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Das PK, Matada GSP, Pal R, Maji L, Dhiwar PS, Manjushree BV, Viji MP. Poly (ADP-ribose) polymerase (PARP) inhibitors as anticancer agents: An outlook on clinical progress, synthetic strategies, biological activity, and structure-activity relationship. Eur J Med Chem 2024; 274:116535. [PMID: 38838546 DOI: 10.1016/j.ejmech.2024.116535] [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: 04/09/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
Poly (ADP-ribose) polymerase (PARP) is considered an essential component in case of DNA (Deoxyribonucleic acid) damage, response by sensing DNA damage and engaging DNA repair proteins. Those proteins repair the damaged DNA via an aspect of posttranslational modification, known as poly (ADP-Ribosyl)ation (PARylation). Specifically, PARP inhibitors (PARPi) have shown better results when administered alone in a variety of cancer types with BRCA (Breast Cancer gene) mutation. The clinical therapeutic benefits of PARP inhibitors have been diminished by their cytotoxicity, progression of drug resistance, and limitation of indication, regardless of their tremendous clinical effectiveness. A growing number of PARP-1 inhibitors, particularly those associated with BRCA-1/2 mutations, have been identified as potential cancer treatments. Recently, several researchers have identified various promising scaffolds, which have resulted in the resuscitation of the faith in PARP inhibitors as cancer therapies. This review provided a comprehensive update on the anatomy and physiology of the PARP enzyme, the profile of FDA (Food and Drug Administration) and CFDA (China Food and Drug Administration)-approved drugs, and small-molecule inhibitors of PARP, including their synthetic routes, biological evaluation, selectivity, and structure-activity relationship.
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Affiliation(s)
- Pronoy Kanti Das
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - Gurubasavaraja Swamy Purawarga Matada
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India.
| | - Rohit Pal
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India.
| | - Lalmohan Maji
- Tarifa Memorial Institute of Pharmacy, Department of Pharmaceutical Chemistry, Murshidabad, 742166, West Bengal, India
| | - Prasad Sanjay Dhiwar
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - B V Manjushree
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - M P Viji
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
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Peng X, Li Y, Qu J, Jiang L, Wu K, Liu D, Chen Y, Peng J, Guo Y, Cao X. High affinity and low PARP-trapping benzimidazole derivatives as a potential warhead for PARP1 degraders. Eur J Med Chem 2024; 271:116405. [PMID: 38678823 DOI: 10.1016/j.ejmech.2024.116405] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
PARPi have been explored and applied in the treatment of various cancers with remarkable efficacy, especially BRCA1/2 mutated ovarian, breast, prostate, and pancreatic cancers. However, PARPi renders inevitable drug resistance and showed high toxicity because of PARP-Trapping with long-term clinic tracking. To overcome the drug resistance and the high toxicity of PARPi, many novel methods have been developed including PROTACs. Being an event-driven technology, PROTACs needs a high affinity, low toxicity warhead with no steric hindrance in binding process. Veliparib shows the lowest PARP-Trapping effect but could hardly to be the warhead of PROTACs because of the strong steric hindrance. Other PARP1 inhibitors showed less steric hindrance but owns high PARP-Trapping effect. Thus, the development of novel warhead with high PARP1 affinity, low PARP1-Trapping, and no steric hindrance would be valuable. In this work, we reserved benzimidazole as the motif to reserve the low PARP1-Trapping effect and substituted the pyrrole by aromatic ring to avoiding the steric hindrance in PARP1 binding cave. Thus, a series of benzimidazole derivates were designed and synthesized, and some biological activities in vitro were evaluated including the inhibition for PARP1 enzyme and the PARP-Trapping effect using MDA-MB-436 cell line. Results showed that the compound 19A10 has higher PARP1 affinity(IC50 = 4.62 nM)) and similar low PARP-Trapping effect compared with Veliparib(IC50 (MDA-MB-436) >100 μM). Docking study showed that the compound 19A10 could avoiding the steric hindrance which was much better than Veliparib. So, the compound 19A10 could potentially be a perfect warhead for PARP1 degraders. Besides, because of the depletion of the PARP1 and the decreasing of the binding capability, we suppose that the PROTACs using 19A10 as the warhead would be no-PARP-Trapping effect. Furthermore, QSAR study showed that to develop novel compounds with high PARP1 binding affinity and low PARP-Trapping, we can choose the skeleton with substituent R1H, R2 = piperiazine, and R3 with large tPSA. And, if we want to develop the compounds with high PARP1 binding affinity and high PARP-Trapping which can possibly improve the lethality against tumor cells, we can choose the skeleton with substituent R1F, R2 = 3-methy-piperiazine, and R3 with large tPSA.
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Affiliation(s)
- Xiaoyu Peng
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Yang Li
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Junfeng Qu
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Lizhi Jiang
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Kaiyue Wu
- Department of Pharmacy, Ezhou Central Hospital, Ezhou, Hubei, China
| | - Dan Liu
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Yuping Chen
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Yu Guo
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China.
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Hirlekar BU, Nuthi A, Singh KD, Murty US, Dixit VA. An overview of compound properties, multiparameter optimization, and computational drug design methods for PARP-1 inhibitor drugs. Eur J Med Chem 2023; 252:115300. [PMID: 36989813 DOI: 10.1016/j.ejmech.2023.115300] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Breast cancer treatment with PARP-1 inhibitors remains challenging due to emerging toxicities, drug resistance, and unaffordable costs of treatment options. How do we invent strategies to design better anti-cancer drugs? A part of the answer is in optimized compound properties, desirability functions, and modern computational drug design methods that drive selectivity and toxicity and have not been reviewed for PARP-1 inhibitors. Nonetheless, comparisons of these compound properties for PARP-1 inhibitors are not available in the literature. In this review, we analyze the physchem, PKPD space to identify inherent desirability functions characteristic of approved drugs that can be valuable for the design of better candidates. Recent literature utilizing ligand, structure-based drug design strategies and matched molecular pair analysis (MMPA) for the discovery of novel PARP-1 inhibitors are also reviewed. Thus, this perspective provides valuable insights into the medchem and multiparameter optimization of PARP-1 inhibitors that might be useful to other medicinal chemists.
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Wu K, Peng X, Li Y, Chen M, Liu Y, Liu D, Jiang L, He Y, Peng J, Cao X. Design, synthesis, and evaluation of 1H-benzo[d]imidazole-4-carboxamide PARP-1 inhibitors using different saturated nitrogen-contained heterocycle as linker group. Chem Biol Drug Des 2023; 101:1335-1347. [PMID: 36752693 DOI: 10.1111/cbdd.14216] [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: 11/04/2022] [Revised: 01/01/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) inhibitors have been successfully applied in the clinical treatment of various cancer. Side effects and drug resistant cases were reported, and more effective PARP-1 inhibitors were required. However, studies on the AD site of PARP-1 inhibitors are currently incomplete. Therefore, to synthesize more potential candidate PARP-1 inhibitors and disclose some AD site SAR of the PARP-1 inhibitors, herein, a series of 2-phenyl-benzimidazole-4-carboxamide derivatives using different saturated nitrogen-contained heterocycles as linker group (6a-6t) have been designed, synthesized, and evaluated PARP-1 inhibitory activity and proliferation inhibitory against BRCA-1 mutant MDA-MB-436 cell line in vitro. The results showed 6b (IC50 = 8.65 nM) exhibited the most PARP-1 enzyme inhibitory activity comparable with Veliparib (IC50 = 15.54 nM) and Olaparib (IC50 = 2.77 nM); 6m exhibited the strongest MDA-MB-436 cell anti-proliferation activity (IC50 = 25.36 ± 6.06 μM) comparable with Olaparib (IC50 = 23.89 ± 3.81 μM). The compounds 6b, 6r, and 6m could be potential candidates for effective PARP-1 inhibitors and valuable for further optimization. The analysis of activity data also showed that the holistically anti-proliferation activity of the 1,4-diazepane group was about~twofold than that of the piperazine group. Meanwhile, the terminal 3-methyl-furanyl group exhibited the most robust PARP-1 inhibitory and anti-proliferation activity. It is hoped that the results could benefitable for further optimization of PARP-1 inhibitors. Furthermore, we note that some compounds (6d,6g,6n,6p,6s) showed poor PARP-1 inhibitory (>500 nM) but relatively good anti-proliferation activity, which indicates the proliferation inhibitory mechanism against MDA-MB-436 cell line was worth investigating in-depth.
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Affiliation(s)
- Kaiyue Wu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Yang Li
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Miaojia Chen
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Yunfan Liu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Dan Liu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Lizhi Jiang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Yan He
- Department of Chemistry, Tsinghua University, Beijing, China.,The State Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, China
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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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Wu K, Chen M, Peng X, Li Y, Tang G, Peng J, Cao X. Recent Progress of the research on the benzimidazole PARP-1 inhibitors. Mini Rev Med Chem 2022; 22:2438-2462. [PMID: 35319364 DOI: 10.2174/1389557522666220321150700] [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: 11/16/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) is a multifunctional protein that plays an important role in DNA repair and genome integrity. PARP-1 inhibitors can be used as effective drugs not only to treat BRCA-1/2 deficient cancers because of the effect of synthetically lethal, but also to treat non-BRCA1/2 deficient tumours because of the effect of PARP capture. Therefore, the PARP inhibitors have become a focus of compelling research. Among these inhibitors, substituted benzimidazole derivatives were mainly concerned lead compounds. However, the commercial available benzimidazole PARP-1 inhibitors have some shortcomings such as serious toxicity in combination with chemotherapy drugs, in vivo cardiovascular side effects such as anemia. Therefore it's crucial for scientists to explore more structure-activity relationships of the benzimidazole PARP-1 inhibitors and access safer and more effective PARP inhibitors. As the binding region of PARP-1 and the substrates is usually characterized as NI site and AD site, the modification of benzimidazoles mainly occurs on the benzimidazole skeleton (NI site), and the side chain of benzimidazole on 2-C position (AD site). Herein, the recent progresses of the researches of benzamides PARP inhibitors were introduced. We noticed that even though many efforts were taken to the modification of NI sites, there were still lacks of optimistic and impressive results. However, the structure-activity relationships of the modification of AD sites have not thoroughly discovered yet. We hope that enlightened by the previous researches, more researches of AD site should be occurred and more effective benzimidazole PARP-1 inhibitors could be designed, synthesized, and applied to clinics.
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Affiliation(s)
- Kaiyue Wu
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Miaojia Chen
- Department of Pharmacy, the first People\'s Hospital, Pingjiang, Yueyang, Hunan, China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yang Li
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Guotao Tang
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Junmei Peng
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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