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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Merighi A. Brain-Derived Neurotrophic Factor, Nociception, and Pain. Biomolecules 2024; 14:539. [PMID: 38785946 PMCID: PMC11118093 DOI: 10.3390/biom14050539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
This article examines the involvement of the brain-derived neurotrophic factor (BDNF) in the control of nociception and pain. BDNF, a neurotrophin known for its essential role in neuronal survival and plasticity, has garnered significant attention for its potential implications as a modulator of synaptic transmission. This comprehensive review aims to provide insights into the multifaceted interactions between BDNF and pain pathways, encompassing both physiological and pathological pain conditions. I delve into the molecular mechanisms underlying BDNF's involvement in pain processing and discuss potential therapeutic applications of BDNF and its mimetics in managing pain. Furthermore, I highlight recent advancements and challenges in translating BDNF-related research into clinical practice.
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Affiliation(s)
- Adalberto Merighi
- Department of Veterinary Sciences, University of Turin, 10095 Turin, Italy
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3
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Tao W, Liu Y, Lin X, Song B, Zeng X. Prediction of multi-relational drug-gene interaction via Dynamic hyperGraph Contrastive Learning. Brief Bioinform 2023; 24:bbad371. [PMID: 37864294 DOI: 10.1093/bib/bbad371] [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: 06/28/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
Drug-gene interaction prediction occupies a crucial position in various areas of drug discovery, such as drug repurposing, lead discovery and off-target detection. Previous studies show good performance, but they are limited to exploring the binding interactions and ignoring the other interaction relationships. Graph neural networks have emerged as promising approaches owing to their powerful capability of modeling correlations under drug-gene bipartite graphs. Despite the widespread adoption of graph neural network-based methods, many of them experience performance degradation in situations where high-quality and sufficient training data are unavailable. Unfortunately, in practical drug discovery scenarios, interaction data are often sparse and noisy, which may lead to unsatisfactory results. To undertake the above challenges, we propose a novel Dynamic hyperGraph Contrastive Learning (DGCL) framework that exploits local and global relationships between drugs and genes. Specifically, graph convolutions are adopted to extract explicit local relations among drugs and genes. Meanwhile, the cooperation of dynamic hypergraph structure learning and hypergraph message passing enables the model to aggregate information in a global region. With flexible global-level messages, a self-augmented contrastive learning component is designed to constrain hypergraph structure learning and enhance the discrimination of drug/gene representations. Experiments conducted on three datasets show that DGCL is superior to eight state-of-the-art methods and notably gains a 7.6% performance improvement on the DGIdb dataset. Further analyses verify the robustness of DGCL for alleviating data sparsity and over-smoothing issues.
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Affiliation(s)
- Wen Tao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Yuansheng Liu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Xuan Lin
- School of Computer Science, Xiangtan University, Xiangtan, 411105 Hunan, China
- Key Laboratory of Intelligent Computing and Information Processing, Ministry of Education (Xiangtan University), Xiangtan, 411105 Hunan, China
| | - Bosheng Song
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082 Hunan, China
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4
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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: 6] [Impact Index Per Article: 6.0] [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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5
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Qin Q, Fu Q, Wang X, Lv R, Lu S, Guo Z, Wu T, Sun Y, Sun Y, Liu N, Zhao D, Cheng M. Design, synthesis and biological evaluation of novel indolin-2-one derivatives as potent second-generation TRKs inhibitors. Eur J Med Chem 2023; 253:115291. [PMID: 37030091 DOI: 10.1016/j.ejmech.2023.115291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023]
Abstract
Tropomyosin receptor kinases (TRKs) are effective targets for anti-cancer drug discovery. The first-generation type I TRKs inhibitors, larotrectinib and entrectinib, exhibit durable disease control in the clinic. The emergence of acquired resistance mediated by secondary mutations in the TRKs domain significantly reduces the therapeutic efficacy of these two drugs, indicating an unmet clinical need. In this study, we designed a potent and orally bioavailable TRK inhibitor, compound 24b, using a molecular hybridization strategy. Compound 24b exhibited significant inhibitory potency against multiple TRK mutants in both biochemical and cellular assays. Furthermore, compound 24b induced apoptosis of Ba/F3-TRKAG595R and Ba/F3-TRKAG667C cells in a dose-dependent manner. Additionally, compound 24b exhibited moderate kinase selectivity. In vitro stability revealed that compound 24b showed excellent plasma stability (t1/2 > 289.1 min) and moderate liver microsomal stability (t1/2 = 44.3 min). Pharmacokinetic studies have revealed that compound 24b is an orally bioavailable TRK inhibitor with a good oral bioavailability of 116.07%. These results indicate that compound 24b be used as a lead molecule for further modifications to overcome drug-resistant mutants of TRK.
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6
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Ito T, Kinoshita K, Tomizawa M, Shinohara S, Nishii H, Matsushita M, Hattori K, Kohchi Y, Kohchi M, Hayase T, Watanabe F, Hasegawa K, Tanaka H, Kuramoto S, Takanashi K, Oikawa N. Discovery of CH7057288 as an Orally Bioavailable, Selective, and Potent pan-TRK Inhibitor. J Med Chem 2022; 65:12427-12444. [PMID: 36066182 DOI: 10.1021/acs.jmedchem.2c01099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinase fusions involving tropomyosin receptor kinases (TRKs) have been proven to act as strong oncogenic drivers and are therefore recognized as attractive therapeutic targets. We screened an in-house kinase-focused library and identified a promising hit compound with a unique tetracyclic scaffold. Compound 1 showed high TRK selectivity but moderate cell growth inhibitory activity as well as a potential risk of inducing CYP3A4. In this report, chemical modification intended to improve TRK inhibition and avoid CYP3A4 induction enabled us to identify an orally bioavailable, selective, and potent TRK inhibitor 7.
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Affiliation(s)
- Toshiya Ito
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Kazutomo Kinoshita
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Masaki Tomizawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Shojiro Shinohara
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Hiroki Nishii
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masayuki Matsushita
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kazuo Hattori
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Yasunori Kohchi
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masami Kohchi
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Tadakatsu Hayase
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Fumio Watanabe
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kiyoshi Hasegawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hiroshi Tanaka
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Shino Kuramoto
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kenji Takanashi
- Research Division, Chugai Pharmaceutical Co. Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Nobuhiro Oikawa
- Research Division, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
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7
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Pan S, Zhang L, Luo X, Nan J, Yang W, Bin H, Li Y, Huang Q, Wang T, Pan Z, Mu B, Wang F, Tian C, Liu Y, Li L, Yang S. Structural Optimization and Structure-Activity Relationship Studies of 6,6-Dimethyl-4-(phenylamino)-6 H-pyrimido[5,4- b][1,4]oxazin-7(8 H)-one Derivatives as A New Class of Potent Inhibitors of Pan-Trk and Their Drug-Resistant Mutants. J Med Chem 2022; 65:2035-2058. [PMID: 35080890 DOI: 10.1021/acs.jmedchem.1c01597] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tropomyosin receptor kinases (TrkA, TrkB, and TrkC) are attractive therapeutic targets for multiple cancers. Two first-generation small-molecule Trks inhibitors, larotrectinib and entrectinib, have just been approved to use clinically. However, the drug-resistance mutations of Trks have already emerged, which calls for new-generation Trks inhibitors. Herein, we report the structural optimization and structure-activity relationship studies of 6,6-dimethyl-4-(phenylamino)-6H-pyrimido[5,4-b][1,4]oxazin-7(8H)-one derivatives as a new class of pan-Trk inhibitors. The prioritized compound 11g exhibited low nanomolar IC50 values against TrkA, TrkB, and TrkC and various drug-resistant mutants. It also showed good kinase selectivity. 11g displayed excellent in vitro antitumor activity and strongly suppressed Trk-mediated signaling pathways in intact cells. In in vivo studies, compound 11g exhibited good antitumor activity in BaF3-TEL-TrkA and BaF3-TEL-TrkCG623R allograft mouse models without exhibiting apparent toxicity. Collectively, 11g could be a promising lead compound for drug discovery targeting Trks and deserves further investigation.
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Affiliation(s)
- Shulei Pan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Liting Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xinling Luo
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jinshan Nan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Wei Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Huachao Bin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yang Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiao Huang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Tianqi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhiling Pan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Bo Mu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Falu Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Chenyu Tian
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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8
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Imidazo[1,2-b]pyridazine as privileged scaffold in medicinal chemistry: An extensive review. Eur J Med Chem 2021; 226:113867. [PMID: 34607244 DOI: 10.1016/j.ejmech.2021.113867] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Imidazo[1,2-b]pyridazine scaffold represents an important class of heterocyclic nucleus which provides various bioactives molecules. Among them, the successful kinase inhibitor ponatinib led to a resurgence of interest in exploring new imidazo[1,2-b]pyridazine-containing derivatives for their putative therapeutic applications in medicine. This present review intends to provide a state-of-the-art of this framework in medicinal chemistry from 1966 to nowadays, unveiling different aspects of its structure-activity relationships (SAR). This extensive literature surveil may guide medicinal chemists for the quest of novel imidazo[1,2-b]pyridazine compounds with enhanced pharmacokinetics profile and efficiency.
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9
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Subramanian G, Duclos B, Johnson PD, Williams T, Ross JT, Bowen SJ, Zhu Y, White JA, Hedke C, Huczek D, Collard W, Javens C, Vairagoundar R, Respondek T, Zachary T, Maddux T, Cox MR, Kamerling S, Gonzales AJ. In Pursuit of an Allosteric Human Tropomyosin Kinase A ( hTrkA) Inhibitor for Chronic Pain. ACS Med Chem Lett 2021; 12:1847-1852. [PMID: 34795875 DOI: 10.1021/acsmedchemlett.1c00483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
Human β-nerve growth factor (β-NGF) and its associated receptor, human tropomyosin receptor kinase A (hTrkA), have been demonstrated to be key factors in the perception of pain. However, efficacious small molecule therapies targeting the intracellularly located hTrkA kinase have not been explored thoroughly for pain management. Herein, we report the pharmacological properties of a selective hTrkA allosteric inhibitor, 1. 1 was shown to be active against the full length hTrkA, showing preferential binding for the inactive kinase, and was confirmed through the X-ray of hTrkA···1 bound complex. 1 was also found to inhibit β-NGF induced neurite outgrowth in rat PC12 cells. Daily oral administration of 1 improved the joint compression threshold of rats injected intra-articularly with monoiodoacetate over a 14-day period. The efficacy of 1 in a relevant chronic pain model of osteoarthritis coupled with in vitro confirmation of target mediation makes allosteric hTrkA inhibitors potential candidates for modulating pain.
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Affiliation(s)
- Govindan Subramanian
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Brian Duclos
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Paul D. Johnson
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Tracey Williams
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Jason T. Ross
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Scott J. Bowen
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Yaqi Zhu
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Julie A. White
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Carolyn Hedke
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Dennis Huczek
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Wendy Collard
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Christopher Javens
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Rajendran Vairagoundar
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Tomasz Respondek
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Theresa Zachary
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Todd Maddux
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Mark R. Cox
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Steven Kamerling
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
| | - Andrea J. Gonzales
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Building 300, Kalamazoo, Michigan 49007, United States
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10
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Nguyen T, Le H, Quinn TP, Nguyen T, Le TD, Venkatesh S. GraphDTA: predicting drug-target binding affinity with graph neural networks. Bioinformatics 2021; 37:1140-1147. [PMID: 33119053 DOI: 10.1093/bioinformatics/btaa921] [Citation(s) in RCA: 284] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/01/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
SUMMARY The development of new drugs is costly, time consuming and often accompanied with safety issues. Drug repurposing can avoid the expensive and lengthy process of drug development by finding new uses for already approved drugs. In order to repurpose drugs effectively, it is useful to know which proteins are targeted by which drugs. Computational models that estimate the interaction strength of new drug-target pairs have the potential to expedite drug repurposing. Several models have been proposed for this task. However, these models represent the drugs as strings, which is not a natural way to represent molecules. We propose a new model called GraphDTA that represents drugs as graphs and uses graph neural networks to predict drug-target affinity. We show that graph neural networks not only predict drug-target affinity better than non-deep learning models, but also outperform competing deep learning methods. Our results confirm that deep learning models are appropriate for drug-target binding affinity prediction, and that representing drugs as graphs can lead to further improvements. AVAILABILITY OF IMPLEMENTATION The proposed models are implemented in Python. Related data, pre-trained models and source code are publicly available at https://github.com/thinng/GraphDTA. All scripts and data needed to reproduce the post hoc statistical analysis are available from https://doi.org/10.5281/zenodo.3603523. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thin Nguyen
- Applied Artificial Intelligence Institute, Deakin University, Geelong, VIC, 3216, Australia
| | - Hang Le
- Faculty of Information Technology, Nha Trang University, Nha Trang, Khanh Hoa, Viet Nam
| | - Thomas P Quinn
- Applied Artificial Intelligence Institute, Deakin University, Geelong, VIC, 3216, Australia
| | - Tri Nguyen
- Applied Artificial Intelligence Institute, Deakin University, Geelong, VIC, 3216, Australia
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, 5095, Australia
| | - Svetha Venkatesh
- Applied Artificial Intelligence Institute, Deakin University, Geelong, VIC, 3216, Australia
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11
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Obeng S, Hiranita T, León F, McMahon LR, McCurdy CR. Novel Approaches, Drug Candidates, and Targets in Pain Drug Discovery. J Med Chem 2021; 64:6523-6548. [PMID: 33956427 DOI: 10.1021/acs.jmedchem.1c00028] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because of the problems associated with opioids, drug discovery efforts have been employed to develop opioids with reduced side effects using approaches such as biased opioid agonism, multifunctional opioids, and allosteric modulation of opioid receptors. Receptor targets such as adrenergic, cannabinoid, P2X3 and P2X7, NMDA, serotonin, and sigma, as well as ion channels like the voltage-gated sodium channels Nav1.7 and Nav1.8 have been targeted to develop novel analgesics. Several enzymes, such as soluble epoxide hydrolase, sepiapterin reductase, and MAGL/FAAH, have also been targeted to develop novel analgesics. In this review, old and recent targets involved in pain signaling and compounds acting at these targets are summarized. In addition, strategies employed to reduce side effects, increase potency, and efficacy of opioids are also elaborated. This review should aid in propelling drug discovery efforts to discover novel analgesics.
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Affiliation(s)
- Samuel Obeng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.,Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Takato Hiranita
- Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Francisco León
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia 29208, United States
| | - Lance R McMahon
- Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.,Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida 32610, United States
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12
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Giraud F, Pereira E, Anizon F, Moreau P. Recent Advances in Pain Management: Relevant Protein Kinases and Their Inhibitors. Molecules 2021; 26:molecules26092696. [PMID: 34064521 PMCID: PMC8124620 DOI: 10.3390/molecules26092696] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
The purpose of this review is to underline the protein kinases that have been established, either in fundamental approach or clinical trials, as potential biological targets in pain management. Protein kinases are presented according to their group in the human kinome: TK (Trk, RET, EGFR, JAK, VEGFR, SFK, BCR-Abl), CMGC (p38 MAPK, MEK, ERK, JNK, ASK1, CDK, CLK2, DYRK1A, GSK3, CK2), AGC (PKA, PKB, PKC, PKMζ, PKG, ROCK), CAMK, CK1 and atypical/other protein kinases (IKK, mTOR). Examples of small molecule inhibitors of these biological targets, demonstrating an analgesic effect, are described. Altogether, this review demonstrates the fundamental role that protein kinase inhibitors could play in the development of new pain treatments.
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13
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Jiang T, Wang G, Liu Y, Feng L, Wang M, Liu J, Chen Y, Ouyang L. Development of small-molecule tropomyosin receptor kinase (TRK) inhibitors for NTRK fusion cancers. Acta Pharm Sin B 2021; 11:355-372. [PMID: 33643817 PMCID: PMC7893124 DOI: 10.1016/j.apsb.2020.05.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Tropomyosin receptor kinase A, B and C (TRKA, TRKB and TRKC), which are well-known members of the cell surface receptor tyrosine kinase (RTK) family, are encoded by the neurotrophic receptor tyrosine kinase 1, 2 and 3 (NTRK1, NTRK2 and NTRK3) genes, respectively. TRKs can regulate cell proliferation, differentiation and even apoptosis through the RAS/MAPKs, PI3K/AKT and PLCγ pathways. Gene fusions involving NTRK act as oncogenic drivers of a broad diversity of adult and pediatric tumors, and TRKs have become promising antitumor targets. Therefore, achieving a comprehensive understanding of TRKs and relevant TRK inhibitors should be urgently pursued for the further development of novel TRK inhibitors for potential clinical applications. This review focuses on summarizing the biological functions of TRKs and NTRK fusion proteins, the development of small-molecule TRK inhibitors with different chemotypes and their activity and selectivity, and the potential therapeutic applications of these inhibitors for future cancer drug discovery efforts.
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Key Words
- AFAP1, actin filament-associated protein 1
- AML, acute myeloid leukemia
- ARHGEF2, Rho/Rac guanine nucleotide exchange factor 2
- BCAN, brevican
- BDNF, brain-derived neurotrophic factor
- BTBD1, BTB (POZ) domain containing 1
- CDK-2, cyclin-dependent kinase 2
- CR, complete response
- CRC, colorectal cancer
- CTCs, sequencing of circulating tumor cells
- DFG, Asp-Phe-Gly
- DOR, durable objective responses
- ETV6, ETS translocation variant 6
- EWG, electron-withdrawing group
- FDA, U.S. Food and Drug Administration
- FISH, fluorescence in situ hybridization
- GBM, glioblastoma multiforme
- HNSCC, head and neck squamous cell carcinoma
- HTS, high-throughput screening
- ICC, intrahepatic cholangiocarcinoma
- IG-C2, Ig-like C2 type I
- LMNA, lamin A/C
- MASC, mammary analogue secretory carcinoma
- MPRIP, myosin phosphatase Rho interacting protein
- NACC2, NACC family member 2
- NCCN, National Comprehensive Cancer Network
- NFASC, neurofascin
- NGF, nerve growth factor
- NGS, next-generation sequencing of tumor tissue
- NSCLC, non-small cell lung cancer
- NT3, neurotrophin-3
- NTRK fusion cancer
- NTRK, neurotrophic receptor tyrosine kinase
- Neurotrophic receptor tyrosine kinase fusions
- OAK, osteoarthritis of the knee
- ORR, overall response rate
- PAN3, poly(A) nuclease 3
- PPL, periplakin
- PROTAC proteolysis targeting chimera, QKI
- RABGTPase activating protein 1-like, RFWD2
- RTK, receptor tyrosine kinase
- SAR, structure–activity relationship
- SBC, secretory breast carcinoma
- SCYL3, SCY1 like pseudokinase 3
- SQSTM1, sequestosome 1
- Small-molecule inhibitor
- TFG, TRK-fused gene
- TP53, tumor protein P53
- TPM3, tropomyosin 3
- TPR, translocated promoter region
- TRIM24, tripartite motif containing 24
- TRK, tropomyosin receptor kinase
- Tropomyosin receptor kinase
- VCL, vinculin
- VEGFR2, vascular endothelial growth factor receptor 2
- quaking I protein, RABGAP1L
- ring finger and WD repeat domain 2, E3 ubiquitin protein ligase
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Affiliation(s)
- Tingting Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Meng Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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15
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Ferrini F, Salio C, Boggio EM, Merighi A. Interplay of BDNF and GDNF in the Mature Spinal Somatosensory System and Its Potential Therapeutic Relevance. Curr Neuropharmacol 2021; 19:1225-1245. [PMID: 33200712 PMCID: PMC8719296 DOI: 10.2174/1570159x18666201116143422] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/17/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022] Open
Abstract
The growth factors BDNF and GDNF are gaining more and more attention as modulators of synaptic transmission in the mature central nervous system (CNS). The two molecules undergo a regulated secretion in neurons and may be anterogradely transported to terminals where they can positively or negatively modulate fast synaptic transmission. There is today a wide consensus on the role of BDNF as a pro-nociceptive modulator, as the neurotrophin has an important part in the initiation and maintenance of inflammatory, chronic, and/or neuropathic pain at the peripheral and central level. At the spinal level, BDNF intervenes in the regulation of chloride equilibrium potential, decreases the excitatory synaptic drive to inhibitory neurons, with complex changes in GABAergic/glycinergic synaptic transmission, and increases excitatory transmission in the superficial dorsal horn. Differently from BDNF, the role of GDNF still remains to be unraveled in full. This review resumes the current literature on the interplay between BDNF and GDNF in the regulation of nociceptive neurotransmission in the superficial dorsal horn of the spinal cord. We will first discuss the circuitries involved in such a regulation, as well as the reciprocal interactions between the two factors in nociceptive pathways. The development of small molecules specifically targeting BDNF, GDNF and/or downstream effectors is opening new perspectives for investigating these neurotrophic factors as modulators of nociceptive transmission and chronic pain. Therefore, we will finally consider the molecules of (potential) pharmacological relevance for tackling normal and pathological pain.
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Affiliation(s)
- Francesco Ferrini
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
- Department of Psychiatry & Neuroscience, Université Laval, Québec, Canada
| | - Chiara Salio
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Elena M. Boggio
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Adalberto Merighi
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
- National Institute of Neuroscience, Grugliasco, Italy
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16
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Subramanian G, Vairagoundar R, Bowen SJ, Roush N, Zachary T, Javens C, Williams T, Janssen A, Gonzales A. Synthetic inhibitor leads of human tropomyosin receptor kinase A ( hTrkA). RSC Med Chem 2020; 11:370-377. [PMID: 33479642 PMCID: PMC7536819 DOI: 10.1039/c9md00554d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/22/2019] [Indexed: 11/21/2022] Open
Abstract
In silico virtual screening followed by in vitro biochemical, biophysical, and cellular screening resulted in the identification of distinctly different hTrkA kinase domain inhibitor scaffolds. X-ray structural analysis of representative inhibitors bound to hTrkA kinase domain defined the binding mode and rationalized the mechanism of action. Preliminary assessment of the sub-type selectivity against the closest hTrkB isoform, and early ADME guided the progression of select inhibitor leads in the screening cascade. The possibility of the actives sustaining to known hTrkA resistance mutations assessed in silico offers initial guidance into the required multiparametric lead optimization to arrive at a clinical candidate.
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Affiliation(s)
- Govindan Subramanian
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Rajendran Vairagoundar
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Scott J Bowen
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Nicole Roush
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Theresa Zachary
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Christopher Javens
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Tracey Williams
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Ann Janssen
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
| | - Andrea Gonzales
- Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA .
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17
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Subramanian G, Zhu Y, Bowen SJ, Roush N, White JA, Huczek D, Zachary T, Javens C, Williams T, Janssen A, Gonzales A. Lead identification and characterization of hTrkA type 2 inhibitors. Bioorg Med Chem Lett 2019; 29:126680. [PMID: 31610943 DOI: 10.1016/j.bmcl.2019.126680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 12/26/2022]
Abstract
Virtual in silico structure-guided modeling, followed by in vitro biochemical screening of a subset of commercially purchasable compound collection resulted in the identification of several human tropomyosin receptor kinase A (hTrkA) inhibitors that bind the orthosteric ATP site and exhibit binding preference for the inactive kinase conformation. The type 2 binding mode with the DFG-out and αC-helix out hTrkA kinase domain conformation was confirmed from X-ray crystallographic solution of a representative inhibitor analog, 1b. Additional hTrkA and hTrkB (selectivity) assays in recombinant cells, neurite outgrowth inhibition using rat PC12 cells, early ADME profiling, and preliminary pharmacokinetic evaluation in rodents guided the lead inhibitor progression in the discovery screening funnel.
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Affiliation(s)
- Govindan Subramanian
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA.
| | - Yaqi Zhu
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Scott J Bowen
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Nicole Roush
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Julie A White
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Dennis Huczek
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Theresa Zachary
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Christopher Javens
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Tracey Williams
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Ann Janssen
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Andrea Gonzales
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
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18
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Subramanian G, Bowen SJ, Zhu Y, Roush N, Zachary T, Javens C, Williams T, Janssen A, Gonzales A. Type 2 inhibitor leads of human tropomyosin receptor kinase (hTrkA). Bioorg Med Chem Lett 2019; 29:126624. [PMID: 31444087 DOI: 10.1016/j.bmcl.2019.126624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
Abstract
In silico virtual screening using the ligand-based ROCS approach and the commercially purchasable compound collection from the ZINC database resulted in the identification of distinctly different and novel acetamide core frameworks with series representatives 1a and 2a exhibiting nanomolar affinity in the kinase domain only hTrkA HTRF biochemical assay. Additional experimental validation using the Caliper technology with either the active or inactive kinase conditions demonstrated the leads, 1a and 2a, to preferentially bind the kinase inactive state. X-ray structural analysis of the kinase domain of hTrkA…1a/2a complexes confirmed the kinase, bind the inhibitor leads in the inactive state and to exhibit a type 2 binding mode with the DFG-out and αC-helix out conformation. The leads also demonstrated sub-micromolar activity in the full length hTrkA cell-based assay and selectivity against the closely related hTrkB isoform. However, the poor microsomal stability and permeability of the leads is suggestive of a multiparametric lead optimization effort requirement for further progression.
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Affiliation(s)
- Govindan Subramanian
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA.
| | - Scott J Bowen
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Yaqi Zhu
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Nicole Roush
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Theresa Zachary
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Christopher Javens
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Tracey Williams
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Ann Janssen
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
| | - Andrea Gonzales
- Veterinary Medicine Research & Development, Zoetis, 333 Portage Street, Bldg. 300, Kalamazoo, MI 49007, USA
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19
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Subramanian G, Johnson PD, Zachary T, Roush N, Zhu Y, Bowen SJ, Janssen A, Duclos BA, Williams T, Javens C, Shalaly ND, Molina DM, Wittwer AJ, Hirsch JL. Deciphering the Allosteric Binding Mechanism of the Human Tropomyosin Receptor Kinase A ( hTrkA) Inhibitors. ACS Chem Biol 2019; 14:1205-1216. [PMID: 31059222 DOI: 10.1021/acschembio.9b00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Access to cryptic binding pockets or allosteric sites on a kinase that present themselves when the enzyme is in a specific conformational state offers a paradigm shift in designing the next generation small molecule kinase inhibitors. The current work showcases an extensive and exhaustive array of in vitro biochemical and biophysical tools and techniques deployed along with structural biology efforts of inhibitor-bound kinase complexes to characterize and confirm the cryptic allosteric binding pocket and docking mode of the small molecule actives identified for hTrkA. Specifically, assays were designed and implemented to lock the kinase in a predominantly active or inactive conformation and the effect of the kinase inhibitor probed to understand the hTrkA binding and hTrkB selectivity. The current outcome suggests that inhibitors with a fast association rate take advantage of the inactive protein conformation and lock the kinase state by also exhibiting a slow off-rate. This in turn shifts the inactive/active state protein conformational equilibrium cycle, affecting the subsequent downstream signaling.
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Affiliation(s)
- Govindan Subramanian
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Paul D. Johnson
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Theresa Zachary
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Nicole Roush
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Yaqi Zhu
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Scott J. Bowen
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Ann Janssen
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Brian A. Duclos
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Tracey Williams
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Christopher Javens
- Veterinary Medicine Research & Development (VMRD), Zoetis, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | | | | | - Arthur J. Wittwer
- Confluence Discovery Technologies, 4320 Forest Park Avenue, St. Louis, Missouri 63108, United States
| | - Jeffrey L. Hirsch
- Confluence Discovery Technologies, 4320 Forest Park Avenue, St. Louis, Missouri 63108, United States
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20
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Hefti F. Pharmacology of nerve growth factor and discovery of tanezumab, an anti-nerve growth factor antibody and pain therapeutic. Pharmacol Res 2019; 154:104240. [PMID: 31026504 DOI: 10.1016/j.phrs.2019.04.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/19/2019] [Indexed: 01/01/2023]
Abstract
The pharmacology of Nerve Growth Factor (NGF) and the discovery and development of tanezumab, a monoclonal anti-NGF antibody for the treatment of pain illustrate the complex and unpredictable nature of modern drug development. Initial efforts attempted to use NGF agonistically for Alzheimer's disease and neuropathies. Most unexpectedly, clinical studies unmasked hyperalgesic effects. These observations together with new data emerging from molecular and animal model studies stimulated the idea of using an NGF antagonist for chronic pain. These events also reflect the advances of neuropharmacology from classical small molecule efforts directed at neurotransmitter receptors to modern biotechnology with significant integration in molecular biology, biochemistry, and protein engineering.
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Affiliation(s)
- Franz Hefti
- Prevail Therapeutics Inc., 430 East 29th Street, New York, NY, 10016, USA.
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21
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Radioligands for Tropomyosin Receptor Kinase (Trk) Positron Emission Tomography Imaging. Pharmaceuticals (Basel) 2019; 12:ph12010007. [PMID: 30609832 PMCID: PMC6469173 DOI: 10.3390/ph12010007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 11/17/2022] Open
Abstract
The tropomyosin receptor kinases family (TrkA, TrkB, and TrkC) supports neuronal growth, survival, and differentiation during development, adult life, and aging. TrkA/B/C downregulation is a prominent hallmark of various neurological disorders including Alzheimer's disease (AD). Abnormally expressed or overexpressed full-length or oncogenic fusion TrkA/B/C proteins were shown to drive tumorigenesis in a variety of neurogenic and non-neurogenic human cancers and are currently the focus of intensive clinical research. Neurologic and oncologic studies of the spatiotemporal alterations in TrkA/B/C expression and density and the determination of target engagement of emerging antineoplastic clinical inhibitors in normal and diseased tissue are crucially needed but have remained largely unexplored due to the lack of suitable non-invasive probes. Here, we review the recent development of carbon-11- and fluorine-18-labeled positron emission tomography (PET) radioligands based on specifically designed small molecule kinase catalytic domain-binding inhibitors of TrkA/B/C. Basic developments in medicinal chemistry, radiolabeling and translational PET imaging in multiple species including humans are highlighted.
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22
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Yan W, Lakkaniga NR, Carlomagno F, Santoro M, McDonald NQ, Lv F, Gunaganti N, Frett B, Li HY. Insights into Current Tropomyosin Receptor Kinase (TRK) Inhibitors: Development and Clinical Application. J Med Chem 2018; 62:1731-1760. [PMID: 30188734 DOI: 10.1021/acs.jmedchem.8b01092] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The use of kinase-directed precision medicine has been heavily pursued since the discovery and development of imatinib. Annually, it is estimated that around ∼20 000 new cases of tropomyosin receptor kinase (TRK) cancers are diagnosed, with the majority of cases exhibiting a TRK genomic rearrangement. In this Perspective, we discuss current development and clinical applications for TRK precision medicine by providing the following: (1) the biological background and significance of the TRK kinase family, (2) a compilation of known TRK inhibitors and analysis of their cocrystal structures, (3) an overview of TRK clinical trials, and (4) future perspectives for drug discovery and development of TRK inhibitors.
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Affiliation(s)
- Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università Federico II , Via S Pansini 5 , 80131 Naples , Italy.,Istituto di Endocrinologia e Oncologia Sperimentale del CNR , Via S Pansini 5 , 80131 Naples , Italy
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università Federico II , Via S Pansini 5 , 80131 Naples , Italy
| | - Neil Q McDonald
- Signaling and Structural Biology Laboratory , The Francis Crick Institute , London NW1 1AT , U.K.,Institute of Structural and Molecular Biology, Department of Biological Sciences , Birkbeck College , Malet Street , London WC1E 7HX , U.K
| | - Fengping Lv
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Naresh Gunaganti
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
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Turk S, Merget B, Eid S, Fulle S. From Cancer to Pain Target by Automated Selectivity Inversion of a Clinical Candidate. J Med Chem 2018; 61:4851-4859. [PMID: 29746776 DOI: 10.1021/acs.jmedchem.8b00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Elimination of inadvertent binding is crucial for inhibitor design targeting conserved protein classes like kinases. Compounds in clinical trials provide a rich source for initiating drug design efforts by exploiting such secondary binding events. Considering both aspects, we shifted the selectivity of tozasertib, originally developed against AurA as cancer target, toward the pain target TrkA. First, selectivity-determining features in binding pockets were identified by fusing interaction grids of several key and off-target conformations. A focused library was subsequently created and prioritized using a multiobjective selection scheme that filters for selective and highly active compounds based on orthogonal methods grounded in computational chemistry and machine learning. Eighteen high-ranking compounds were synthesized and experimentally tested. The top-ranked compound has 10000-fold improved selectivity versus AurA, nanomolar cellular activity, and is highly selective in a kinase panel. This was achieved in a single round of automated in silico optimization, highlighting the power of recent advances in computer-aided drug design to automate design and selection processes.
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Affiliation(s)
- Samo Turk
- BioMed X Innovation Center , Im Neuenheimer Feld 515 , 69120 Heidelberg , Germany
| | - Benjamin Merget
- BioMed X Innovation Center , Im Neuenheimer Feld 515 , 69120 Heidelberg , Germany
| | - Sameh Eid
- BioMed X Innovation Center , Im Neuenheimer Feld 515 , 69120 Heidelberg , Germany
| | - Simone Fulle
- BioMed X Innovation Center , Im Neuenheimer Feld 515 , 69120 Heidelberg , Germany
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Abstract
PURPOSE OF REVIEW Opioid use and abuse has led to a worldwide opioid epidemic. And while opioids are clinically useful when appropriately indicated, they are associated with a wide range of dangerous side effects and whether they are effective at treating or eliminating chronic pain is controversial. There has long been a need for the development of nonopioid alternative treatments for patients that live in pain, and until recently, only a few effective treatments were available. Today, there are a wide range of nonopioid treatments available including NSAIDs, acetaminophen, corticosteroids, nerve blocks, SSRIs, neurostimulators, and anticonvulsants. However, these treatments are still not entirely effective at treating pain, which has sparked a new exploration of novel nonopioid pharmacotherapies. RECENT FINDINGS This manuscript will outline the most recent trends in novel nonopioid pharmacotherapy development including tramadol/dexketoprofen, TrkA inhibitors, tapentadol, opioid agonists, Nektar 181, TRV 130, ßarrestin2, bisphosphonates, antibodies, sodium channel blockers, NMDA antagonists, TRP receptors, transdermal vitamin D, AAK1 kinase inhibition, calcitonin gene-related peptide (CGRP), TRPV4 antagonists, cholecystokinin, delta opioid receptor, neurokinin, and gene therapy. The pharmacotherapies discussed in this manuscript outline promising opioid alternatives which can change the future of chronic pain treatment.
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Shahin R, Mansi I, Swellmeen L, Alwidyan T, Al-Hashimi N, Al-Qarar'h Y, Shaheen O. Ligand-based computer aided drug design reveals new tropomycin receptor kinase a (TrkA) inhibitors. J Mol Graph Model 2018; 80:327-352. [PMID: 29454290 DOI: 10.1016/j.jmgm.2018.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/26/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
Targeting tropomycin kinase A (TrkA) by small molecule inhibitors is considered as a promising strategy for treating several human cancers. To achieve this goal, a ligand based QSAR model was applied using the Discovery studio 4.5 (DS 4.5). Hence, a total list of 161 TrkA inhibitors was investigated. The TrkA inhibitors were extensively explored to detect their optimal physicochemical properties and pharmacophoric binding modes, which were converted into numeric descriptors and allowed to compete within the context of the Genetic Function Algorithm (GFA) approximations to find the subset of terms that correlates best with the activity. The resulted successful QSAR equation had statistical criteria of (r2129=0.67, r2LOO=0.61 r2PRESS against 32 external test inhibitors=0.50). Afterwards, the most successful pharmacophore: HypoB-T5-3, was used to screen compounds within the National Cancer institute (NCI) database. Only 41 compounds were retrieved and 21 of them exhibited anti-TrkA activity. The most potent hit had an IC50 value of 2.4μM. Later, upon docking the active hits into the TrkA binding pocket, important interactions were revealed including hydrogen bonding with the amino acids Asp668 and Lys544 in addition to the cation-π interactions with the sidechain of Arg559.
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Affiliation(s)
- Rand Shahin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical sciences, Hashemite University, Zarqa, Jordan.
| | - Iman Mansi
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical sciences, Hashemite University, Zarqa, Jordan.
| | - Lubna Swellmeen
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Zarqa University, Zarqa, Jordan.
| | - Tahani Alwidyan
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical sciences, Hashemite University, Zarqa, Jordan
| | - Nabil Al-Hashimi
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical sciences, Hashemite University, Zarqa, Jordan
| | - Yaser Al-Qarar'h
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical sciences, Hashemite University, Zarqa, Jordan
| | - Omar Shaheen
- Department of Pharmacology, Faculty of Medicine, University of Jordan, Amman, Jordan.
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Affiliation(s)
- Franziska Denk
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, King's College London, London SE1 1UL, United Kingdom
| | - David L. Bennett
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Stephen B. McMahon
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, King's College London, London SE1 1UL, United Kingdom
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27
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Price EA, Krasowska-Zoladek A, Nanda KK, Stachel SJ, Henze DA. Development of a pharmacodynamic biomarker to measure target engagement from inhibition of the NGF-TrkA pathway. J Neurosci Methods 2017; 282:34-42. [PMID: 28279735 DOI: 10.1016/j.jneumeth.2017.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/02/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND NGF signaling through TrkA triggers pathways involved in a wide range of biological effects. Clinical trials targeting either NGF or TrkA are ongoing to treat various diseases in the areas of oncology, neuroscience, and for pain, but there is no described measure of target engagement of TrkA in these studies. NEW METHOD We have developed custom ELISA assays to measure NGF-induced phosphorylation of TrkA specific for rodent and human receptors. Optimized tissue processing methods allow for detection in both the brain and in skin. In addition, TrkB and TrkC assays have been in established to evaluate selectivity against other neurotrophin receptors. RESULTS In a preclinical NGF-induced pain model, we show that pre-dosing with a TrkA inhibitor prevents phosphorylation of TrkA in the skin at a dose that is efficacious in reversal of thermal hypersensitivity. In addition, we show data in non-human primate and human skin supporting the potential use of this approach to enable translational target engagement. Comparison with existing methods: Existing methods involve animal models expressing TrkA tumors or injection of over-expressing TrkA recombinant cells into animals. Our method can measure target engagement in both normal and disease tissues in preclinical animal models and human skin. CONCLUSIONS We have developed methods to assess target engagement for drug programs aimed at disrupting NGF-induced TrkA signaling. This includes preclinical determination of selectivity against other neurotrophin receptors and estimation of functional peripheral restriction. Preliminary data supports this method can be translated into a clinical pharmacodynamic readout using human skin biopsies.
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Affiliation(s)
- Eric A Price
- Departments of Neuroscience Pain and Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc, West Point, PA 19486, USA.
| | - Alicja Krasowska-Zoladek
- Departments of Neuroscience Pain and Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc, West Point, PA 19486, USA
| | - Kausik K Nanda
- Departments of Neuroscience Pain and Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc, West Point, PA 19486, USA
| | - Shawn J Stachel
- Departments of Neuroscience Pain and Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc, West Point, PA 19486, USA
| | - Darrell A Henze
- Departments of Neuroscience Pain and Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc, West Point, PA 19486, USA
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Bailey JJ, Schirrmacher R, Farrell K, Bernard-Gauthier V. Tropomyosin receptor kinase inhibitors: an updated patent review for 2010-2016 - Part II. Expert Opin Ther Pat 2017; 27:831-849. [PMID: 28270021 DOI: 10.1080/13543776.2017.1297797] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION TrkA/B/C receptor activation supports growth, survival, and differentiation of discrete neuronal populations during development, adult life, and ageing but also plays numerous roles in human disease onset and progression. Trk-specific inhibitors have therapeutic applications in cancer and pain and thus constitute a growing area of interest in oncology and neurology. There has been substantial growth in the number of structural classes of Trk inhibitors and the number of industrial entrants to the Trk inhibitor field over the past six years. Areas covered: In Part II of this two-part review, the discussion of recent patent literature covering Trk family inhibitors is continued from Part I and clinical research with Trk inhibitors is considered. Expert opinion: Trk has been molecularly targeted for over a decade resulting in the progressive evolution of structurally diversified Trk inhibitors arising from scaffold hopping and HTS efforts. Correspondingly, there have been a growing number of clinical investigations utilizing Trk inhibitors in recent years, with a particular focus on the treatment of NTRK-fusion positive cancers and chronic pain. The observed potential of Trk inhibitors to cause adverse CNS side effects however suggests the need for a more rigorous consideration of BBB permeation capabilities during drug development.
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Affiliation(s)
- Justin J Bailey
- a Faculty of Medicine & Dentistry, Department of Oncology , University of Alberta , Edmonton , Canada
| | - Ralf Schirrmacher
- a Faculty of Medicine & Dentistry, Department of Oncology , University of Alberta , Edmonton , Canada
| | - Kristen Farrell
- a Faculty of Medicine & Dentistry, Department of Oncology , University of Alberta , Edmonton , Canada
| | - Vadim Bernard-Gauthier
- a Faculty of Medicine & Dentistry, Department of Oncology , University of Alberta , Edmonton , Canada
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29
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Bailey JJ, Schirrmacher R, Farrell K, Bernard-Gauthier V. Tropomyosin receptor kinase inhibitors: an updated patent review for 2010-2016 - Part I. Expert Opin Ther Pat 2017; 27:733-751. [PMID: 28270010 DOI: 10.1080/13543776.2017.1297796] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Tropomyosin receptor kinases (TrkA/B/C) play crucial roles in the development and maintenance of the nervous system, and aberrant expression of Trk has been implicated in neurological disorders as well as neural and non-neural neoplasms. Patent activity encompassing Trk inhibitors has grown substantially over the last 6 years, recognized by a rise in the number of pharmaceutical entrants to the field and the escalation of novel inhibitor chemotypes. Area covered: In Part I of this two part review, a biological and structural overview of Trk is provided in the context of Trk as a therapeutic target for cancer and pain, followed by the report of recent patent literature claiming small molecule inhibitors of Trk family kinases or which describe inhibitors developed for other kinase targets but include noteworthy Trk inhibition/application. The discussion of the patent literature continues in Part II of this review, which includes an in-depth view of the current clinical applications of Trk inhibitors. Expert opinion: Substantial synthetic efforts in Trk inhibitor development has propagated numerous and diverse inhibitor chemotypes, including TrkA-specific inhibitors. While many novel Trk inhibitors remain the original progeny of Trk-specific development programs, kinase inhibitors initially developed for other kinases have also been successfully repositioned for Trk.
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Affiliation(s)
- Justin J Bailey
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
| | - Ralf Schirrmacher
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
| | - Kristen Farrell
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
| | - Vadim Bernard-Gauthier
- a Faculty of Medicine & Dentistry , University of Alberta, Department of Oncology , Edmonton , AB , Canada
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30
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Furuya N, Momose T, Katsuno K, Fushimi N, Muranaka H, Handa C, Ozawa T, Kinoshita T. The juxtamembrane region of TrkA kinase is critical for inhibitor selectivity. Bioorg Med Chem Lett 2017; 27:1233-1236. [DOI: 10.1016/j.bmcl.2017.01.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 12/19/2022]
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31
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Kim D, Park JY, Kim JH. Docking-based In SilicoScreening for Identification of Micromolar Inhibitors of Tropomyosin-related Kinase A from Natural Origin. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Daehyun Kim
- Department of Chemistry; Chung-Ang University; Seoul 06974 Korea
| | - Jung Youl Park
- Industry-Academic Cooperation Foundation; Hanbat National University; Daejeon 34158 Korea
| | - Ji-Hyun Kim
- National CRI-Center for Chemical Dynamics in Living Cells; Chung-Ang University; Seoul 06974 Korea
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32
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Structural characterization of nonactive site, TrkA-selective kinase inhibitors. Proc Natl Acad Sci U S A 2016; 114:E297-E306. [PMID: 28039433 DOI: 10.1073/pnas.1611577114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of-but adjacent to-the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.
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33
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Crystal Structures of Neurotrophin Receptors Kinase Domain. VITAMINS AND HORMONES 2016; 104:1-18. [PMID: 28215291 DOI: 10.1016/bs.vh.2016.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neurotrophins and their receptors (Trk) play key roles in the development of the nervous system and in cell survival. Trk receptors are therefore attractive pharmacological targets for brain disorders as well as for cancers. While the druggability of the extracellular domain of the receptors, that specifically binds neurotrophins, is yet to be proven, the intracellular kinase domains are attractive targets for small-molecule binding. The recent crystal structures of the three isoforms of the Trk family, TrkA, TrkB, and TrkC have been described in their apo forms and in complex with potent and selective pan-Trk inhibitors. The description of the kinase domain of each of the isoforms will be discussed in their apo forms or bound to potent inhibitors of interest in cancer therapy. Nononcology indications and selectivity issues will also be discussed.
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34
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Norman BH, McDermott JS. Targeting the Nerve Growth Factor (NGF) Pathway in Drug Discovery. Potential Applications to New Therapies for Chronic Pain. J Med Chem 2016; 60:66-88. [DOI: 10.1021/acs.jmedchem.6b00964] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bryan H. Norman
- Discovery Chemistry
Research and Technologies and ‡Neurophysiology, Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, Lilly
Corporate Center, Indiana 46285, United States
| | - Jeff S. McDermott
- Discovery Chemistry
Research and Technologies and ‡Neurophysiology, Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, Lilly
Corporate Center, Indiana 46285, United States
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35
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Sami N, Kumar V, Islam A, Ali S, Ahmad F, Hassan I. Exploring Missense Mutations in Tyrosine Kinases Implicated with Neurodegeneration. Mol Neurobiol 2016; 54:5085-5106. [PMID: 27544236 DOI: 10.1007/s12035-016-0046-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022]
Abstract
Protein kinases are one of the largest families of evolutionarily related proteins and the third most common protein class of human genome. All the protein kinases share the same structural organization. They are made up of an extracellular domain, transmembrane domain and an intra cellular kinase domain. Missense mutations in these kinases have been studied extensively and correlated with various neurological disorders. Individual mutations in the kinase domain affect the functions of protein. The enhanced or reduced expression of protein leads to hyperactivation or inactivation of the signalling pathways, resulting in neurodegeneration. Here, we present extensive analyses of missense mutations in the tyrosine kinase focussing on the neurodegenerative diseases encompassing structure function relationship. This is envisaged to enhance our understanding about the neurodegeneration and possible therapeutic measures.
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Affiliation(s)
- Neha Sami
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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36
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Choe H, Son YH, Byun BJ, Choi SU, Lee K. Identification of Pyrrole[3,4-c]pyrazoles as Potent Tropomyosin Receptor Kinase A (TrkA) Inhibitors. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10862] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hyeonjeong Choe
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology; Daejeon 34114 Korea
- Department of Chemistry; KAIST; Daejeon 34141 Korea
| | - You Hwa Son
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology; Daejeon 34114 Korea
| | - Byung Jin Byun
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology; Daejeon 34114 Korea
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame IN 46556 USA
| | - Sang Un Choi
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology; Daejeon 34114 Korea
| | - Kwangho Lee
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology; Daejeon 34114 Korea
- Medicinal Chemistry & Pharmacology; Korea University of Science & Technology; Daejeon 34113 Korea
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37
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El-Damasy AK, Cho NC, Nam G, Pae AN, Keum G. Discovery of a Nanomolar Multikinase Inhibitor (KST016366): A New Benzothiazole Derivative with Remarkable Broad-Spectrum Antiproliferative Activity. ChemMedChem 2016; 11:1587-95. [PMID: 27405013 DOI: 10.1002/cmdc.201600224] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/25/2016] [Indexed: 01/07/2023]
Abstract
Herein we report the discovery of compound 6 [KST016366; 4-((2-(3-(4-((4-ethylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)ureido)benzo[d]thiazol-6-yl)oxy)picolinamide] as a new potent multikinase inhibitor through minor structural modification of our previously reported RAF kinase inhibitor A. In vitro anticancer evaluation of 6 showed substantial broad-spectrum antiproliferative activity against 60 human cancer cell lines. In particular, it showed GI50 values of 51.4 and 19 nm against leukemia K-562 and colon carcinoma KM12 cell lines, respectively. Kinase screening of compound 6 revealed its nanomolar-level inhibitory activity of certain oncogenic kinases implicated in both tumorigenesis and angiogenesis. Interestingly, 6 displays IC50 values of 0.82, 3.81, and 53 nm toward Tie2, TrkA, and ABL-1 (wild-type and T315I mutant) kinases, respectively. Moreover, 6 is orally bioavailable with a favorable in vivo pharmacokinetic profile. Compound 6 may serve as a promising candidate for further development of potent anticancer chemotherapeutics.
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Affiliation(s)
- Ashraf Kareem El-Damasy
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.,Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon, 305-350, Republic of Korea.,Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt
| | - Nam-Chul Cho
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea
| | - Ghilsoo Nam
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.,Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon, 305-350, Republic of Korea
| | - Ae Nim Pae
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea.,Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon, 305-350, Republic of Korea
| | - Gyochang Keum
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul, 136-791, Republic of Korea. .,Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon, 305-350, Republic of Korea.
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El-Damasy AK, Cho NC, Pae AN, Kim EE, Keum G. Novel 5-substituted-2-anilinoquinolines with 3-(morpholino or 4-methylpiperazin-1-yl)propoxy moiety as broad spectrum antiproliferative agents: Synthesis, cell based assays and kinase screening. Bioorg Med Chem Lett 2016; 26:3307-3312. [PMID: 27241691 DOI: 10.1016/j.bmcl.2016.05.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 11/30/2022]
Abstract
A series of new 2-anilinoquinolines possessing 3-(morpholino or 4-methylpiperazin-1-yl)propoxy moiety at C5 of quinoline has been designed and synthesized as potential anticancer agents. Their antiproliferative activities were evaluated against a panel of 60 cancer cell lines at NCI and compared with gefitinib as a reference compound. Most of the tested compounds displayed potent and broad spectrum antiproliferative activities. Compounds 7d, 7f and 7g showed strong inhibitory and lethal effects at 10μM concentration. Moreover, they manifested superior potencies and efficacies than gefitinib across the most tested cell lines. Compound 7d, with 4-chloro-3-trifluoromethylphenyl group, proved to be the most potent and efficacious derivative in this series, with mean GI50 and TGI values of 1.62μM and 3.47μM, respectively. Kinase screening of 7d against a panel of 47 oncogenic kinases revealed its selective inhibitory effect (96% inhibition) towards TrkA kinase. Furthermore, the most potent compounds showed low cytotoxic effects against HFF-1 normal cell line.
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Affiliation(s)
- Ashraf Kareem El-Damasy
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon 305-350, Republic of Korea; Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
| | - Nam-Chul Cho
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Ae Nim Pae
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon 305-350, Republic of Korea
| | - Eunice Eunkyeong Kim
- Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon 305-350, Republic of Korea; Biomedical Research Institute, KIST, Republic of Korea
| | - Gyochang Keum
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, Korea University of Science and Technology (UST), Gajungro 217, Youseong-gu, Daejeon 305-350, Republic of Korea.
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New approaches to treating pain. Bioorg Med Chem Lett 2016; 26:1103-19. [DOI: 10.1016/j.bmcl.2015.12.103] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/11/2022]
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40
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Recent Advances in the Development and Application of Radiolabeled Kinase Inhibitors for PET Imaging. Molecules 2015; 20:22000-27. [PMID: 26690113 PMCID: PMC6332294 DOI: 10.3390/molecules201219816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/18/2015] [Accepted: 12/01/2015] [Indexed: 12/20/2022] Open
Abstract
Over the last 20 years, intensive investigation and multiple clinical successes targeting protein kinases, mostly for cancer treatment, have identified small molecule kinase inhibitors as a prominent therapeutic class. In the course of those investigations, radiolabeled kinase inhibitors for positron emission tomography (PET) imaging have been synthesized and evaluated as diagnostic imaging probes for cancer characterization. Given that inhibitor coverage of the kinome is continuously expanding, in vivo PET imaging will likely find increasing applications for therapy monitoring and receptor density studies both in- and outside of oncological conditions. Early investigated radiolabeled inhibitors, which are mostly based on clinically approved tyrosine kinase inhibitor (TKI) isotopologues, have now entered clinical trials. Novel radioligands for cancer and PET neuroimaging originating from novel but relevant target kinases are currently being explored in preclinical studies. This article reviews the literature involving radiotracer design, radiochemistry approaches, biological tracer evaluation and nuclear imaging results of radiolabeled kinase inhibitors for PET reported between 2010 and mid-2015. Aspects regarding the usefulness of pursuing selective vs. promiscuous inhibitor scaffolds and the inherent challenges associated with intracellular enzyme imaging will be discussed.
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Bernard-Gauthier V, Schirrmacher R. Evaluation of WO2015042088 A1 - a novel urea-based scaffold for TrkA inhibition. Expert Opin Ther Pat 2015; 26:291-5. [DOI: 10.1517/13543776.2016.1118062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Jeong Y, Lim SM, Hong S. Discovery of wrightiadione as a novel template for the TrkA kinase inhibitors. Bioorg Med Chem Lett 2015; 25:5186-9. [PMID: 26442778 DOI: 10.1016/j.bmcl.2015.09.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 11/19/2022]
Abstract
Enzymatic kinase assays and docking simulation studies have shown that the natural product wrightiadione displays inhibitory activity toward TrkA and PLK3. In this study, the template of wrightiadione served as a starting point for Trk inhibitor development campaigns. Molecular simulation provided structural insights for the design of derivatives that were efficiently generated by our recently developed 3-step tandem synthetic approach, resulting in the discovery of compound 2h with biochemical potency at the single-digit micromolar level.
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Affiliation(s)
- Yujeong Jeong
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea; Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Min Lim
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea; Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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Efficient Syntheses of 1,2,3-Triazoloamide Derivatives Using Solid- and Solution-Phase Synthetic Approaches. Molecules 2015; 20:19984-20013. [PMID: 26556332 PMCID: PMC6332172 DOI: 10.3390/molecules201119673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/17/2022] Open
Abstract
Efficient synthetic routes for the preparation of secondary and tertiary 1,2,3-triazoloamide derivatives were developed. A secondary α-1,2,3-triazoloamide library was constructed and expanded by a previously developed solid-phase synthetic route and a tertiary 1,2,3-triazoloamide library was constructed by a parallel solution-phase synthetic route. The synthetic routes rely on amide formation with secondary amines and chloro-acid chlorides; SN2 reaction with sodium azide; and the selective [3 + 2] Hüisgen cycloaddition with appropriate terminal alkynes. The target secondary and tertiary 1,2,3-triazoloamide derivatives were obtained with three-diversity points in excellent overall yields and purities using the reported solid- and solution-phase synthetic routes, respectively.
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Hirose M, Kuroda Y, Murata E. NGF/TrkA Signaling as a Therapeutic Target for Pain. Pain Pract 2015; 16:175-82. [PMID: 26452158 DOI: 10.1111/papr.12342] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 06/15/2015] [Indexed: 01/03/2023]
Abstract
Nerve growth factor (NGF) was first discovered approximately 60 years ago by Rita Levi-Montalcini as a protein that induces the growth of nerves. It is now known that NGF is also associated with Alzheimer's disease and intractable pain, and hence, it, along with its high-affinity receptor, tropomyosin receptor kinase (Trk) A, is considered to be 1 of the new targets for therapies being developed to treat these diseases. Anti-NGF antibody and TrkA inhibitors are known drugs that suppress NGF/TrkA signaling, and many drugs of these classes have been developed thus far. Interestingly, local anesthetics also possess TrkA inhibitory effects. This manuscript describes the development of an analgesic that suppresses NGF/TrkA signaling, which is anticipated to be 1 of the new methods to treat intractable pain.
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Affiliation(s)
- Munetaka Hirose
- Department of Anesthesiology and Pain Medicine, Hyogo College of Medicine, Hyogo, Japan
| | - Yoshihiro Kuroda
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Hyogo, Japan
| | - Eri Murata
- Department of Anesthesiology and Reanimatology, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
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Choi HS, Rucker PV, Wang Z, Fan Y, Albaugh P, Chopiuk G, Gessier F, Sun F, Adrian F, Liu G, Hood T, Li N, Jia Y, Che J, McCormack S, Li A, Li J, Steffy A, Culazzo A, Tompkins C, Phung V, Kreusch A, Lu M, Hu B, Chaudhary A, Prashad M, Tuntland T, Liu B, Harris J, Seidel HM, Loren J, Molteni V. (R)-2-Phenylpyrrolidine Substituted Imidazopyridazines: A New Class of Potent and Selective Pan-TRK Inhibitors. ACS Med Chem Lett 2015; 6:562-7. [PMID: 26005534 DOI: 10.1021/acsmedchemlett.5b00050] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/16/2015] [Indexed: 02/07/2023] Open
Abstract
Deregulated kinase activities of tropomyosin receptor kinase (TRK) family members have been shown to be associated with tumorigenesis and poor prognosis in a variety of cancer types. In particular, several chromosomal rearrangements involving TRKA have been reported in colorectal, papillary thyroid, glioblastoma, melanoma, and lung tissue that are believed to be the key oncogenic driver in these tumors. By screening the Novartis compound collection, a novel imidazopyridazine TRK inhibitor was identified that served as a launching point for drug optimization. Structure guided drug design led to the identification of (R)-2-phenylpyrrolidine substituted imidazopyridazines as a series of potent, selective, orally bioavailable pan-TRK inhibitors achieving tumor regression in rats bearing KM12 xenografts. From this work the (R)-2-phenylpyrrolidine has emerged as an ideal moiety to incorporate in bicyclic TRK inhibitors by virtue of its shape complementarity to the hydrophobic pocket of TRKs.
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Affiliation(s)
- Ha-Soon Choi
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Paul V. Rucker
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Zhicheng Wang
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Yi Fan
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Pamela Albaugh
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Greg Chopiuk
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Francois Gessier
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Fangxian Sun
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Francisco Adrian
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Guoxun Liu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Tami Hood
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Yong Jia
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Jianwei Che
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Susan McCormack
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Allen Li
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Jie Li
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Auzon Steffy
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - AnneMarie Culazzo
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Celine Tompkins
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Van Phung
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Andreas Kreusch
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Min Lu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Bin Hu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Apurva Chaudhary
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Mahavir Prashad
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Tove Tuntland
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Bo Liu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Jennifer Harris
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - H. Martin Seidel
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Jon Loren
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Valentina Molteni
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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Bernard-Gauthier V, Bailey JJ, Aliaga A, Kostikov A, Rosa-Neto P, Wuest M, Brodeur GM, Bedell BJ, Wuest F, Schirrmacher R. Development of subnanomolar radiofluorinated (2-pyrrolidin-1-yl)imidazo[1,2-b]pyridazine pan-Trk inhibitors as candidate PET imaging probes. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00388a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dysregulation of tropomyosin receptor kinases (TrkA/B/C) expression and signalling is recognized as a hallmark of numerous neurodegenerative diseases including Parkinson's, Huntington's and Alzheimer's disease.
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Affiliation(s)
| | | | - Arturo Aliaga
- Translational Neuroimaging Laboratory
- McGill Centre for Studies in Aging
- Douglas Mental Health University Institute
- Montreal
- Canada
| | - Alexey Kostikov
- McConnell Brain Imaging Centre
- Montreal Neurological Institute
- McGill University
- Montreal
- Canada
| | - Pedro Rosa-Neto
- Translational Neuroimaging Laboratory
- McGill Centre for Studies in Aging
- Douglas Mental Health University Institute
- Montreal
- Canada
| | - Melinda Wuest
- Department of Oncology
- University of Alberta
- Edmonton
- Canada
| | | | - Barry J. Bedell
- Biospective Inc
- Montreal
- Canada
- Research Institute of the McGill University Health Centre
- Montreal
| | - Frank Wuest
- Department of Oncology
- University of Alberta
- Edmonton
- Canada
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Wang L, Liu N, Dai B. Metal-free site-selective C–N bond-forming reaction of polyhalogenated pyridines and pyrimidines. RSC Adv 2015. [DOI: 10.1039/c5ra18653f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A metal-free method for highly site-selective C–N bond-formation of polyhalogenated pyridines and pyrimidines is developed.
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Affiliation(s)
- Lei Wang
- School of Chemistry and Chemical Engineering
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan
- Shihezi University
- Shihezi
- China
| | - Ning Liu
- School of Chemistry and Chemical Engineering
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan
- Shihezi University
- Shihezi
- China
| | - Bin Dai
- School of Chemistry and Chemical Engineering
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan
- Shihezi University
- Shihezi
- China
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