1
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Xiong Y, Yu J. LRRK2 in Parkinson's disease: upstream regulation and therapeutic targeting. Trends Mol Med 2024; 30:982-996. [PMID: 39153957 PMCID: PMC11466701 DOI: 10.1016/j.molmed.2024.07.003] [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: 02/12/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 08/19/2024]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common causes of Parkinson's disease (PD) to date. Dysfunction in LRRK2 enzymatic activities and elevated protein levels are associated with the disease. How is LRRK2 activated, and what downstream molecular and cellular processes does LRRK2 regulate? Addressing these questions is crucial to decipher the disease mechanisms. In this review we focus on the upstream regulations and briefly discuss downstream substrates of LRRK2 as well as the cellular consequences caused by these regulations. Building on these basic findings, we discuss therapeutic strategies targeting LRRK2 and highlight the challenges in clinical trials. We further highlight the important questions that remains to be answered in the LRRK2 field.
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Affiliation(s)
- Yulan Xiong
- Department of Neuroscience, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
| | - Jianzhong Yu
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269, USA
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2
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Naskar A, Roy RK, Srivastava D, Patra N. Decoding Inhibitor Egression from Wild-Type and G2019S Mutant LRRK2 Kinase: Insights into Unbinding Mechanisms for Precision Drug Design in Parkinson's Disease. J Phys Chem B 2024; 128:6657-6669. [PMID: 38822803 DOI: 10.1021/acs.jpcb.4c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) remains a viable target for drug development since the discovery of the association of its mutations with Parkinson's disease (PD). G2019S (in the kinase domain) is the most common mutation for LRRK2-based PD. Though various types of inhibitors have been developed for the kinase domain to reduce the effect of the mutation, understanding the working of these inhibitors at the molecular level is still ongoing. This study focused on the exploration of the dissociation mechanism (pathways) of inhibitors from (WT and G2019S) LRRK2 kinase (using homology model CHK1 kinase), which is one of the crucial aspects in drug discovery. Here, two ATP-competitive type I inhibitors, PF-06447475 and MLi-2 (Comp1 and Comp2 ), and one non-ATP-competitive type II inhibitor, rebastinib (Comp3), were considered for this investigation. To study the unbinding process, random accelerated molecular dynamics simulations were performed. The binding free energies of the three inhibitors for different egression paths were determined using umbrella sampling. This work found four major egression pathways that were adopted by the inhibitors Comp1 (path1, path2, and path3), Comp2 (path1, path2 and path3), and Comp3 (path3 and path4). Also, the mechanism of unbinding for each path and key residues involved in unbinding were explored. Mutation was not observed to impact the preference of the particular egression pathways for both LRRK2-Comp1 and -Comp2 systems. However, the findings suggested that the size of the inhibitor molecules might have an effect on the preference of the egression pathways. The binding energy and residence time of the inhibitors followed a similar trend to experimental observations. The findings of this work might provide insight into designing more potent inhibitors for the G2019S LRRK2 kinase.
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Affiliation(s)
- Avigyan Naskar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Rakesh K Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Diship Srivastava
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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3
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Cao R, Chen C, Wen J, Zhao W, Zhang C, Sun L, Yuan L, Wu C, Shan L, Xi M, Sun H. Recent advances in targeting leucine-rich repeat kinase 2 as a potential strategy for the treatment of Parkinson's disease. Bioorg Chem 2023; 141:106906. [PMID: 37837728 DOI: 10.1016/j.bioorg.2023.106906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/24/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. Several single gene mutations involved in PD have been identified such as leucine-rich repeat kinase 2 (LRRK2), the most common cause of sporadic and familial PD. Its mutations have attracted much attention to therapeutically targeting this kinase. To date, many compounds including small chemical molecules with diverse scaffolds and RNA agents have been developed with significant amelioration in preclinical PD models. Currently, five candidates, DNL201, DNL151, WXWH0226, NEU-723 and BIIB094, have advanced to clinical trials for PD treatment. In this review, we describe the structure, pathogenic mutations and the mechanism of LRRK2, and summarize the development of LRRK2 inhibitors in preclinical and clinical studies, trying to provide an insight into targeting LRRK2 for PD intervention in future.
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Affiliation(s)
- Ruiwei Cao
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Caiping Chen
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Jing Wen
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Weihe Zhao
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | | | - Longhui Sun
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Liyan Yuan
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Chunlei Wu
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China
| | - Lei Shan
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China
| | - Meiyang Xi
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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4
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Naskar A, Bhanja KK, Roy RK, Patra N. Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study. Chemphyschem 2023; 24:e202300306. [PMID: 37584472 DOI: 10.1002/cphc.202300306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/17/2023]
Abstract
Mutations in multi-domain leucine-rich repeat kinase 2 (LRRK2) have been an interest to researchers as these mutations are associated with Parkinson's disease. G2019S mutation in LRRK2 kinase domain leads to the formation of additional hydrogen bonds by S2019 which results in stabilization of the active state of the kinase, thereby increasing kinase activity. Two additional hydrogen bonds of S2019 are reported separately. Here, a mechanistic picture of the formation of additional hydrogen bonds of S2019 with Q1919 (also with E1920) is presented using 'active' Roco4 kinase as a homology model and its relationship with the stabilization of the 'active' G2019S LRRK2 kinase. A conformational flipping of residue Q1919 was found which helped to form stable hydrogen bond with S2019 and made 'active' state more stable in G2019S LRRK2. Two different states were found within the 'active' kinase with respect to the conformational change (flipping) in Q1919. Two doubly-mutated systems, G2019S/Q1919A and G2019S/E1920 K, were studied separately to check the effect of Q1919 and E1920. For both cases, the stable S2 state was not formed, leading to a decrease in kinase activity. These results indicate that both the additional hydrogen bonds of S2019 (with Q1919 and E1920) are necessary to stabilize the active G2019S LRRK2.
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Affiliation(s)
- Avigyan Naskar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
| | - Kousik Kumar Bhanja
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
| | - Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad, 826004, India
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5
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Hu J, Zhang D, Tian K, Ren C, Li H, Lin C, Huang X, Liu J, Mao W, Zhang J. Small-molecule LRRK2 inhibitors for PD therapy: Current achievements and future perspectives. Eur J Med Chem 2023; 256:115475. [PMID: 37201428 DOI: 10.1016/j.ejmech.2023.115475] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that orchestrates a diverse array of cellular processes, including vesicle transport, autophagy, lysosome degradation, neurotransmission, and mitochondrial activity. Hyperactivation of LRRK2 triggers vesicle transport dysfunction, neuroinflammation, accumulation of α-synuclein, mitochondrial dysfunction, and the loss of cilia, ultimately leading to Parkinson's disease (PD). Therefore, targeting LRRK2 protein is a promising therapeutic strategy for PD. The clinical translation of LRRK2 inhibitors was historically impeded by issues surrounding tissue specificity. Recent studies have identified LRRK2 inhibitors that have no effect on peripheral tissues. Currently, there are four small-molecule LRRK2 inhibitors undergoing clinical trials. This review provides a summary of the structure and biological functions of LRRK2, along with an overview of the binding modes and structure-activity relationships (SARs) of small-molecule inhibitors targeting LRRK2. It offers valuable references for developing novel drugs targeting LRRK2.
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Affiliation(s)
- Jiarui Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Keyue Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Changyu Ren
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Heng Li
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaoli Huang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wuyu Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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6
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Tang X, Xing S, Ma M, Xu Z, Guan Q, Chen Y, Feng F, Liu W, Chen T, Chen Y, Sun H. The Development and Design Strategy of Leucine-Rich Repeat Kinase 2 Inhibitors: Promising Therapeutic Agents for Parkinson's Disease. J Med Chem 2023; 66:2282-2307. [PMID: 36758171 DOI: 10.1021/acs.jmedchem.2c01552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting millions of people worldwide. Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are the most common genetic risk factor for PD. Elevated LRRK2 kinase activity is found in idiopathic and familial PD cases. LRRK2 mutations are involved in multiple PD pathogeneses, including dysregulation of mitochondrial homeostasis, ciliogenesis, etc. Here, we provide a comprehensive overview of the biological function, structure, and mutations of LRRK2. We also examine recent advances and challenges in developing LRRK2 inhibitors and address prospective protein-based targeting strategies. The binding mechanisms, structure-activity relationships, and pharmacokinetic features of inhibitors are emphasized to provide a comprehensive compendium on the rational design of LRRK2 inhibitors. We hope that this publication can serve as a guide for designing novel LRRK2 inhibitors based on the summarized facts and perspectives.
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Affiliation(s)
- Xu Tang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Shuaishuai Xing
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Mingkang Ma
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Ziwei Xu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Qianwen Guan
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yuting Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People's Republic of China
- Jiangsu Food and Pharmaceuticals Science College, Institute of Food and Pharmaceuticals Research, Huai'an 223005, People's Republic of China
| | - Wenyuan Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
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7
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Tan S, Lu R, Yao D, Wang J, Gao P, Xie G, Liu H, Yao X. Identification of LRRK2 Inhibitors through Computational Drug Repurposing. ACS Chem Neurosci 2023; 14:481-493. [PMID: 36649061 DOI: 10.1021/acschemneuro.2c00672] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder that affects more than ten million people worldwide. However, the current PD treatments are still limited and alternative treatment strategies are urgently required. Leucine-rich repeat kinase 2 (LRRK2) has been recognized as a promising target for PD treatment. However, there are no approved LRRK2 inhibitors on the market. To rapidly identify potential drug repurposing candidates that inhibit LRRK2 kinase, we report a structure-based drug repurposing workflow that combines molecular docking, recursive partitioning model, molecular dynamics (MD) simulation, and molecular mechanics-generalized Born surface area (MM-GBSA) calculation. Thirteen compounds screened from our drug repurposing workflow were further evaluated through the experiment. The experimental results showed six drugs (Abivertinib, Aumolertinib, Encorafenib, Bosutinib, Rilzabrutinib, and Mobocertinib) with IC50 less than 5 μM that were identified as potential LRRK2 kinase inhibitors. The most potent compound Abivertinib showed potent inhibitions with IC50 toward G2019S mutation and wild-type LRRK2 of 410.3 nM and 177.0 nM, respectively. Our combination screening strategy had a 53% hit rate in this repurposing task. MD simulations and MM-GBSA free energy analysis further revealed the atomic binding mechanism between the identified drugs and G2019S LRRK2. In summary, the results showed that our drug repurposing workflow could be used to identify potent compounds for LRRK2. The potent inhibitors discovered in our work can be a starting point to develop more effective LRRK2 inhibitors.
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Affiliation(s)
- Shuoyan Tan
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou730000, China
| | - Ruiqiang Lu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou730000, China
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen518060, China
| | - Jun Wang
- Ping An Healthcare Technology, Beijing100000, China
| | - Peng Gao
- Ping An Healthcare Technology, Beijing100000, China
| | - Guotong Xie
- Ping An Healthcare Technology, Beijing100000, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou730000, China.,State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
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8
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Lesniak RK, Nichols RJ, Montine TJ. Development of mutation-selective LRRK2 kinase inhibitors as precision medicine for Parkinson's disease and other diseases for which carriers are at increased risk. Front Neurol 2022; 13:1016040. [PMID: 36388213 PMCID: PMC9643380 DOI: 10.3389/fneur.2022.1016040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Robert K. Lesniak
- Medicinal Chemistry Knowledge Center, Sarafan Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, United States
- Department of Pathology, Stanford University, Stanford, CA, United States
- *Correspondence: Robert K. Lesniak
| | - R. Jeremy Nichols
- Department of Pathology, Stanford University, Stanford, CA, United States
- R. Jeremy Nichols
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, United States
- Thomas J. Montine
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9
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Smith LJ, Lee CY, Menozzi E, Schapira AHV. Genetic variations in GBA1 and LRRK2 genes: Biochemical and clinical consequences in Parkinson disease. Front Neurol 2022; 13:971252. [PMID: 36034282 PMCID: PMC9416236 DOI: 10.3389/fneur.2022.971252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Variants in the GBA1 and LRRK2 genes are the most common genetic risk factors associated with Parkinson disease (PD). Both genes are associated with lysosomal and autophagic pathways, with the GBA1 gene encoding for the lysosomal enzyme, glucocerebrosidase (GCase) and the LRRK2 gene encoding for the leucine-rich repeat kinase 2 enzyme. GBA1-associated PD is characterized by earlier age at onset and more severe non-motor symptoms compared to sporadic PD. Mutations in the GBA1 gene can be stratified into severe, mild and risk variants depending on the clinical presentation of disease. Both a loss- and gain- of function hypothesis has been proposed for GBA1 variants and the functional consequences associated with each variant is often linked to mutation severity. On the other hand, LRRK2-associated PD is similar to sporadic PD, but with a more benign disease course. Mutations in the LRRK2 gene occur in several structural domains and affect phosphorylation of GTPases. Biochemical studies suggest a possible convergence of GBA1 and LRRK2 pathways, with double mutant carriers showing a milder phenotype compared to GBA1-associated PD. This review compares GBA1 and LRRK2-associated PD, and highlights possible genotype-phenotype associations for GBA1 and LRRK2 separately, based on biochemical consequences of single variants.
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Affiliation(s)
- Laura J. Smith
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Chiao-Yin Lee
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Elisa Menozzi
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Anthony H. V. Schapira
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
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10
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Thakur G, Kumar V, Lee KW, Won C. Structural Insights and Development of LRRK2 Inhibitors for Parkinson's Disease in the Last Decade. Genes (Basel) 2022; 13:1426. [PMID: 36011337 PMCID: PMC9408223 DOI: 10.3390/genes13081426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/01/2022] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disease, characterized by the specific loss of dopaminergic neurons in the midbrain. The pathophysiology of PD is likely caused by a variety of environmental and hereditary factors. Many single-gene mutations have been linked to this disease, but a significant number of studies indicate that mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are a potential therapeutic target for both sporadic and familial forms of PD. Consequently, the identification of potential LRRK2 inhibitors has been the focus of drug discovery. Various investigations have been conducted in academic and industrial organizations to investigate the mechanism of LRRK2 in PD and further develop its inhibitors. This review summarizes the role of LRRK2 in PD and its structural details, especially the kinase domain. Furthermore, we reviewed in vitro and in vivo findings of selected inhibitors reported to date against wild-type and mutant versions of the LRRK2 kinase domain as well as the current trends researchers are employing in the development of LRRK2 inhibitors.
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Affiliation(s)
- Gunjan Thakur
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Vikas Kumar
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea
| | - Keun Woo Lee
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea
| | - Chungkil Won
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
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11
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12
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Kluss JH, Lewis PA, Greggio E. Leucine-rich repeat kinase 2 (LRRK2): an update on the potential therapeutic target for Parkinson's disease. Expert Opin Ther Targets 2022; 26:537-546. [PMID: 35642531 DOI: 10.1080/14728222.2022.2082937] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AREAS COVERED In this review, we will provide an update on the current status of drugs and other technologies that have emerged in recent years and provide an overview of their efficacy in ameliorating LRRK2 kinase activity and overall safety in animal models and humans. EXPERT OPINION The growth of both target discovery and innovative drug design has sparked a lot of excitement for the future of how we treat Parkinson's disease. Given the immense focus on LRRK2 as a therapeutic target, it is expected within the next decade to determine its therapeutic properties, or lack thereof, for PD.
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Affiliation(s)
- Jillian H Kluss
- School of Pharmacy, University of Reading, Whiteknights, Reading, UK.,Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Patrick A Lewis
- School of Pharmacy, University of Reading, Whiteknights, Reading, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.,Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy.,Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
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13
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Discovery of G2019S-Selective Leucine Rich Repeat Protein Kinase 2 inhibitors with in vivo efficacy. Eur J Med Chem 2021; 229:114080. [PMID: 34992038 DOI: 10.1016/j.ejmech.2021.114080] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/20/2022]
Abstract
Mutations in the Leucine Rich Repeat Protein Kinase 2 gene (LRRK2) are the most common genetic causes of Parkinson's Disease (PD). The G2019S mutation is the most common inherited LRRK2 mutation, occurs in the kinase domain, and results in increased kinase activity. We report the discovery and development of compound 38, an indazole-based, G2019S-selective (>2000-fold vs. WT) LRRK2 inhibitor capable of entering rodent brain (Kp = 0.5) and selectively inhibiting G2019S-LRRK2. The compounds disclosed herein present a starting point for further development of brain penetrant G2019S selective inhibitors that hopefully reduce lung phenotype side-effects and pave the way to providing a precision medicine for people with PD who carry the G2019S mutation.
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14
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Tasegian A, Singh F, Ganley IG, Reith AD, Alessi DR. Impact of Type II LRRK2 inhibitors on signaling and mitophagy. Biochem J 2021; 478:3555-3573. [PMID: 34515301 PMCID: PMC8589421 DOI: 10.1042/bcj20210375] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/21/2023]
Abstract
Much effort has been devoted to the development of selective inhibitors of the LRRK2 as a potential treatment for LRRK2 driven Parkinson's disease. In this study, we first compare the properties of Type I (GSK3357679A and MLi-2) and Type II (GZD-824, Rebastinib and Ponatinib) kinase inhibitors that bind to the closed or open conformations of the LRRK2 kinase domain, respectively. We show that Type I and Type II inhibitors suppress phosphorylation of Rab10 and Rab12, key physiological substrates of LRRK2 and also promote mitophagy, a process suppressed by LRRK2. Type II inhibitors also display higher potency towards wild-type LRRK2 compared with pathogenic mutants. Unexpectedly, we find that Type II inhibitors, in contrast with Type I compounds, fail to induce dephosphorylation of a set of well-studied LRRK2 biomarker phosphorylation sites at the N-terminal region of LRRK2, including Ser935. These findings emphasize that the biomarker phosphorylation sites on LRRK2 are likely reporting on the open vs closed conformation of LRRK2 kinase and that only inhibitors which stabilize the closed conformation induce dephosphorylation of these biomarker sites. Finally, we demonstrate that the LRRK2[A2016T] mutant which is resistant to MLi-2 Type 1 inhibitor, also induces resistance to GZD-824 and Rebastinib suggesting this mutation could be exploited to distinguish off target effects of Type II inhibitors. Our observations provide a framework of knowledge to aid with the development of more selective Type II LRRK2 inhibitors.
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Affiliation(s)
- Anna Tasegian
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Francois Singh
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Ian G. Ganley
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Alastair D. Reith
- GlaxoSmithKline Pharmaceuticals R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Dario R. Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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15
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Allosteric inhibition of LRRK2, where are we now. Biochem Soc Trans 2021; 48:2185-2194. [PMID: 33079169 PMCID: PMC7609032 DOI: 10.1042/bst20200424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. In recent years, it has been shown that leucine-rich repeat kinase 2 (LRRK2) has a crucial function in both familial and sporadic forms of PD. LRRK2 pathogenic mutations are thought to result in an increase in LRRK2 kinase activity. Thus, inhibiting LRRK2 kinase activity has become a main therapeutic target. Many compounds capable of inhibiting LRRK2 kinase activity with high selectivity and brain availability have been described. However, the safety of long-term use of these ATP-competitive LRRK2 kinase inhibitors has been challenged by several studies. Therefore, alternative ways of targeting LRRK2 activity will have a great benefit. In this review, we discuss the recent progress in the development of allosteric inhibitors of LRRK2, mainly via interfering with GTPase activity, and propose potential new intra and interprotein interactions targets that can lead to open doors toward new therapeutics.
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16
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Azeggagh S, Berwick DC. The development of inhibitors of leucine-rich repeat kinase 2 (LRRK2) as a therapeutic strategy for Parkinson's disease: the current state of play. Br J Pharmacol 2021; 179:1478-1495. [PMID: 34050929 DOI: 10.1111/bph.15575] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/29/2022] Open
Abstract
Current therapeutic approaches for Parkinson's disease (PD) are based around treatments that alleviate symptoms but do not slow or prevent disease progression. As such, alternative strategies are needed. A promising approach is the use of molecules that reduce the function of leucine-rich repeat kinase (LRRK2). Gain-of-function mutations in LRRK2 account for a notable proportion of familial Parkinson's disease cases, and significantly, elevated LRRK2 kinase activity is reported in idiopathic Parkinson's disease. Here, we describe progress in finding therapeutically effective LRRK2 inhibitors, summarising studies that range from in vitro experiments to clinical trials. LRRK2 is a complex protein with two enzymatic activities and a myriad of functions. This creates opportunities for a rich variety of strategies and also increases the risk of unintended consequences. We comment on the strength and limitations of the different approaches and conclude that with two molecules under clinical trial and a diversity of alternative options in the pipeline, there is cause for optimism.
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Affiliation(s)
- Sonia Azeggagh
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Daniel C Berwick
- Institute of Medical and Biomedical Education, St George's, University of London, London, UK
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17
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Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE. Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature 2020; 588:344-349. [PMID: 32814344 PMCID: PMC7726071 DOI: 10.1038/s41586-020-2673-2] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease1 and is also linked to its idiopathic form2. LRRK2 has been proposed to function in membrane trafficking3 and colocalizes with microtubules4. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure5. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors.
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Affiliation(s)
- C K Deniston
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - J Salogiannis
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - S Mathea
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - D M Snead
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - I Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
| | - M Matyszewski
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - O Donosa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - R Watanabe
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - J Böhning
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | - A K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - E Villa
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.
| | - A E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA.
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18
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Ditsiou A, Cilibrasi C, Simigdala N, Papakyriakou A, Milton-Harris L, Vella V, Nettleship JE, Lo JH, Soni S, Smbatyan G, Ntavelou P, Gagliano T, Iachini MC, Khurshid S, Simon T, Zhou L, Hassell-Hart S, Carter P, Pearl LH, Owen RL, Owens RJ, Roe SM, Chayen NE, Lenz HJ, Spencer J, Prodromou C, Klinakis A, Stebbing J, Giamas G. The structure-function relationship of oncogenic LMTK3. SCIENCE ADVANCES 2020; 6:6/46/eabc3099. [PMID: 33188023 PMCID: PMC7673765 DOI: 10.1126/sciadv.abc3099] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/30/2020] [Indexed: 05/10/2023]
Abstract
Elucidating signaling driven by lemur tyrosine kinase 3 (LMTK3) could help drug development. Here, we solve the crystal structure of LMTK3 kinase domain to 2.1Å resolution, determine its consensus motif and phosphoproteome, unveiling in vitro and in vivo LMTK3 substrates. Via high-throughput homogeneous time-resolved fluorescence screen coupled with biochemical, cellular, and biophysical assays, we identify a potent LMTK3 small-molecule inhibitor (C28). Functional and mechanistic studies reveal LMTK3 is a heat shock protein 90 (HSP90) client protein, requiring HSP90 for folding and stability, while C28 promotes proteasome-mediated degradation of LMTK3. Pharmacologic inhibition of LMTK3 decreases proliferation of cancer cell lines in the NCI-60 panel, with a concomitant increase in apoptosis in breast cancer cells, recapitulating effects of LMTK3 gene silencing. Furthermore, LMTK3 inhibition reduces growth of xenograft and transgenic breast cancer mouse models without displaying systemic toxicity at effective doses. Our data reinforce LMTK3 as a druggable target for cancer therapy.
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Affiliation(s)
- Angeliki Ditsiou
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Chiara Cilibrasi
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Nikiana Simigdala
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos," 15341 Athens, Greece
| | - Leanne Milton-Harris
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Viviana Vella
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Joanne E Nettleship
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics Headington, Oxford OX3 7BN, UK
- Protein Production UK, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Jae Ho Lo
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Goar Smbatyan
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Panagiota Ntavelou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Teresa Gagliano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Maria Chiara Iachini
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Sahir Khurshid
- Faculty of Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Thomas Simon
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Storm Hassell-Hart
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Philip Carter
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London W12 0NN, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Raymond J Owens
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics Headington, Oxford OX3 7BN, UK
- Protein Production UK, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- The Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, UK
| | - S Mark Roe
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Naomi E Chayen
- Faculty of Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Chrisostomos Prodromou
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Apostolos Klinakis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Justin Stebbing
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London W12 0NN, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
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19
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Abstract
Introduction: Disease-modifying treatment for Parkinson's disease (PD) to halt or revert the disease progression remains an unmet medical need. LRRK2 kinase activity is abnormally elevated in PD patients carrying LRRK2 mutations, with G2019S as the most frequent one. Small molecules to inhibit LRRK2 kinase activity might provide a potential disease-modifying strategy for PD.Areas covered: This review provides an update of small molecule LRRK2 inhibitors in patents published from January 2014 to October 2019. The molecules are classified by their structural scaffolds.Expert opinion: Despite the tremendous efforts to push small molecule LRRK2 inhibitors toward clinical trials, the overall progress is somewhat disappointing due to the challenges in compound optimization and the putative concern of target-related adverse effects. It is challenging to optimize multiple parameters including kinase selectivity, CNS penetration, and unbound fraction in brain simultaneously. In addition, the on-target effect of morphologic changes observed in lung/kidney in pre-clinical studies for several frontrunner ATP-competitive inhibitors prevented their further development. With this regard, non-ATP-competitive inhibitors may provide a different safety profile for development. DNL201 and DNL151 have entered early clinical trials to evaluate tolerability and target engagement biomarkers. This will pave the way for the development for future LRRK2 inhibitors.
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Affiliation(s)
- Xiao Ding
- Department of Chemistry and Biology, Shanghai Medicilon Inc., Shanghai, China
| | - Feng Ren
- Department of Chemistry and Biology, Shanghai Medicilon Inc., Shanghai, China
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20
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The dynamic switch mechanism that leads to activation of LRRK2 is embedded in the DFGψ motif in the kinase domain. Proc Natl Acad Sci U S A 2019; 116:14979-14988. [PMID: 31292254 PMCID: PMC6660771 DOI: 10.1073/pnas.1900289116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Little is known about the regulation of Leucine-rich repeat kinase 2 (LRRK2) associated with familial Parkinson’s disease (PD). To test whether the kinase domain drives LRRK2 activation, we applied the spine concept that describes the core architecture of every protein kinase. We discovered that mutation of Y2018, a regulatory spine residue, to Phe in the DFGψ motif created a hyperactive kinase similar to the PD-associated mutation G2019S. The hydroxyl moiety of Y2018 thus serves as a “brake,” stabilizing the inactive conformation; simply removing it destroys a key inhibitory hydrogen-bonding node. These data reveal an LRRK2-specific regulatory mechanism, confirming that the kinase domain functions as a classical kinase that controls overall conformational dynamics in full-length LRRK2 and drives therapeutic strategies. Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein, and LRRK2 mutants are recognized risk factors for Parkinson’s disease (PD). Although the precise mechanisms that control LRRK2 regulation and function are unclear, the importance of the kinase domain is strongly implicated, since 2 of the 5 most common familial LRRK2 mutations (G2019S and I2020T) are localized to the conserved DFGψ motif in the kinase core, and kinase inhibitors are under development. Combining the concept of regulatory (R) and catalytic (C) spines with kinetic and cell-based assays, we discovered a major regulatory mechanism embedded within the kinase domain and show that the DFG motif serves as a conformational switch that drives LRRK2 activation. LRRK2 is quite unusual in that the highly conserved Phe in the DFGψ motif, which is 1 of the 4 R-spine residues, is replaced with tyrosine (DY2018GI). A Y2018F mutation creates a hyperactive phenotype similar to the familial mutation G2019S. The hydroxyl moiety of Y2018 thus serves as a “brake” that stabilizes an inactive conformation; simply removing it destroys a key hydrogen-bonding node. Y2018F, like the pathogenic mutant I2020T, spontaneously forms LRRK2-decorated microtubules in cells, while the wild type and G2019S require kinase inhibitors to form filaments. We also explored 3 different mechanisms that create kinase-dead pseudokinases, including D2017A, which further emphasizes the highly synergistic role of key hydrophobic and hydrophilic/charged residues in the assembly of active LRRK2. We thus hypothesize that LRRK2 harbors a classical protein kinase switch mechanism that drives the dynamic activation of full-length LRRK2.
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21
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Agrahari AK, Doss GPC, Siva R, Magesh R, Zayed H. Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. J Theor Biol 2019; 469:163-171. [PMID: 30844370 DOI: 10.1016/j.jtbi.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. However, no computational study deeply investigated the possible impact of the G2019S substitution on the kinase domain in its Apo conformation. Therefore, in this study, we used 200 ns molecular dynamic simulation using the GROMACS 5.1.4 package software to investigate the impact of the G2019S substitution on the structure of the kinase domain of LRRK2. Our results indicate that the G2019S substitution affects the dynamics and stability of LRRK2 by decreasing the flexibility and increasing the compactness of the kinase domain and showing its tendency to be in an active conformation for long time interval because of the high energy barrier between active and inactive conformation. This study predicts the molecular pathogenicity mechanism of the G2019S on patients with PD and provides a potential platform for developing therapeutics for patients with PD that harbor this amino acid substitution.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University (DU), Porur, Chennai, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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22
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Shore DGM, Sweeney ZK, Beresford A, Chan BK, Chen H, Drummond J, Gill A, Kleinheinz T, Liu X, Medhurst AD, McIver EG, Moffat JG, Zhu H, Estrada AA. Discovery of potent azaindazole leucine-rich repeat kinase 2 (LRRK2) inhibitors possessing a key intramolecular hydrogen bond - Part 2. Bioorg Med Chem Lett 2019; 29:674-680. [PMID: 30522953 DOI: 10.1016/j.bmcl.2018.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 11/28/2022]
Abstract
The discovery of disease-modifying therapies for Parkinson's Disease (PD) represents a critical need in neurodegenerative medicine. Genetic mutations in LRRK2 are risk factors for the development of PD, and some of these mutations have been linked to increased LRRK2 kinase activity and neuronal toxicity in cellular and animal models. As such, research towards brain-permeable kinase inhibitors of LRRK2 has received much attention. In the course of a program to identify structurally diverse inhibitors of LRRK2 kinase activity, a 5-azaindazole series was optimized for potency, metabolic stability and brain penetration. A key design element involved the incorporation of an intramolecular hydrogen bond to increase permeability and potency against LRRK2. This communication will outline the structure-activity relationships of this matched pair series including the challenge of obtaining a desirable balance between metabolic stability and brain penetration.
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Affiliation(s)
- Daniel G M Shore
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Zachary K Sweeney
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alan Beresford
- Department of Drug Metabolism and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, Essex CB10 1XL, UK
| | - Bryan K Chan
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Huifen Chen
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason Drummond
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Andrew Gill
- Department of Biochemical and Cellular Pharmacology, BioFocus, Chesterford Research Park, Saffron Walden, Essex CB10 1XL, UK
| | - Tracy Kleinheinz
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xingrong Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Andrew D Medhurst
- Department of Biochemical and Cellular Pharmacology, BioFocus, Chesterford Research Park, Saffron Walden, Essex CB10 1XL, UK
| | - Edward G McIver
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage SG1 2FX, UK
| | - John G Moffat
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Haitao Zhu
- Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anthony A Estrada
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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23
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Kelly K, Wang S, Boddu R, Liu Z, Moukha-Chafiq O, Augelli-Szafran C, West AB. The G2019S mutation in LRRK2 imparts resiliency to kinase inhibition. Exp Neurol 2018; 309:1-13. [PMID: 30048714 DOI: 10.1016/j.expneurol.2018.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/18/2018] [Accepted: 07/21/2018] [Indexed: 12/13/2022]
Abstract
The G2019S mutation in LRRK2 is one of the most common known genetic causes of neurodegeneration and Parkinson disease (PD). LRRK2 mutations are thought to enhance LRRK2 kinase activity. Efficacious small molecule LRRK2 kinase inhibitors with favorable drug properties have recently been developed for pre-clinical studies in rodent models, and inhibitors have advanced to safety trials in humans. Rats that express human G2019S-LRRK2 protein and G2019S-LRRK2 knock-in mice provide newly characterized models to better understand the ostensible target for inhibitors. Herein, we explore the relationships between LRRK2 kinase inhibition in the brain and the periphery to establish the link between LRRK2 kinase activity and protein stability, induction of lysosomal defects in kidney and lung, and how G2019S-LRRK2 expression impacts these phenotypes. Using a novel ultra-sensitive scalable assay based on protein capillary electrophoresis with LRRK2 kinase inhibitors included in-diet, G2019S-LRRK2 protein was resilient to inhibition compared to wild-type (WT)-LRRK2 protein, particularly in the brain. Whereas WT-LRRK2 kinase activity could be completed blocked without lowering LRRK2 protein levels, higher inhibitor concentrations were necessary to fully reduce G2019S-LRRK2 activity. G2019S-LRRK2 expression afforded robust protection from inhibitor-induced kidney lysosomal defects, suggesting a gain-of-function for the mutation in this phenotype. In rodents treated with inhibitors, parallel measurements of phospho-Rab10 revealed a poor correlation to phospho-LRRK2, likely due to cells that express Rab10 but poorly express LRRK2 in heterogenous tissues and cell isolates. In summary, our results highlight several challenges associated with the inhibition of the G2019S-LRRK2 kinase that might be considered in initial clinical efforts.
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Affiliation(s)
- Kaela Kelly
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Shijie Wang
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Ravindra Boddu
- Division of Nephrology, Nephrology Research and Training Center, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Zhiyong Liu
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | | | - Andrew B West
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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24
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Bhayye SS, Roy K, Saha A. Molecular dynamics simulation study reveals polar nature of pathogenic mutations responsible for stabilizing active conformation of kinase domain in leucine-rich repeat kinase II. Struct Chem 2017. [DOI: 10.1007/s11224-017-1059-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Williamson DS, Smith GP, Acheson-Dossang P, Bedford ST, Chell V, Chen IJ, Daechsel JCA, Daniels Z, David L, Dokurno P, Hentzer M, Herzig MC, Hubbard RE, Moore JD, Murray JB, Newland S, Ray SC, Shaw T, Surgenor AE, Terry L, Thirstrup K, Wang Y, Christensen KV. Design of Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Crystallographic Surrogate Derived from Checkpoint Kinase 1 (CHK1). J Med Chem 2017; 60:8945-8962. [PMID: 29023112 DOI: 10.1021/acs.jmedchem.7b01186] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2), such as G2019S, are associated with an increased risk of developing Parkinson's disease. Surrogates for the LRRK2 kinase domain based on checkpoint kinase 1 (CHK1) mutants were designed, expressed in insect cells infected with baculovirus, purified, and crystallized. X-ray structures of the surrogates complexed with known LRRK2 inhibitors rationalized compound potency and selectivity. The CHK1 10-point mutant was preferred, following assessment of surrogate binding affinity with LRRK2 inhibitors. Fragment hit-derived arylpyrrolo[2,3-b]pyridine LRRK2 inhibitors underwent structure-guided optimization using this crystallographic surrogate. LRRK2-pSer935 HEK293 IC50 data for 22 were consistent with binding to Ala2016 in LRRK2 (equivalent to Ala147 in CHK1 10-point mutant structure). Compound 22 was shown to be potent, moderately selective, orally available, and brain-penetrant in wild-type mice, and confirmation of target engagement was demonstrated, with LRRK2-pSer935 IC50 values for 22 in mouse brain and kidney being 1.3 and 5 nM, respectively.
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Affiliation(s)
- Douglas S Williamson
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | | | | | - Simon T Bedford
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Victoria Chell
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - I-Jen Chen
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | | | - Zoe Daniels
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | | | - Pawel Dokurno
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | | | | | - Roderick E Hubbard
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Jonathan D Moore
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - James B Murray
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Samantha Newland
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Stuart C Ray
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Terry Shaw
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Allan E Surgenor
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Lindsey Terry
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Kenneth Thirstrup
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
| | - Yikang Wang
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge, CB21 6GB, United Kingdom
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26
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Salado IG, Zaldivar-Diez J, Sebastián-Pérez V, Li L, Geiger L, González S, Campillo NE, Gil C, Morales AV, Perez DI, Martinez A. Leucine rich repeat kinase 2 (LRRK2) inhibitors based on indolinone scaffold: Potential pro-neurogenic agents. Eur J Med Chem 2017; 138:328-342. [PMID: 28688273 DOI: 10.1016/j.ejmech.2017.06.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is one of the most pursued targets for Parkinson's disease (PD) therapy. Moreover, it has recently described its role in regulating Wnt signaling and thus, it may be involved in adult neurogenesis. This new hypothesis could give rise to double disease-modifying agents firstly by the benefits of inhibiting LRRK2 and secondly by promoting adult neurogenesis. Herein we report, the design, synthesis, biological evaluation, SAR and potential binding mode of indoline-like LRRK2 inhibitors and their preliminary neurogenic effect in neural precursor cells isolated from adult mice ventricular-subventricular zone. These results open new therapeutic horizons for the use of LRRK2 inhibitors as neuroregenerative agents. Moreover, the indolinone derivatives here prepared, inhibitors of the kinase activity of LRRK2, may be considered as pharmacological probes to study the potential neuroregeneration of the damaged brain.
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Affiliation(s)
- Irene G Salado
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Josefa Zaldivar-Diez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Víctor Sebastián-Pérez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Lingling Li
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal-CSIC, Madrid, Spain
| | - Larissa Geiger
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Silvia González
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Nuria E Campillo
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Carmen Gil
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Aixa V Morales
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal-CSIC, Madrid, Spain
| | - Daniel I Perez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.
| | - Ana Martinez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.
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27
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Abstract
INTRODUCTION Leucine-rich repeat kinase 2 (LRRK2) is a member of the Tyrosine Kinase-Like (TKL) branch of the kinome tree and is a multi-domain protein that includes GTPase and kinase activity. While genome-wide association studies (GWAS) has linked LRRK2 with Crohn's disease and leprosy, it has received the greatest attention due to it being implicated as one of the genetic loci associated with autosomal dominant inheritance in Parkinson's disease (PD). Areas covered: In this review, the small molecule patent literature from 2014-2016 with a focus on composition of matter and use patents was surveyed. Scifinder was primarily searched using 'LRRK2' as the query to identify all relevant literature and then triaged for small molecule patents. Expert opinion: The patent landscape around LRRK2 continues to develop. The early patents covered using existing kinase inhibitors for use against LRRK2. This evolved to compounds specifically designed for selectivity against LRRK2, but key exemplified compounds lacked sufficient brain exposure to affect sufficient efficacy. More recent compounds have addressed this deficiency and show greater potential for treating PD. While potency will be necessary to generate medicines with low human daily doses, brain penetration and safety will be the key differentiators for ultimately determining the most effective LRRK2 disease-modifying treatment for PD.
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Affiliation(s)
- Paul Galatsis
- a Worldwide Medicinal Chemistry , Pfizer Worldwide Research & Development , Cambridge , MA , USA
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28
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Christensen KV, Smith GP, Williamson DS. Development of LRRK2 Inhibitors for the Treatment of Parkinson's Disease. PROGRESS IN MEDICINAL CHEMISTRY 2017; 56:37-80. [PMID: 28314412 DOI: 10.1016/bs.pmch.2016.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Linkage and genome-wide association studies have identified a genetic risk locus for late-onset Parkinson's disease in chromosome 12, originally identified as PARK6. The causative gene was identified to code for a large multifunctional protein, LRRK2 (leucine-rich repeat kinase 2). The combined genetic and biochemical evidence supports a hypothesis in which the LRRK2 kinase function is causally involved in the pathogenesis of sporadic and familial forms of PD, and therefore that LRRK2 kinase inhibitors could be useful for treatment. Although LRRK2 has so far not been crystallised, the use of homology modelling and crystallographic surrogates has allowed the optimisation of chemical structures such that compounds of high selectivity with good brain penetration and appropriate pharmacokinetic properties are now available for understanding the biology of LRRK2 in vitro and in vivo. This chapter reviews LRRK2 biology, the structural biology of LRRK2 and gives an overview of inhibitors of LRRK2.
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Affiliation(s)
- K V Christensen
- Neuroscience Drug Discovery, H. Lundbeck A/S, Valby, Denmark
| | - G P Smith
- Neuroscience Drug Discovery, H. Lundbeck A/S, Valby, Denmark
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29
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The dual enzyme LRRK2 hydrolyzes GTP in both its GTPase and kinase domains in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:274-280. [PMID: 27939437 DOI: 10.1016/j.bbapap.2016.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/11/2016] [Accepted: 12/06/2016] [Indexed: 11/20/2022]
Abstract
The evolutionarily conserved enzyme encoded by the leucine-rich repeat kinase 2 gene, LRRK2, harbors both a Rab-like GTPase domain and a serine/threonine protein kinase domain. Pathogenic mutations in either the GTPase or kinase domain can cause neurodegeneration and Parkinson disease. No high-resolution structure of the human LRRK2 kinase domain is available but the most common mutation, G2019S in the kinase domain, is predicted to alter the ATP-binding pocket structure and interaction with divalent cations. Here we find that the manganese-bound kinase domain acquires a robust ability to utilize both GTP as well as ATP in autophosphorylation of the GTPase domain and phosphorylation of peptide substrates in vitro. The G2019S LRRK2 mutation increases the efficiency of GTP-mediated kinase activity ten-fold compared to WT LRRK2 activity. Moreover, GTP-dependent phosphorylation alters autophosphorylation-site preference in vitro. While additional studies are required to determine the physiological relevance of these observations, LRRK2 is one of the only known kinases to be able to utilize GTP as a phospho-donor at physiological levels in vitro, and thus one of the only known proteins to be able to hydrolyze GTP in two distinct domains within the same protein.
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30
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Inzelberg R, Flash S, Friedman E, Azizi E. Cutaneous malignant melanoma and Parkinson disease: Common pathways? Ann Neurol 2016; 80:811-820. [PMID: 27761938 DOI: 10.1002/ana.24802] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/03/2016] [Accepted: 10/10/2016] [Indexed: 12/25/2022]
Abstract
The mechanisms underlying the high prevalence of cutaneous malignant melanoma (CMM) in Parkinson disease (PD) are unclear, but plausibly involve common pathways. 129Ser-phosphorylated α-synuclein, a pathological PD hallmark, is abundantly expressed in CMM, but not in normal skin. In inherited PD, PARK genes harbor germline mutations; the same genes are somatically mutated in CMM, or their encoded proteins are involved in melanomagenesis. Conversely, genes associated with CMM affect PD risk. PD/CMM-targeted cells share neural crest origin and melanogenesis capability. Pigmentation gene variants may underlie their susceptibility. We review putative genetic intersections that may be suggestive of shared pathways in neurodegeneration/melanomagenesis. Ann Neurol 2016;80:811-820.
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Affiliation(s)
- Rivka Inzelberg
- Department of Neurology and Neurosurgery, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv
- Center of Advanced Technologies in Rehabilitation, Sheba Medical Center, Tel Hashomer
| | - Shira Flash
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv
| | - Eitan Friedman
- Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Sheba Medical Center, Tel Hashomer
- Departments of Internal Medicine and Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv
| | - Esther Azizi
- Department of Dermatology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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31
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Bosc N, Wroblowski B, Aci-Sèche S, Meyer C, Bonnet P. A Proteometric Analysis of Human Kinome: Insight into Discriminant Conformation-dependent Residues. ACS Chem Biol 2015; 10:2827-40. [PMID: 26411811 DOI: 10.1021/acschembio.5b00555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Because of the success of imatinib, the first type-II kinase inhibitor approved by the FDA in 2001, sustained efforts have been made by the pharmaceutical industry to discover novel compounds stabilizing the inactive conformation of protein kinases. On the seven type-II inhibitors having reached the market, four were released in 2012, suggesting an acceleration of the research of such a class of compounds. Still, they represent less than a third of the protein kinase inhibitors available to patients today. The identification of key residues involved in the binding of this type of ligands in the kinase active site might ease the design of potent and selective type-II inhibitors. In order to identify those discriminant residues, we have developed a proteometric approach combining residue descriptors of protein kinase sequences and biological activities of various type-II kinase inhibitors. We applied Partial Least Squares (PLS) regression to identify 29 key residues that influence the binding of four type-II inhibitors to most proteins of the kinome. The gatekeeper residue was found to be the most relevant, confirming an essential role in ligand binding as well as in protein kinase conformational changes. Using the newly developed proteometric model, we predicted the propensity of each protein kinase to be inhibited by type-II ligands. The model was further validated using an external data set of protein/ligand activity pairs. Other residues present in the kinase domain, and more specifically in the binding site, have been highlighted by this approach, but their role in biological mechanisms is still unknown.
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Affiliation(s)
- Nicolas Bosc
- Institut
de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans
BP 6759, 45067 Orléans
Cedex 2, France
| | - Berthold Wroblowski
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Samia Aci-Sèche
- Institut
de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans
BP 6759, 45067 Orléans
Cedex 2, France
| | - Christophe Meyer
- Centre de Recherche Janssen-Cilag, Campus de Maigremont - CS
10615, 27106 Val de
Reuil Cedex, France
| | - Pascal Bonnet
- Institut
de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans
BP 6759, 45067 Orléans
Cedex 2, France
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32
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Anusuya S, Velmurugan D, Gromiha MM. Identification of dengue viral RNA-dependent RNA polymerase inhibitor using computational fragment-based approaches and molecular dynamics study. J Biomol Struct Dyn 2015; 34:1512-32. [DOI: 10.1080/07391102.2015.1081620] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Shanmugam Anusuya
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
- Bioinformatics Infrastructure Facility (BIF), University of Madras, Guindy Campus, Chennai 600 025, India
| | - M. Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
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33
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Zinovjev K, Tuñón I. Transition state ensemble optimization for reactions of arbitrary complexity. J Chem Phys 2015; 143:134111. [DOI: 10.1063/1.4931596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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34
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Shanley MR, Hawley D, Leung S, Zaidi NF, Dave R, Schlosser KA, Bandopadhyay R, Gerber SA, Liu M. LRRK2 Facilitates tau Phosphorylation through Strong Interaction with tau and cdk5. Biochemistry 2015; 54:5198-208. [PMID: 26268594 DOI: 10.1021/acs.biochem.5b00326] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) and tau have been identified as risk factors of Parkinson's disease (PD). As LRRK2 is a kinase and tau is hyperphosphorylated in some LRRK2 mutation carriers of PD patients, the obvious hypothesis is that tau could be a substrate of LRRK2. Previous reports that LRRK2 phosphorylates free tau or tubulin-associated tau provide direct support for this proposition. By comparing LRRK2 with cdk5, we show that wild-type LRRK2 and the G2019S mutant phosphorylate free recombinant full-length tau protein with specific activity 480- and 250-fold lower than cdk5, respectively. More strikingly tau binds to wt LRRK2 or the G2019S mutant 140- or 200-fold more strongly than cdk5. The extremely low activity of LRRK2 but strong binding affinity with tau suggests that LRRK2 may facilitate tau phosphorylation as a scaffold protein rather than as a major tau kinase. This hypothesis is further supported by the observation that (i) cdk5 or tau coimmunoprecipitates with endogenous LRRK2 in SH-SY5Y cells, in mouse brain tissue, and in human PBMCs; (ii) knocking down endogenous LRRK2 by its siRNA in SH-SY5Y cells reduces tau phosphorylation at Ser396 and Ser404; (iii) inhibiting LRRK2 kinase activity by its inhibitors has no effect on tau phosphorylation at these two sites; and (iv) overexpressing wt LRRK2, the G2019S mutant, or the D1994A kinase-dead mutant in SH-SY5Y cells has no effect on tau phosphorylation. Our results suggest that LRRK2 facilitates tau phosphorylation indirectly by recruiting tau or cdk5 rather than by directly phosphorylating tau.
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Affiliation(s)
- Mary R Shanley
- Neurology Department, Brigham and Women's Hospital, Harvard Medical School , 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Dillon Hawley
- Neurology Department, Brigham and Women's Hospital, Harvard Medical School , 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Shirley Leung
- Neurology Department, Brigham and Women's Hospital, Harvard Medical School , 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Nikhat F Zaidi
- Neurology Department, Brigham and Women's Hospital, Harvard Medical School , 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Roshni Dave
- Neurology Department, Brigham and Women's Hospital, Harvard Medical School , 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Kate A Schlosser
- Department of Genetics and of Biochemistry, Geisel School of Medicine at Dartmouth , One Medical Center Drive HB-7937, Lebanon, New Hampshire 03756, United States
| | - Rina Bandopadhyay
- Reta Lila, Weston Institute of Neurological Studies Department of Molecular Neuroscience UCL, Institute of Neurology 1 , Wakefield Street, London WC1N 1PJ, U.K
| | - Scott A Gerber
- Department of Genetics and of Biochemistry, Geisel School of Medicine at Dartmouth , One Medical Center Drive HB-7937, Lebanon, New Hampshire 03756, United States
| | - Min Liu
- Neurology Department, Brigham and Women's Hospital, Harvard Medical School , 65 Landsdowne Street, Fourth Floor, Cambridge, Massachusetts 02139, United States
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35
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Discovery of LRRK2 inhibitors using sequential in silico joint pharmacophore space (JPS) and ensemble docking. Bioorg Med Chem Lett 2015; 25:2713-9. [DOI: 10.1016/j.bmcl.2015.04.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 11/22/2022]
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36
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Estrada AA, Sweeney ZK. Chemical Biology of Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors. J Med Chem 2015; 58:6733-46. [PMID: 25915084 DOI: 10.1021/acs.jmedchem.5b00261] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is an urgent need for the development of Parkinson's disease (PD) treatments that can slow disease progression. The leucine-rich repeat kinase 2 (LRRK2) protein has been genetically and functionally linked to PD, and modulation of LRRK2 enzymatic activity has been proposed as a novel therapeutic strategy. In this review, we describe the bioactivity of selected small molecules that have been used to inhibit LRRK2 kinase activity in vitro or in vivo. These compounds are important tools for understanding the cellular biology of LRRK2 and for evaluating the potential of LRRK2 inhibitors as disease-modifying PD therapies.
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Affiliation(s)
- Anthony A Estrada
- Department of Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Zachary K Sweeney
- Department of Discovery Chemistry, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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37
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Ryan BJ, Hoek S, Fon EA, Wade-Martins R. Mitochondrial dysfunction and mitophagy in Parkinson's: from familial to sporadic disease. Trends Biochem Sci 2015; 40:200-10. [PMID: 25757399 DOI: 10.1016/j.tibs.2015.02.003] [Citation(s) in RCA: 381] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder characterised by the preferential loss of dopaminergic neurons in the substantia nigra. Mitochondrial dysfunction is increasingly appreciated as a key determinant of dopaminergic neuronal susceptibility in PD and is a feature of both familial and sporadic disease, as well as in toxin-induced Parkinsonism. Recently, the mechanisms by which PD-associated mitochondrial proteins phosphatase and tensin homolog deleted on chromosome 10 (PTEN)-induced putative kinase 1 (PINK1) and parkin function and induce neurodegeneration have been identified. In addition, increasing evidence implicates other PD-associated proteins such as α-synuclein (α-syn) and leucine-rich repeat kinase 2 (LRRK2) in mitochondrial dysfunction in genetic cases of PD with the potential for a large functional overlap with sporadic disease. This review highlights how recent advances in understanding familial PD-associated proteins have identified novel mechanisms and therapeutic strategies for addressing mitochondrial dysfunction in PD.
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Affiliation(s)
- Brent J Ryan
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Selim Hoek
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Edward A Fon
- McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, Le Gros Clark Building, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK.
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38
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Li JQ, Tan L, Yu JT. The role of the LRRK2 gene in Parkinsonism. Mol Neurodegener 2014; 9:47. [PMID: 25391693 PMCID: PMC4246469 DOI: 10.1186/1750-1326-9-47] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/21/2014] [Indexed: 12/13/2022] Open
Abstract
Parkinson’s disease (PD), like many common age-related conditions, has been recognized to have a substantial genetic component. Multiple lines of evidence suggest that Leucine-rich repeat kinase 2 (LRRK2) is a crucial factor to understanding the etiology of PD. LRRK2 is a large, widely expressed, multi-domain and multifunctional protein. LRRK2 mutations are the major cause to inherited and sporadic PD. In this review, we discuss the pathology and clinical features which show diversity and variability of LRRK2-associated PD. In addition, we do a thorough literature review and provide theoretical data for gene counseling. Further, we present the evidence linking LRRK2 to various possible pathogenic mechanism of PD such as α-synuclein, tau, inflammatory response, oxidative stress, mitochondrial dysfunction, synaptic dysfunction as well as autophagy-lysosomal system. Based on the above work, we investigate activities both within GTPase and outside enzymatic regions in order to obtain a potential therapeutic approach to solve the LRRK2 problem.
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Affiliation(s)
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, No, 5 Donghai Middle Road, Qingdao 266071, PR China.
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39
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Rudenko IN, Cookson MR. Heterogeneity of leucine-rich repeat kinase 2 mutations: genetics, mechanisms and therapeutic implications. Neurotherapeutics 2014; 11:738-50. [PMID: 24957201 PMCID: PMC4391379 DOI: 10.1007/s13311-014-0284-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Variation within and around the leucine-rich repeat kinase 2 (LRRK2) gene is associated with familial and sporadic Parkinson's disease (PD). Here, we discuss the prevalence of LRRK2 substitutions in different populations and their association with PD, as well as molecular and cellular mechanisms of pathologically relevant LRRK2 mutations. Kinase activation was proposed as a universal molecular mechanism for all pathogenic LRRK2 mutations, but later reports revealed heterogeneity in the effect of mutations on different activities of LRRK2. One mutation (G2019S) increases kinase activity, whereas mutations in the Ras of complex proteins (ROC)-C-terminus of ROC (COR) bidomain impair the GTPase function of LRRK2. Some risk factor variants, including G2385R in the WD40 domain, actually decrease the kinase activity of LRRK2. We suggest a model where LRRK2 mutations exert different molecular mechanisms but interfere with normal cellular function of LRRK2 at different levels of the same downstream pathway. Finally, we discuss the current state of therapeutic approaches for LRRK2-related PD.
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Affiliation(s)
- Iakov N. Rudenko
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
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Sirin S, Kumar R, Martinez C, Karmilowicz MJ, Ghosh P, Abramov YA, Martin V, Sherman W. A computational approach to enzyme design: predicting ω-aminotransferase catalytic activity using docking and MM-GBSA scoring. J Chem Inf Model 2014; 54:2334-46. [PMID: 25005922 DOI: 10.1021/ci5002185] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Enzyme design is an important area of ongoing research with a broad range of applications in protein therapeutics, biocatalysis, bioengineering, and other biomedical areas; however, significant challenges exist in the design of enzymes to catalyze specific reactions of interest. Here, we develop a computational protocol using an approach that combines molecular dynamics, docking, and MM-GBSA scoring to predict the catalytic activity of enzyme variants. Our primary focuses are to understand the molecular basis of substrate recognition and binding in an S-stereoselective ω-aminotransferase (ω-AT), which naturally catalyzes the transamination of pyruvate into alanine, and to predict mutations that enhance the catalytic efficiency of the enzyme. The conversion of (R)-ethyl 5-methyl-3-oxooctanoate to (3S,5R)-ethyl 3-amino-5-methyloctanoate in the context of several ω-AT mutants was evaluated using the computational protocol developed in this work. We correctly identify the mutations that yield the greatest improvements in enzyme activity (20-60-fold improvement over wild type) and confirm that the computationally predicted structure of a highly active mutant reproduces key structural aspects of the variant, including side chain conformational changes, as determined by X-ray crystallography. Overall, the protocol developed here yields encouraging results and suggests that computational approaches can aid in the redesign of enzymes with improved catalytic efficiency.
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Affiliation(s)
- Sarah Sirin
- Schrödinger, Inc. , 120 West 45th Street, 29th Floor, New York, New York 10036, United States
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41
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Selvaraj C, Bharathi Priya R, Singh SK. Communication of γ Phage Lysin plyG Enzymes Binding toward SrtA for Inhibition ofBacillus Anthracis: Protein–Protein Interaction and Molecular Dynamics Study. ACTA ACUST UNITED AC 2014; 21:257-65. [DOI: 10.3109/15419061.2014.927444] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ray S, Bender S, Kang S, Lin R, Glicksman MA, Liu M. The Parkinson disease-linked LRRK2 protein mutation I2020T stabilizes an active state conformation leading to increased kinase activity. J Biol Chem 2014; 289:13042-53. [PMID: 24695735 DOI: 10.1074/jbc.m113.537811] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effect of leucine-rich repeat kinase 2 (LRRK2) mutation I2020T on its kinase activity has been controversial, with both increased and decreased effects being reported. We conducted steady-state and pre-steady-state kinetic studies on LRRKtide and its analog LRRKtide(S). Their phosphorylation differs by the rate-limiting steps: product release is rate-limiting for LRRKtide and phosphoryl transfer is rate-limiting for LRRKtide(S). As a result, we observed that the I2020T mutant is more active than wild type (WT) LRRK2 for LRRKtide(S) phosphorylation, whereas it is less active than WT for LRRKtide phosphorylation. Our pre-steady-state kinetic data suggest that (i) the I2020T mutant accelerates the rates of phosphoryl transfer of both reactions by 3-7-fold; (ii) this increase is masked by a rate-limiting product release step for LRRKtide phosphorylation; and (iii) the observed lower activity of the mutant for LRRKtide phosphorylation is a consequence of its instability: the concentration of the active form of the mutant is 3-fold lower than WT. The I2020T mutant has a dramatically low KATP and therefore leads to resistance to ATP competitive inhibitors. Two well known DFG-out or type II inhibitors are also weaker toward the mutant because they inhibit the mutant in an unexpected ATP competitive mechanism. The I2020 residue lies next to the DYG motif of the activation loop of the LRRK2 kinase domain. Our modeling and metadynamic simulations suggest that the I2020T mutant stabilizes the DYG-in active conformation and creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP competitive fashion.
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Affiliation(s)
- Soumya Ray
- From the Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, and
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43
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Silva RG, Geoghegan KF, Qiu X, Aulabaugh A. A continuous and direct assay to monitor leucine-rich repeat kinase 2 activity. Anal Biochem 2014; 450:63-9. [DOI: 10.1016/j.ab.2014.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 12/01/2022]
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44
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Mills RD, Mulhern TD, Liu F, Culvenor JG, Cheng HC. Prediction of the Repeat Domain Structures and Impact of Parkinsonism-Associated Variations on Structure and Function of all Functional Domains of Leucine-Rich Repeat Kinase 2 (LRRK2). Hum Mutat 2014; 35:395-412. [DOI: 10.1002/humu.22515] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 01/08/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Ryan D. Mills
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Terrence D. Mulhern
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Fei Liu
- Department of Chemistry & Biomolecular Sciences; Macquarie University; NSW Australia
| | - Janetta G. Culvenor
- Department of Pathology; University of Melbourne; Parkville Victoria Australia
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
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45
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Cardona F, Tormos-Pérez M, Pérez-Tur J. Structural and functional in silico analysis of LRRK2 missense substitutions. Mol Biol Rep 2014; 41:2529-42. [PMID: 24488318 DOI: 10.1007/s11033-014-3111-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/10/2014] [Indexed: 11/27/2022]
Abstract
The LRRK2 gene (Leucine-Rich Repeat Kinase 2, PARK8) is mutated in a significant number of cases of autosomal dominant Parkinson's disease (PD) and in some sporadic cases of late-onset PD. LRRK2 is a large, complex protein that comprises several interaction domains: armadillo, ankyrin, leucine-rich repeats and WD40 domains; two catalytic domains: ROC-GTPase and serine/threonine kinase; and a COR domain (unknown function). Pathogenic mutations are scattered all over the domains of LRRK2, although the prevalence of mutations in some domains is higher (ROC-GTPase, COR and kinase). In this work, we model the structure of each domain to predict and explore the effects of described missense mutations and polymorphisms. The results allow us to postulate the possible effects of pathogenic mutations in the function of the protein, and hypothesize the importance of some polymorphisms that have not been linked directly to PD, but act as risk factors for the disease. In our analysis, we also study the effects of PD-related mutations in the kinase domain structure and in the phosphorylation of the activation loop to determine effects on kinase activity.
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Affiliation(s)
- Fernando Cardona
- Unitat de Genètica Molecular, Institut de Biomedicina de València, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain,
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46
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Estrada AA, Chan BK, Baker-Glenn C, Beresford A, Burdick DJ, Chambers M, Chen H, Dominguez SL, Dotson J, Drummond J, Flagella M, Fuji R, Gill A, Halladay J, Harris SF, Heffron TP, Kleinheinz T, Lee DW, Pichon CEL, Liu X, Lyssikatos JP, Medhurst AD, Moffat JG, Nash K, Scearce-Levie K, Sheng Z, Shore DG, Wong S, Zhang S, Zhang X, Zhu H, Sweeney ZK. Discovery of Highly Potent, Selective, and Brain-Penetrant Aminopyrazole Leucine-Rich Repeat Kinase 2 (LRRK2) Small Molecule Inhibitors. J Med Chem 2014; 57:921-36. [DOI: 10.1021/jm401654j] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Anthony A. Estrada
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Bryan K. Chan
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Charles Baker-Glenn
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Alan Beresford
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Daniel J. Burdick
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Mark Chambers
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Huifen Chen
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Sara L. Dominguez
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Jennafer Dotson
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Jason Drummond
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Michael Flagella
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Reina Fuji
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Andrew Gill
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Jason Halladay
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Seth F. Harris
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Timothy P. Heffron
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Tracy Kleinheinz
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Donna W. Lee
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Claire E. Le Pichon
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Xingrong Liu
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Joseph P. Lyssikatos
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Andrew D. Medhurst
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - John G. Moffat
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Kevin Nash
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Kimberly Scearce-Levie
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Zejuan Sheng
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Daniel G. Shore
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Susan Wong
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Shuo Zhang
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Xiaolin Zhang
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Haitao Zhu
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
| | - Zachary K. Sweeney
- Departments of †Discovery Chemistry, ‡Neurosciences, §Biochemical and Cellular
Pharmacology, ∥Drug Metabolism
and Pharmacokinetics, ⊥Safety Assessment, and #Structural Biology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
- Departments
of ∇Chemistry, ○Biochemical and
Cellular Pharmacology, and ◆Drug Metabolism
and Pharmacokinetics, BioFocus, Chesterford Research Park, Saffron Walden, CB10 1XL, United Kingdom
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48
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The development of CNS-active LRRK2 inhibitors using property-directed optimisation. Bioorg Med Chem Lett 2013; 23:3690-6. [PMID: 23721803 DOI: 10.1016/j.bmcl.2013.04.086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/23/2013] [Accepted: 04/30/2013] [Indexed: 12/20/2022]
Abstract
Mutations in PARK8/LRRK2 are the most common genetic cause of Parkinson's disease. Inhibition of LRRK2 kinase activity has neuroprotective benefits, and provides a means of addressing the underlying biochemical cause of Parkinson's disease for the first time. Initial attempts to develop LRRK2 inhibitors were largely unsuccessful and highlight shortcomings intrinsic to traditional, high throughput screening methods of lead discovery. Recently, amino-pyrimidine GNE-7915 was reported as a potent (IC50=9 nM) selective (1/187 kinases), brain-penetrant and non-toxic inhibitor of LRRK2. The use of in silico modelling, extensive in vitro assays and resource-efficient in vivo techniques to produce GNE-7915, reflects a trend towards the concerted optimisation of potency, selectivity and pharmacokinetic properties in early-stage drug development.
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49
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Madhavi Sastry G, Adzhigirey M, Day T, Annabhimoju R, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 2013; 27:221-34. [DOI: 10.1007/s10822-013-9644-8] [Citation(s) in RCA: 2913] [Impact Index Per Article: 264.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 04/03/2013] [Indexed: 12/11/2022]
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