1
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Qin Q, Lu S, Guo Z, Li Z, Fu Q, Wang X, Wu T, Sun Y, Liu N, Zhang H, Zhao D, Cheng M. Discovery of novel indazole derivatives as second-generation TRK inhibitors. Eur J Med Chem 2024; 276:116640. [PMID: 39033612 DOI: 10.1016/j.ejmech.2024.116640] [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: 05/06/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024]
Abstract
NTRK gene fusion leads to the activation of downstream signaling pathways, which is a oncogenic driver in various cancers. NTRK fusion-positive cancers can be treated with the first-generation TRK inhibitors, larotrectinib and entrectinib. Unfortunately, the patients eventually face the dilemma of no drugs available as the emergence of certain resistance mutations. The development of efficient and broad-spectrum second-generation TRK inhibitors is still of great significance. Here, we analyzed the binding modes of compounds 6, 10 with TRKA protein, respectively, a series of novel indazole TRK inhibitors were designed and synthesized using molecular hybridization strategy. Among them, the optimal compound B31 showed strong antiproliferative activities against Km-12, Ba/F3-TRKAG595R, and Ba/F3-TRKAG667C cell lines with IC50 values of 0.3, 4.7, and 9.9 nM, respectively. And the inhibitory effect against TRKAG667C (IC50 = 9.9 nM) was better than that of selitrectinib (IC50 = 113.1 nM). Further, compound B31 exhibited moderate kinase selectivity and excellent plasma stability (t1/2 > 480 min). In vivo pharmacokinetic studies in Sprague-Dawley rats showed that B31 had acceptable pharmacokinetic properties.
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Affiliation(s)
- 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
| | - Shuyu Lu
- 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
| | - Zhiqiang Guo
- 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
| | - Zhuo Li
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Haoyu 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
| | - 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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2
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Liu ZQ, Zhang Q, Liu YL, Yu XQ, Chui RH, Zhang LL, Zhao B, Ma LY. Recent contributions of pyridazine as a privileged scaffold of anticancer agents in medicinal chemistry: An updated review. Bioorg Med Chem 2024; 111:117847. [PMID: 39121679 DOI: 10.1016/j.bmc.2024.117847] [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: 06/22/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Pyridazine, as a privileged scaffold, has been extensively utilized in drug development due to its multiple biological activities. Especially around its distinctive anticancer property, a massive number of pyridazine-containing compounds have been synthesized and evaluated that target a diverse array of biological processes involved in cancer onset and progression. These include glutaminase 1 (GLS1) inhibitors, tropomyosin receptor kinase (TRK) inhibitors, and bromodomain containing protein (BRD) inhibitors, targeting aberrant tumor metabolism, cell signal transduction and epigenetic modifications, respectively. Pyridazine moieties functioned as either core frameworks or warheads in the above agents, exhibiting promising potential in cancer treatment. Therefore, the review aims to summarize the recent contributions of pyridazine derivatives as potent anticancer agents between 2020 and 2024, focusing mainly on their structure-activity relationships (SARs) and development strategies, with a view to show that the application of the pyridazine scaffold by different medicinal chemists provides new insights into the rational design of anticancer drugs.
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Affiliation(s)
- Zi-Qiang Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Qian Zhang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Yu-Lin Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Xiao-Qian Yu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Rui-Hao Chui
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Lin-Lin Zhang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China
| | - Bing Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China.
| | - Li-Ying Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China, School of Pharmaceutical Science and Institute of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, PR China; China Meheco Topfond Pharmaceutical Co., Key Laboratory of Cardio-cerebrovascular Drug, Zhumadian 463000, PR China.
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3
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Jin X, Ding N, Guo HY, Hu Q. Macrocyclic-based strategy in drug design: From lab to the clinic. Eur J Med Chem 2024; 277:116733. [PMID: 39098132 DOI: 10.1016/j.ejmech.2024.116733] [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: 07/05/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Macrocyclic compounds have emerged as potent tools in the field of drug design, offering unique advantages for enhancing molecular recognition, improving pharmacokinetic properties, and expanding the chemical space accessible to medicinal chemists. This review delves into the evolutionary trajectory of macrocyclic-based strategies, tracing their journey from laboratory innovations to clinical applications. Beginning with an exploration of the defining structural features of macrocycles and their impact on drug-like characteristics, this discussion progresses to highlight key design principles that have facilitated the development of diverse macrocyclic drug candidates. Through a series of illustrative representative case studies from approved macrocyclic drugs and candidates spanning various therapeutic areas, particular emphasis is placed on their efficacy in targeting challenging protein-protein interactions, enzymes, and receptors. Additionally, this review thoroughly examines how macrocycles effectively address critical issues such as metabolic stability, oral bioavailability and selectivity. Valuable insights into optimization strategies employed during both approved and clinical phases underscore successful translation of promising leads into efficacious therapies while providing valuable perspectives on harnessing the full potential of macrocycles in drug discovery and development endeavors.
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Affiliation(s)
- Xin Jin
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ning Ding
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hong-Yu Guo
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Hu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
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4
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Darlami O, Pun R, Ahn SH, Kim SH, Shin D. Macrocyclization strategy for improving candidate profiles in medicinal chemistry. Eur J Med Chem 2024; 272:116501. [PMID: 38754142 DOI: 10.1016/j.ejmech.2024.116501] [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: 04/06/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Macrocycles are defined as cyclic compounds with 12 or more members. In medicinal chemistry, they are categorized based on their core chemistry into cyclic peptides and macrocycles. Macrocycles are advantageous because of their structural diversity and ability to achieve high affinity and selectivity towards challenging targets that are often not addressable by conventional small molecules. The potential of macrocyclization to optimize drug-like properties while maintaining adequate bioavailability and permeability has been emphasized as a key innovation in medicinal chemistry. This review provides a detailed case study of the application of macrocyclization over the past 5 years, starting from the initial analysis of acyclic active compounds to optimization of the resulting macrocycles for improved efficacy and drug-like properties. Additionally, it illustrates the strategic value of macrocyclization in contemporary drug discovery efforts.
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Affiliation(s)
- Om Darlami
- College of Pharmacy, Gachon University, Hambakmoe-ro 191, Yeunsu-gu, Incheon, 21935, Republic of Korea
| | - Rabin Pun
- College of Pharmacy, Gachon University, Hambakmoe-ro 191, Yeunsu-gu, Incheon, 21935, Republic of Korea
| | - Sung-Hoon Ahn
- College of Pharmacy, Kangwon National University, Gangwondaehak-gil 1, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Seok-Ho Kim
- College of Pharmacy, Kangwon National University, Gangwondaehak-gil 1, Chuncheon, Gangwon-do, 24341, Republic of Korea.
| | - Dongyun Shin
- College of Pharmacy, Gachon University, Hambakmoe-ro 191, Yeunsu-gu, Incheon, 21935, Republic of Korea.
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5
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Zheng X, Chen Z, Guo M, Liang H, Song X, Liu Y, Liao Z, Zhang Y, Guo J, Zhou Y, Zhang ZM, Tu Z, Zhang Y, Chen Y, Zhang Z, Lu X. Structure-Based Optimization of Pyrazinamide-Containing Macrocyclic Derivatives as Fms-like Tyrosine Kinase 3 (FLT3) Inhibitors to Overcome Clinical Mutations. ACS Pharmacol Transl Sci 2024; 7:1485-1506. [PMID: 38751627 PMCID: PMC11092118 DOI: 10.1021/acsptsci.4c00071] [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: 02/08/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Secondary mutations in Fms-like tyrosine kinase 3-tyrosine kinase domain (FLT3-TKD) (e.g., D835Y and F691L) have become a major on-target resistance mechanism of FLT3 inhibitors, which present a significant clinical challenge. To date, no effective drugs have been approved to simultaneously overcome clinical resistance caused by these two mutants. Thus, a series of pyrazinamide macrocyclic compounds were first designed and evaluated to overcome the secondary mutations of FLT3. The representative 8v exhibited potent inhibitory activities against FLT3D835Y and FLT3D835Y/F691L with IC50 values of 1.5 and 9.7 nM, respectively. 8v also strongly suppressed the proliferation against Ba/F3 cells transfected with FLT3-ITD, FLT3-ITD-D835Y, FLT3-ITD-F691L, FLT3-ITD-D835Y-F691L, and MV4-11 acute myeloid leukemia (AML) cell lines with IC50 values of 12.2, 10.5, 24.6, 16.9, and 6.8 nM, respectively. Furthermore, 8v demonstrated ideal anticancer efficacy in a Ba/F3-FLT3-ITD-D835Y xenograft model. The results suggested that 8v can serve as a promising macrocycle-based FLT3 inhibitor for the treatment of AML.
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Affiliation(s)
- Xuan Zheng
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhiwen Chen
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ming Guo
- Department
of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local
Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hong Liang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Song
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yiling Liu
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhenling Liao
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yan Zhang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jing Guo
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhi-min Zhang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhengchao Tu
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ye Zhang
- Guangxi
Key Laboratory of Drug Discovery and Optimization, School of Pharmacy, Guilin Medical University, Guilin 541199, China
| | - Yongheng Chen
- Department
of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local
Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhang Zhang
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaoyun Lu
- State
Key Laboratory of Bioactive Molecules and Druggability Assessment,
International Cooperative Laboratory of Traditional Chinese Medicine
Modernization and Innovative Drug Discovery of Chinese Ministry of
Education, Guangzhou City Key Laboratory of Precision Chemical Drug
Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
- Department
of Hematology, Guangdong Second Provincial General Hospital, Jinan University, Guangzhou 510632, China
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6
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [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: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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7
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Xiang S, Lu X. Selective type II TRK inhibitors overcome xDFG mutation mediated acquired resistance to the second-generation inhibitors selitrectinib and repotrectinib. Acta Pharm Sin B 2024; 14:517-532. [PMID: 38322338 PMCID: PMC10840435 DOI: 10.1016/j.apsb.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/15/2023] [Accepted: 10/24/2023] [Indexed: 02/08/2024] Open
Abstract
Neurotrophic receptor kinase (NTRK) fusions are actionable oncogenic drivers of multiple pediatric and adult solid tumors, and tropomyosin receptor kinase (TRK) has been considered as an attractive therapeutic target for "pan-cancer" harboring these fusions. Currently, two generations TRK inhibitors have been developed. The representative second-generation inhibitors selitrectinib and repotrectinib were designed to overcome clinic acquired resistance of the first-generation inhibitors larotrectinib or entrectinib resulted from solvent-front and gatekeeper on-target mutations. However, xDFG (TRKAG667C/A/S, homologous TRKCG696C/A/S) and some double mutations still confer resistance to selitrectinib and repotrectinib, and overcoming these resistances represents a major unmet clinical need. In this review, we summarize the acquired resistance mechanism of the first- and second-generation TRK inhibitors, and firstly put forward the emerging selective type II TRK inhibitors to overcome xDFG mutations mediated resistance. Additionally, we concluded our perspectives on new challenges and future directions in this field.
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Affiliation(s)
- Shuang Xiang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
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8
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Sun JG, Nie P, Herdewijn P, Li XJ. Exploring the synthetic approaches and clinical prowess of established macrocyclic pharmaceuticals. Eur J Med Chem 2024; 264:116051. [PMID: 38104377 DOI: 10.1016/j.ejmech.2023.116051] [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: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Macrocyclic compounds, characterized by cyclic structures, often originate from either modified forms of unicyclic canonical molecules or natural products. Within the field of medicinal chemistry, there has been a growing fascination with drug-like macrocycles in recent years, primarily due to compelling evidence indicating that macrocyclization can significantly influence both the biological and physiochemical properties, as well as the selectivity, when compared to their acyclic counterparts. The approval of contemporary pharmaceutical agents like Lorlatinib underscore the notable clinical relevance of drug-like macrocycles. Nonetheless, the synthesis of these drug-like macrocycles poses substantial challenges, primarily stemming from the complexity of ring-closing reactions, which are inherently dependent on the size and geometry of the bridging linker, impacting overall yields. Nevertheless, macrocycles offer a promising avenue for expanding the synthetic toolkit in medicinal chemistry, enabling the creation of bioactive compounds. To shed light on the subject, we delve into the clinical prowess of established macrocyclic drugs, spanning various therapeutic areas, including oncology, and infectious diseases. Case studies of clinically approved macrocyclic agents illustrate their profound impact on patient care and disease management. As we embark on this journey through the world of macrocyclic pharmaceuticals, we aim to provide a comprehensive overview of their synthesis and clinical applications, shedding light on the pivotal role they play in modern medicine.
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Affiliation(s)
- Jian-Gang Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Peng Nie
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Xiao-Jing Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
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9
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Zhao X, Kong Y, Ji Y, Xin X, Chen L, Chen G, Yu C. Classification models for predicting the bioactivity of pan-TRK inhibitors and SAR analysis. Mol Divers 2023:10.1007/s11030-023-10735-2. [PMID: 37910346 DOI: 10.1007/s11030-023-10735-2] [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: 07/14/2023] [Accepted: 09/22/2023] [Indexed: 11/03/2023]
Abstract
Tropomyosin receptor kinases (TRKs) are important broad-spectrum anticancer targets. The oncogenic rearrangement of the NTRK gene disrupts the extracellular structural domain and epitopes for therapeutic antibodies, making small-molecule inhibitors essential for treating NTRK fusion-driven tumors. In this work, several algorithms were used to construct descriptor-based and nondescriptor-based models, and the models were evaluated by outer 10-fold cross-validation. To find a model with good generalization ability, the dataset was partitioned by random and cluster-splitting methods to construct in- and cross-domain models, respectively. Among the 48 models built, the model with the combination of the deep neural network (DNN) algorithm and extended connectivity fingerprints 4 (ECFP4) descriptors achieved excellent performance in both dataset divisions. The results indicate that the DNN algorithm has a strong generalization prediction ability, and the richness of features plays a vital role in predicting unknown spatial molecules. Additionally, we combined the clustering results and decision tree models of fingerprint descriptors to perform structure-activity relationship analysis. It was found that nitrogen-containing aromatic heterocyclic and benzo heterocyclic structures play a crucial role in enhancing the activity of TRK inhibitors. Workflow for generating predictive models for TRK inhibitors.
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Affiliation(s)
- Xiaoman Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing, 100029, People's Republic of China
- College of Bio engineering, No. 9 Liangshuihe 1st Street, Beijing, 100176, People's Republic of China
| | - Yue Kong
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing, 100029, People's Republic of China
| | - Yueshan Ji
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing, 100029, People's Republic of China
| | - Xiulan Xin
- College of Bio engineering, No. 9 Liangshuihe 1st Street, Beijing, 100176, People's Republic of China
| | - Liang Chen
- College of Bio engineering, No. 9 Liangshuihe 1st Street, Beijing, 100176, People's Republic of China
| | - Guang Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing, 100029, People's Republic of China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, Beijing, 100029, People's Republic of China.
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10
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Wang Z, Wang J, Wang Y, Xiang S, Zhou H, Song S, Song X, Tu Z, Zhou Y, Ding K, Zhang ZM, Zhang Z, Lu X. Structure-Based Optimization of the Third Generation Type II Macrocycle TRK Inhibitors with Improved Activity against Solvent-Front, xDFG, and Gatekeeper Mutations. J Med Chem 2023; 66:12950-12965. [PMID: 37676745 DOI: 10.1021/acs.jmedchem.3c00899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The solvent-front (SF), gatekeeper, and xDFG motif mutations of tropomyosin receptor kinase (TRK) mediating acquired resistance of larotrectinib and entrectinib represent an unmet clinical need. To date, no effective drugs are being approved to overcome these mutants. Thus, a series of macrocycle compounds were designed and synthesized as new type II TRK inhibitors to combat clinically relevant mutations. The representative compound 10g exhibited excellent potency against wide type TRKA/C, TRKAG595R, TRKAG667C, and TRKAF589L with IC50 values of 5.21, 4.51, 6.77, 1.42, and 6.13 nM, respectively, and a good kinome selectivity against 378 kinases. 10g also strongly suppressed the proliferation of Ba/F3 cells transfected with SF, GK, xDFG, and others (Val to Met) single mutants with IC50 values of 1.43-47.56 nM. Moreover, 10g demonstrated ideal antitumor efficacy in both BaF3-CD74-NTRK1G595R and BaF3-CD74-NTRK1G667C xenograft models. The study provides a promising lead compound for pan-anticancer drug discovery.
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Affiliation(s)
- Zuqin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jie Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yongjin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Shuang Xiang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Hengliang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Shukai Song
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Song
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhengchao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
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El-Nassan HB, Al-Qadhi MA. Recent advances in the discovery of tropomyosin receptor kinases TRKs inhibitors: A mini review. Eur J Med Chem 2023; 258:115618. [PMID: 37413881 DOI: 10.1016/j.ejmech.2023.115618] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023]
Abstract
The tropomyosin receptor tyrosine kinases (TRKs) control the cell proliferation mainly in the nervous system and are encoded by NTRK genes. Fusion and mutation of NTRK genes were detected in various types of cancers. Many small molecules TRK inhibitors have been discovered during the last two decades and some of them have entered clinical trials. Moreover, two of these inhibitors; larotrectinib and entrectinib; were approved by FDA for the treatment of TRK-fusion positive solid tumors. However, mutation of TRK enzymes resulted in resistance to both drugs. Therefore, next generation TRK inhibitors were discovered to overcome the acquired drug resistance. Additionally, the off-target and on-target adverse effects on the brain initiated the need for selective TRK subtype inhibitors. Indeed, some molecules were recently reported as selective TRKA or TRKC inhibitors with minimal CNS side effects. The current review highlighted the efforts done during the last three years in the design and discovery of novel TRK inhibitors.
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Affiliation(s)
- Hala B El-Nassan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| | - Mustafa A Al-Qadhi
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
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12
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Zheng J, Li B, Wu Y, Wu X, Wang Y. Targeting Arginine Methyltransferase PRMT5 for Cancer Therapy: Updated Progress and Novel Strategies. J Med Chem 2023. [PMID: 37366223 DOI: 10.1021/acs.jmedchem.3c00250] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
As a predominant type II protein arginine methyltransferase, PRMT5 plays critical roles in various normal cellular processes by catalyzing the mono- and symmetrical dimethylation of a wide range of histone and nonhistone substrates. Clinical studies have revealed that high expression of PRMT5 is observed in different solid tumors and hematological malignancies and is closely associated with cancer initiation and progression. Accordingly, PRMT5 is becoming a promising anticancer target and has received great attention in both the pharmaceutical industry and the academic community. In this Perspective, we comprehensively summarize recent advances in the development of first-generation PRMT5 enzymatic inhibitors and highlight novel strategies targeting PRMT5 in the past 5 years. We also discuss the challenges and opportunities of PRMT5 inhibition, with the aim of shedding light on future PRMT5 drug discovery.
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Affiliation(s)
- Jiahong Zheng
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bang Li
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yingqi Wu
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiaoshuang Wu
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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13
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Cao Z, Zhang J, Guo M, Shao B, Wei X, Li S, Wang P, Zhai X. Discovery of novel phenyl triazole analogs as TRK/ALK dual inhibitors with prospective antitumor effects. Bioorg Chem 2023; 136:106563. [PMID: 37121107 DOI: 10.1016/j.bioorg.2023.106563] [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: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
The exploration of novel anaplastic lymphoma kinase (ALK) and tropomyosin receptor kinase (TRK) dual inhibitors tended to serve as targeted treatment of cancer. Herein, a series of phenyl triazole derivatives were designed and synthesized as ALK/TRK dual regulators based on structure-based drug design (SBDD) strategy and were evaluated for antiproliferative activity by MTT assay. Accordingly, all compounds showed surprising cytotoxicity with IC50 values below 10 μM on KM12, H2228 and KARPAS299 cell lines. Among them, compound 13a bearing (2-(4-methylpiperazin-1-yl)phenyl)morpholinomethanone moiety was identified as the optimal hit in enzymatic screening with IC50 values of 1.9 nM (TRKA), 7.2 nM (ALK) and 65.2 nM (ALKL1196M), respectively. Furthermore, 13a could inhibit KM12 cell migration and colony formation in a dose dependent manner. Meanwhile, AO/EB staining indicated that the pro-apoptotic effect of 13a was comparable to that of Entrectinib at the dose of 200 nM. Ultimately, the binding model of 13a with TRKA and ALK well established its mode of action which accounted for the superior activities as a promising antitumor candidate.
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Affiliation(s)
- Zhi Cao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiahao Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengrao Guo
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bin Shao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiujian Wei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Sen Li
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Peng Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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14
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Wang G, Wu Y, Wu C, Shuai W, Jiang T, Wang A, Bu F, Sun Q, Ouyang L. Rational design and crystallographic analysis of novel isoform-selective TRKA inhibitors for cancer therapy. Acta Pharm Sin B 2023; 13:440-443. [PMID: 36815052 PMCID: PMC9939310 DOI: 10.1016/j.apsb.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022] Open
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15
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Xiang S, Wang J, Huang H, Wang Z, Song X, Zhou Y, Jin F, He X, Zhang ZM, Tu Z, Ding K, Zhang Z, Lu X. Switch type I to type II TRK inhibitors for combating clinical resistance induced by xDFG mutation for cancer therapy. Eur J Med Chem 2022; 245:114899. [DOI: 10.1016/j.ejmech.2022.114899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/13/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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16
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Gong Y, Wu FX, Wang MS, Xu HC, Zhuo LS, Yang GF, Huang W. Discovery of 3-pyrazolyl-substituted pyrazolo[1,5-a]pyrimidine derivatives as potent TRK inhibitors to overcome clinically acquired resistance. Eur J Med Chem 2022; 241:114654. [DOI: 10.1016/j.ejmech.2022.114654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022]
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