hybridization, substituent installation, scaffold hopping, isosteric replacement, high-throughput screening, induction and separation of chirality, structure modifications of phytoconstituents and use of structural templates have been exhaustively leveraged in the last decade to load the chemical toolbox of PARP inhibitors. Resultantly, numerous promising scaffolds have been pinpointed that in turn have led to the resuscitation of the credence to PARP inhibitors as cancer therapeutics. This review briefly presents the physiological functions of PARPs, the pharmacokinetics, and pharmacodynamics, and the interaction profiles of FDA-approved PARP inhibitors. Comprehensively covered is the section on the drug design strategies employed by drug discovery enthusiasts for furnishing PARP inhibitors. The impact of structural variations in the template of designed scaffolds on enzymatic and cellular activity (structure-activity relationship studies) has been discussed. The insights gained through the biological evaluation such as profiling of physicochemical properties andin vitroADME properties, PK assessments, and high-dose pharmacology are covered.
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Affiliation(s)
- Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Mandeep Rana
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Ritika
- College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Jacob Mathew
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Sanya Nepali
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chun-Hsu Pan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan.
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9
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Yang Y, Chen S, Wang Q, Niu MM, Qu Y, Zhou Y. Identification of novel and potent dual-targeting HDAC1/SPOP inhibitors using structure-based virtual screening, molecular dynamics simulation and evaluation of in vitro and in vivo antitumor activity. Front Pharmacol 2023; 14:1208740. [PMID: 37492092 PMCID: PMC10363607 DOI: 10.3389/fphar.2023.1208740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023] Open
Abstract
Cancer is one of the important factors threatening human health. Hence, it is essential to create novel potent drugs to treat it. Due to the strong correlation among histone deacetylase1 (HDAC1), speckle-type POZ protein (SPOP) and cancers, dual inhibition of HDAC1 and SPOP may be a promising strategy for cancer treatment. In this study, we successfully identified four potential dual-targeting HDAC1/SPOP candidate compounds with structure-based virtual screening. In vitro inhibition experiments confirmed that the four compounds had dual inhibitory effects on HDAC1 and SPOP. Among them, compound HS-2 had a stronger inhibitory effect on HDAC1 and SPOP than the positive controls. Further molecular dynamics simulations indicated that HS-2 could stably bind to HDAC1 and SPOP. In addition, MTT assay indicated that HS-2 inhibited the growth of tumor cells in the micromolar range. In vivo evaluation showed that HS-2 could obviously inhibit the growth of tumor in nude mice without obvious toxicity. These findings suggest that HS-2 is a novel and potent dual-targeting HDAC1/SPOP inhibitor for cancer treatment.
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Affiliation(s)
- Yingxue Yang
- Department of Gastroenterology, The First People’s Hospital of Kunshan, Suzhou, China
| | - Shutong Chen
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Qinghua Wang
- Department of Gastroenterology, The First People’s Hospital of Kunshan, Suzhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yuanqian Qu
- Department of Pathology, Department of Gastrointestinal Surgery, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China
| | - Yang Zhou
- Department of Pathology, Department of Gastrointestinal Surgery, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China
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10
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Rana M, Thakur A, Kaur C, Pan CH, Lee SB, Liou JP, Nepali K. Prudent tactics to sail the boat of PARP inhibitors as therapeutics for diverse malignancies. Expert Opin Drug Discov 2023; 18:1169-1193. [PMID: 37525475 DOI: 10.1080/17460441.2023.2241818] [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: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
INTRODUCTION PARP inhibitors block the DNA-repairing mechanism of PARP and represent a promising class of anti-cancer therapy. The last decade has witnessed FDA approvals of several PARP inhibitors, with some undergoing advanced-stage clinical investigation. Medicinal chemists have invested much effort to expand the structure pool of PARP inhibitors. Issues associated with the use of PARP inhibitors that make their standing disconcerting in the pharmaceutical sector have been addressed via the design of new structural assemblages. AREA COVERED In this review, the authors present a detailed account of the medicinal chemistry campaigns conducted in the recent past for the construction of PARP1/PARP2 inhibitors, PARP1 biased inhibitors, and PARP targeting bifunctional inhibitors as well as PARP targeting degraders (PROTACs). Limitations associated with FDA-approved PARP inhibitors and strategies to outwit the limitations are also discussed. EXPERT OPINION The PARP inhibitory field has been rejuvenated with numerous tractable entries in the last decade. With numerous magic bullets in hand coupled with unfolded tactics to outwit the notoriety of cancer cells developing resistance toward PARP inhibitors, the dominance of PARP inhibitors as a sagacious option of targeted therapy is highly likely to be witnessed soon.
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Affiliation(s)
- Mandeep Rana
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Charanjit Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Chun-Hsu Pan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
| | - Sung-Bau Lee
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical, University, Taipei, Taiwan
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11
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Zhang J, Zhang J, Li H, Chen L, Yao D. Dual-target inhibitors of PARP1 in cancer therapy: a drug discovery perspective. Drug Discov Today 2023; 28:103607. [PMID: 37146962 DOI: 10.1016/j.drudis.2023.103607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1), a key enzyme in DNA repair, has emerged as a promising anticancer druggable target. An increasing number of PARP1 inhibitors have been discovered to treat cancer, most notably those characterized by BRCA1/2 mutations. Although PARP1 inhibitors have achieved great clinical success, their cytotoxicity, development of drug resistance, and restriction of indication have weakened their clinical therapeutic effects. To address these issues, dual PARP1 inhibitors have been documented as a promising strategy. Here, we review recent progress in the development of dual PARP1 inhibitors, summarize the different designs of dual-target inhibitors, and introduce their antitumor pharmacology, shedding light on the discovery of dual PARP1 inhibitors for cancer treatment.
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Affiliation(s)
- Jiahui Zhang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; These authors contributed equally to this work
| | - Jin Zhang
- School of Pharmaceutical Sciences of Medical School, Shenzhen University, Shenzhen, 518000, China; These authors contributed equally to this work
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China.
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Yedla P, Babalghith AO, Andra VV, Syed R. PROTACs in the Management of Prostate Cancer. Molecules 2023; 28:molecules28093698. [PMID: 37175108 PMCID: PMC10179857 DOI: 10.3390/molecules28093698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Cancer treatments with targeted therapy have gained immense interest due to their low levels of toxicity and high selectivity. Proteolysis-Targeting Chimeras (PROTACs) have drawn special attention in the development of cancer therapeutics owing to their unique mechanism of action, their ability to target undruggable proteins, and their focused target engagement. PROTACs selectively degrade the target protein through the ubiquitin-proteasome system, which describes a different mode of action compared to conventional small-molecule inhibitors or even antibodies. Among different cancer types, prostate cancer (PC) is the most prevalent non-cutaneous cancer in men. Genetic alterations and the overexpression of several genes, such as FOXA1, AR, PTEN, RB1, TP53, etc., suppress the immune response, resulting in drug resistance to conventional drugs in prostate cancer. Since the progression of ARV-110 (PROTAC for PC) into clinical phases, the focus of research has quickly shifted to protein degraders targeting prostate cancer. The present review highlights an overview of PROTACs in prostate cancer and their superiority over conventional inhibitors. We also delve into the underlying pathophysiology of the disease and explain the structural design and linkerology strategies for PROTAC molecules. Additionally, we touch on the various targets for PROTAC in prostate cancer, including the androgen receptor (AR) and other critical oncoproteins, and discuss the future prospects and challenges in this field.
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Affiliation(s)
- Poornachandra Yedla
- Department of Pharmacogenomics, Institute of Translational Research, Asian Healthcare Foundation, Asian Institute of Gastroenterology Hospitals, Gachibowli, Hyderabad 500082, India
| | - Ahmed O Babalghith
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Vindhya Vasini Andra
- Department of Medical Oncology, Omega Hospitals, Gachibowli, Hyderabad 500032, India
| | - Riyaz Syed
- Department of Chemiinformatics, Centella Scientific, JHUB, Jawaharlal Nehru Technological University, Hyderabad 500085, India
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Wang Y, Zhang H, Li J, Niu MM, Zhou Y, Qu Y. Discovery of potent and noncovalent KRAS G12D inhibitors: Structure-based virtual screening and biological evaluation. Front Pharmacol 2022; 13:1094887. [PMID: 36618907 PMCID: PMC9815544 DOI: 10.3389/fphar.2022.1094887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of pancreatic cancer. Herein, we identified four potent and noncovalent KRASG12D inhibitors (hits 1-4) by using structure-based virtual screening and biological evaluation. The in vitro assays indicated that the four compounds had sub-nanomolar affinities for KRASG12D and showed a dose-dependent inhibitory effect on human pancreatic cancer cells. In particular, the hit compound 3 was the most promising candidate and significantly inhibited the tumor growth of pancreatic cancer in tumor-bearing mice. The hit compound 3 represented a promising starting point for structural optimization in hit-to-lead development. This study shows that hit compound 3 provides a basis for the development of the treatment of cancer driven by KRASG12D.
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Affiliation(s)
- Yuting Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Hai Zhang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jindong Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yang Zhou
- Department of Pathology, Department of Gastrointestinal Surgery, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China,*Correspondence: Yang Zhou, ; Yuanqian Qu,
| | - Yuanqian Qu
- Department of Pathology, Department of Gastrointestinal Surgery, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China,*Correspondence: Yang Zhou, ; Yuanqian Qu,
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Zhang Y, Yang K, Ye S, Tang W, Chang X, Wang Y, Wang C, Wang Y, Wu Y, Miao Z. Application of a fluorine strategy in the lead optimization of betulinic acid to the discovery of potent CD73 inhibitors. Steroids 2022; 188:109112. [PMID: 36150476 DOI: 10.1016/j.steroids.2022.109112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 01/11/2023]
Abstract
The ecto-5'-nucleotidase (CD73) is an important enzyme in the adenosine pathway and catalyzes the extracellular hydrolysis of adenosine monophosphate (AMP) yielding adenosine which is involved in the inflammation and immunosuppression. Inhibitors of CD73 have potential as novel immunotherapy agents for the treatment of cancer and infection. In this study, we discovered a series of fluorinated betulinic acid derivatives as potent CD73 inhibitors by a fluorine scanning strategy. Among these, three compounds ZM522, ZM553 and ZM557 exhibited inhibitory activity with IC50 values of 0.56 uM, 0.74 uM and 0.47 uM, respectively. In addition, these compounds showed a 7-fold, 5-fold and 8-fold increase in activity compared to the positive control drug α, β-methylene adenosine diphosphate (APCP) against the human CD73 enzyme. Two of these (ZM522 and ZM553) also exhibited effective interferon gamma (INF-γ) elevation and indicated the regulation of rescued T cell activation. Therefore, our study provides both a lead optimization strategy and potential compounds for further development of small molecule CD73 inhibitors.
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Affiliation(s)
- Yanming Zhang
- School of Pharmacy, The Second Military Medical University, 325 Guohe Road, Shanghai 200433, PR China
| | - Keli Yang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai 201418, PR China
| | - Shuang Ye
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Wenmin Tang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai 201418, PR China
| | - Xuliang Chang
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, PR China
| | - Yuan Wang
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, PR China
| | - Chuanhao Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai 201418, PR China
| | - Ying Wang
- Department of Dermatology, The First Affiliated Hospital of Second Military Medical University, Shanghai 200433, PR China.
| | - Yuelin Wu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Haiquan Road, Shanghai 201418, PR China.
| | - Zhenyuan Miao
- School of Pharmacy, The Second Military Medical University, 325 Guohe Road, Shanghai 200433, PR China.
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Lin Y, Zhang Y, Wang D, Yang B, Shen YQ. Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 107:154481. [PMID: 36215788 DOI: 10.1016/j.phymed.2022.154481] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/14/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Traditional Chinese medicine (TCM), as a significant part of the global pharmaceutical science, the abundant molecular compounds it contains is a valuable potential source of designing and screening new drugs. However, due to the un-estimated quantity of the natural molecular compounds and diversity of the related problems drug discovery such as precise screening of molecular compounds or the evaluation of efficacy, physicochemical properties and pharmacokinetics, it is arduous for researchers to design or screen applicable compounds through old methods. With the rapid development of computer technology recently, especially artificial intelligence (AI), its innovation in the field of virtual screening contributes to an increasing efficiency and accuracy in the process of discovering new drugs. PURPOSE This study systematically reviewed the application of computational approaches and artificial intelligence in drug virtual filtering and devising of TCM and presented the potential perspective of computer-aided TCM development. STUDY DESIGN We made a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Then screening the most typical articles for our research. METHODS The systematic review was performed by following the PRISMA guidelines. The databases PubMed, EMBASE, Web of Science, CNKI were used to search for publications that focused on computer-aided drug virtual screening and design in TCM. RESULT Totally, 42 corresponding articles were included in literature reviewing. Aforementioned studies were of great significance to the treatment and cost control of many challenging diseases such as COVID-19, diabetes, Alzheimer's Disease (AD), etc. Computational approaches and AI were widely used in virtual screening in the process of TCM advancing, which include structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS). Besides, computational technologies were also extensively applied in absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction of candidate drugs and new drug design in crucial course of drug discovery. CONCLUSIONS The applications of computer and AI play an important role in the drug virtual screening and design in the field of TCM, with huge application prospects.
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Affiliation(s)
- Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - You Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dongyang Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Wang H, Wen J, Yang Y, Liu H, Wang S, Ding X, Zhou C, Zhang X. Identification of highly effective inhibitors against SARS-CoV-2 main protease: From virtual screening to in vitro study. Front Pharmacol 2022; 13:1036208. [PMID: 36467060 PMCID: PMC9715617 DOI: 10.3389/fphar.2022.1036208] [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: 09/04/2022] [Accepted: 11/07/2022] [Indexed: 05/29/2024] Open
Abstract
Background and Objective: The public's safety has been significantly jeopardized by the pandemic of COVID-19, which is brought on by the highly virulent and contagious SARS-CoV-2 virus. Finding novel antiviral drugs is currently of utmost importance for the treatment of patients with COVID-19. Main protease (3CLpro) of SARS-CoV-2 is involved in replication of virus, so it is considered as a promising target. Using small molecules to inhibit SARS-CoV-2-3CLpro activity may be an effective way to prevent viral replication to fight COVID-19. Despite the fact that some SARS-CoV-2-3CLpro inhibitors have been described, only few of them have high levels of inhibition at nanomolar concentrations. In this study, we aimed to screen out effective SARS-CoV-2-3CLpro inhibitors. Methods: To identify highly effective SARS-CoV-2-3CLpro inhibitors, a pharmacophore mapping and multiple-conformation docking were efficiently applied to find novel hit compounds from a database. Then, the stability of the 3CLpro-hit complexes was validated by using molecular dynamics simulation. Finally, biological assay was used to assess the inhibition effects of hit compounds on SARS-CoV-2-3CLpro. Results: Four hit compounds were identified by using computer-assisted strategy. Molecular dynamics simulation suggested that these hits bound stably to the 3CLpro-active pocket. Bioassay showed that all the hits had potent inhibition against SARS-CoV-2-3CLpro with IC50 values in the range of 0.017-0.83 μM. Particularly, hit one was the best 3CLpro inhibitor and its inhibition effect of SARS-CoV-2-3CLpro (IC50 = 0.017 ± 0.003 µM) was about 236 times stronger than that of ML300 (IC50 = 4.01 ± 0.66 µM). Conclusion: These data indicate that hit one could be regarded as an anti-SARS-CoV-2 candidate worth exploring further for the treatment of COVID-19.
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Affiliation(s)
- Hu Wang
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Jun Wen
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Yang Yang
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Hailin Liu
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Song Wang
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Xiaoli Ding
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Chunqiao Zhou
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Xuelin Zhang
- Department of Pharmacy, The First People’s Hospital of Chongqing Liang Jiang New Area, Chongqing, China
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Yin S, Mei S, Li Z, Xu Z, Wu Y, Chen X, Liu D, Niu MM, Li J. Non-covalent cyclic peptides simultaneously targeting Mpro and NRP1 are highly effective against Omicron BA.2.75. Front Pharmacol 2022; 13:1037993. [PMID: 36408220 PMCID: PMC9666779 DOI: 10.3389/fphar.2022.1037993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022] Open
Abstract
Available vaccine-based immunity may at high risk of being evaded due to substantial mutations in the variant Omicron. The main protease (Mpro) of SARS-CoV-2 and human neuropilin-1 (NRP1), two less mutable proteins, have been reported to be crucial for SARS-CoV-2 replication and entry into host cells, respectively. Their dual blockade may avoid vaccine failure caused by continuous mutations of the SARS-CoV-2 genome and exert synergistic antiviral efficacy. Herein, four cyclic peptides non-covalently targeting both Mpro and NRP1 were identified using virtual screening. Among them, MN-2 showed highly potent affinity to Mpro (Kd = 18.2 ± 1.9 nM) and NRP1 (Kd = 12.3 ± 1.2 nM), which was about 3,478-fold and 74-fold stronger than that of the positive inhibitors Peptide-21 and EG3287. Furthermore, MN-2 exhibited significant inhibitory activity against Mpro and remarkable anti-infective activity against the pseudotyped variant Omicron BA.2.75 without obvious cytotoxicity. These data demonstrated that MN-2, a novel non-covalent cyclic peptide, is a promising agent against Omicron BA.2.75.
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Affiliation(s)
- Shengnan Yin
- Department of Pharmacy, Taizhou Hospital Affiliated to Nanjing University of Chinese Medicine, Taizhou, China
| | - Shuang Mei
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Zhiqin Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Zhen Xu
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yuting Wu
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Xiujuan Chen
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Dongmei Liu
- Department of Pharmacy, Taizhou Hospital Affiliated to Nanjing University of Chinese Medicine, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Jindong Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
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Ai D, Wu J, Cai H, Zhao D, Chen Y, Wei J, Xu J, Zhang J, Wang L. A multi-task FP-GNN framework enables accurate prediction of selective PARP inhibitors. Front Pharmacol 2022; 13:971369. [DOI: 10.3389/fphar.2022.971369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
PARP (poly ADP-ribose polymerase) family is a crucial DNA repair enzyme that responds to DNA damage, regulates apoptosis, and maintains genome stability; therefore, PARP inhibitors represent a promising therapeutic strategy for the treatment of various human diseases including COVID-19. In this study, a multi-task FP-GNN (Fingerprint and Graph Neural Networks) deep learning framework was proposed to predict the inhibitory activity of molecules against four PARP isoforms (PARP-1, PARP-2, PARP-5A, and PARP-5B). Compared with baseline predictive models based on four conventional machine learning methods such as RF, SVM, XGBoost, and LR as well as six deep learning algorithms such as DNN, Attentive FP, MPNN, GAT, GCN, and D-MPNN, the evaluation results indicate that the multi-task FP-GNN method achieves the best performance with the highest average BA, F1, and AUC values of 0.753 ± 0.033, 0.910 ± 0.045, and 0.888 ± 0.016 for the test set. In addition, Y-scrambling testing successfully verified that the model was not results of chance correlation. More importantly, the interpretability of the multi-task FP-GNN model enabled the identification of key structural fragments associated with the inhibition of each PARP isoform. To facilitate the use of the multi-task FP-GNN model in the field, an online webserver called PARPi-Predict and its local version software were created to predict whether compounds bear potential inhibitory activity against PARPs, thereby contributing to design and discover better selective PARP inhibitors.
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Malebari AM, Duffy Morales G, Twamley B, Fayne D, Khan MF, McLoughlin EC, O’Boyle NM, Zisterer DM, Meegan MJ. Synthesis, Characterisation and Mechanism of Action of Anticancer 3-Fluoroazetidin-2-ones. Pharmaceuticals (Basel) 2022; 15:ph15091044. [PMID: 36145265 PMCID: PMC9501633 DOI: 10.3390/ph15091044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
The stilbene combretastatin A-4 (CA-4) is a potent microtubule-disrupting agent interacting at the colchicine-binding site of tubulin. In the present work, the synthesis, characterisation and mechanism of action of a series of 3-fluoro and 3,3-difluoro substituted β-lactams as analogues of the tubulin-targeting agent CA-4 are described. The synthesis was achieved by a convenient microwave-assisted Reformatsky reaction and is the first report of 3-fluoro and 3,3-difluoro β-lactams as CA-4 analogues. The β-lactam compounds 3-fluoro-4-(3-hydroxy-4-methoxyphenyl)-1-(3,4,5-trimethoxy phenyl)azetidin-2-one 32 and 3-fluoro-4-(3-fluoro-4-methoxyphenyl)-1-(3,4,5-trimethoxyphenyl)azetidin-2-one) 33 exhibited potent activity in MCF-7 human breast cancer cells with IC50 values of 0.075 µM and 0.095 µM, respectively, and demonstrated low toxicity in non-cancerous cells. Compound 32 also demonstrated significant antiproliferative activity at nanomolar concentrations in the triple-negative breast cancer cell line Hs578T (IC50 0.033 μM), together with potency in the invasive isogenic subclone Hs578Ts(i)8 (IC50 = 0.065 μM), while 33 was also effective in MDA-MB-231 cells (IC50 0.620 μM). Mechanistic studies demonstrated that 33 inhibited tubulin polymerisation, induced apoptosis in MCF-7 cells, and induced a downregulation in the expression of anti-apoptotic Bcl2 and survivin with corresponding upregulation in the expression of pro-apoptotic Bax. In silico studies indicated the interaction of the compounds with the colchicine-binding site, demonstrating the potential for further developing novel cancer therapeutics as microtubule-targeting agents.
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Affiliation(s)
- Azizah M. Malebari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Trinity Biomedical Sciences Institute, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Gabriela Duffy Morales
- Trinity Biomedical Sciences Institute, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Brendan Twamley
- School of Chemistry, Trinity College Dublin, Dublin 2, D02 PN40 Dublin, Ireland
| | - Darren Fayne
- Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Mohemmed Faraz Khan
- Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Eavan C. McLoughlin
- Trinity Biomedical Sciences Institute, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Niamh M. O’Boyle
- Trinity Biomedical Sciences Institute, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Daniela M. Zisterer
- Trinity Biomedical Sciences Institute, School of Biochemistry and Immunology, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
| | - Mary J. Meegan
- Trinity Biomedical Sciences Institute, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590 Dublin, Ireland
- Correspondence:
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Recent advances in structural types and medicinal chemistry of PARP-1 inhibitors. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02919-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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