1
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Li N, Liu YH, Wu J, Liu QG, Niu JB, Zhang Y, Fu XJ, Song J, Zhang SY. Strategies that regulate Hippo signaling pathway for novel anticancer therapeutics. Eur J Med Chem 2024; 276:116694. [PMID: 39047607 DOI: 10.1016/j.ejmech.2024.116694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/29/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
As a highly conserved signaling network across different species, the Hippo pathway is involved in various biological processes. Dysregulation of the Hippo pathway could lead to a wide range of diseases, particularly cancers. Extensive researches have demonstrated the close association between dysregulated Hippo signaling and tumorigenesis as well as tumor progression. Consequently, targeting the Hippo pathway has emerged as a promising strategy for cancer treatment. In fact, there has been an increasing number of reports on small molecules that target the Hippo pathway, exhibiting therapeutic potential as anticancer agents. Importantly, some of Hippo signaling pathway inhibitors have been approved for the clinical trials. In this work, we try to provide an overview of the core components and signal transduction mechanisms of the Hippo signaling pathway. Furthermore, we also analyze the relationship between Hippo signaling pathway and cancers, as well as summarize the small molecules with proven anti-tumor effects in clinical trials or reported in literatures. Additionally, we discuss the anti-tumor potency and structure-activity relationship of the small molecule compounds, providing a valuable insight for further development of anticancer agents against this pathway.
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Affiliation(s)
- Na Li
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Yun-He Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Ji Wu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Qiu-Ge Liu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jin-Bo Niu
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yan Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiang-Jing Fu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China.
| | - Jian Song
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Sai-Yang Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention &Treatment, Zhengzhou, 450001, China.
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2
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Logan KM, Kaplan W, Simov V, Zhou H, Li D, Torres L, Morriello GJ, Acton JJ, Pio B, Chen YH, Keylor MH, Johnson R, Kattar SD, Chau R, Yan X, Ardolino M, Zarate C, Otte KM, Palte RL, Xiong T, McMinn SE, Lin S, Neelamkavil SF, Liu P, Su J, Hegde LG, Woodhouse JD, Moy LY, Ciaccio PJ, Piesvaux J, Zebisch M, Henry C, Barker J, Wood HB, Kennedy ME, DiMauro EF, Fell MJ, Fuller PH. Discovery and Optimization of N-Heteroaryl Indazole LRRK2 Inhibitors. J Med Chem 2024; 67:16807-16819. [PMID: 39231262 DOI: 10.1021/acs.jmedchem.4c01627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Inhibition of leucine-rich repeat kinase 2 is a genetically supported mechanism for the treatment of Parkinson's disease. We previously disclosed the discovery of an indazole series lead that demonstrated both safety and translational risks. The safety risks were hypothesized to be of unknown origin, so structural diversity in subsequent chemical matter was prioritized. The translational risks were identified due to a low brain Kpu,u in nonhuman primate studies, which raised concern over the use of an established peripheral biomarker as a surrogate for central target engagement. Given these challenges, the team sought to leverage structure- and property-based drug design and expanded efflux transporter profiling to identify structurally distinct leads with enhanced CNS drug-likeness. Herein, we describe the discovery of a "reinvented" indazole series with improved physicochemical properties and efflux transporter profiles while maintaining excellent potency and off-target kinase selectivity, which resulted in advanced lead, compound 23.
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Affiliation(s)
- Kaitlyn M Logan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Will Kaplan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Hua Zhou
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derun Li
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Luis Torres
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - John J Acton
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Barbara Pio
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Yi-Heng Chen
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cayetana Zarate
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Shishi Lin
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | | | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthias Zebisch
- Evotec (U.K.) Ltd., 90 Park Drive, Milton Park, Abingdon OX14 4RZ, Oxfordshire, U.K
| | - Clare Henry
- Evotec (U.K.) Ltd., 90 Park Drive, Milton Park, Abingdon OX14 4RZ, Oxfordshire, U.K
| | - John Barker
- Evotec (U.K.) Ltd., 90 Park Drive, Milton Park, Abingdon OX14 4RZ, Oxfordshire, U.K
| | - Harold B Wood
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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3
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Tan S, Gong X, Liu H, Yao X. Identification of novel LRRK2 inhibitors by structure-based virtual screening and alchemical free energy calculation. Phys Chem Chem Phys 2024; 26:19775-19786. [PMID: 38984923 DOI: 10.1039/d4cp01762e] [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: 07/11/2024]
Abstract
The Leucine-rich repeat kinase 2 (LRRK2) target has been identified as a promising drug target for Parkinson's disease (PD) treatment. This study focuses on optimizing the activity of LRRK2 inhibitors using alchemical relative binding free energy (RBFE) calculations. Initially, we assessed various free energy calculation methods across different LRRK2 kinase inhibitor scaffolds. The results indicate that alchemical free energy calculations are promising for prospective predictions on LRRK2 inhibitors, especially for the aminopyrimidine scaffold with an RMSE of 1.15 kcal mol-1 and Rp of 0.83. Following this, we optimized a potent LRRK2 kinase inhibitor identified from previous virtual screenings, featuring a novel scaffold. Guided by RBFE predictions using alchemical methods, this optimization led to the discovery of compound LY2023-001. This compound, with a [1,2,4]triazolo[5,6-b]indole scaffold, exhibited enhanced inhibitory activity against G2019S LRRK2 (IC50 = 12.9 nM). Molecular dynamics (MD) simulations revealed that LY2023-001 formed stable hydrogen bonds with Glu1948, and Ala1950 in the G2019S LRRK2 protein. Additionally, its phenyl substituents engage in strong electrostatic interactions with Lys1906 and van der Waals interactions with Leu1885, Phe1890, Val1893, Ile1933, Met1947, Leu1949, Leu2001, Ala2016, and Asp2017. Our findings underscore the potential of computational methods in the successful optimization of small molecules, offering important insights for the development of novel LRRK2 inhibitors.
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Affiliation(s)
- Shuoyan Tan
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xiaoqing Gong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, 999078, China.
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, 999078, China.
| | - Xiaojun Yao
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, 999078, China.
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4
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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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5
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Elhadi A, Zhao D, Ali N, Sun F, Zhong S. Multi-method computational evaluation of the inhibitors against leucine-rich repeat kinase 2 G2019S mutant for Parkinson's disease. Mol Divers 2024:10.1007/s11030-024-10808-w. [PMID: 38396210 DOI: 10.1007/s11030-024-10808-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/07/2024] [Indexed: 02/25/2024]
Abstract
Leucine-rich repeat kinase 2 G2019S mutant (LRRK2 G2019S) is a potential target for Parkinson's disease therapy. In this work, the computational evaluation of the LRRK2 G2019S inhibitors was conducted via a combined approach which contains a preliminary screening of a large database of compounds via similarity and pharmacophore, a secondary selection via structure-based affinity prediction and molecular docking, and a rescoring treatment for the final selection. MD simulations and MM/GBSA calculations were performed to check the agreement between different prediction methods for these inhibitors. 331 experimental ligands were collected, and 170 were used to build the structure-activity relationship. Eight representative ligand structural models were employed in similarity searching and pharmacophore screening over 14 million compounds. The process for selecting proper molecular descriptors provides a successful sample which can be used as a general strategy in QSAR modelling. The rescoring used in this work presents an alternative useful treatment for ranking and selection.
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Affiliation(s)
- Ahmed Elhadi
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, People's Republic of China
| | - Dan Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, People's Republic of China
| | - Noman Ali
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, People's Republic of China
| | - Fusheng Sun
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, People's Republic of China
| | - Shijun Zhong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, People's Republic of China.
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6
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Baidya AT, Deshwal S, Das B, Mathew AT, Devi B, Sandhir R, Kumar R. Catalyzing a Cure: Discovery and development of LRRK2 inhibitors for the treatment of Parkinson's disease. Bioorg Chem 2024; 143:106972. [PMID: 37995640 DOI: 10.1016/j.bioorg.2023.106972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
Parkinson's disease (PD) is an age-related second most common progressive neurodegenerative disorder that affects millions of people worldwide. Despite decades of research, no effective disease modifying therapeutics have reached clinics for treatment/management of PD. Leucine-rich repeat kinase 2 (LRRK2) which controls membrane trafficking and lysosomal function and its variant LRRK2-G2019S are involved in the development of both familial and sporadic PD. LRRK2, is therefore considered as a legitimate target for the development of therapeutics against PD. During the last decade, efforts have been made to develop effective, safe and selective LRRK2 inhibitors and also our understanding about LRRK2 has progressed. However, there is an urge to learn from the previously designed and reported LRRK2 inhibitors in order to effectively approach designing of new LRRK2 inhibitors. In this review, we have aimed to cover the pre-clinical studies undertaken to develop small molecule LRRK2 inhibitors by screening the patents and other available literature in the last decade. We have highlighted LRRK2 as targets in the progress of PD and subsequently covered detailed design, synthesis and development of diverse scaffolds as LRRK2 inhibitors. Moreover, LRRK2 inhibitors under clinical development has also been discussed. LRRK2 inhibitors seem to be potential targets for future therapeutic interventions in the treatment and management of PD and this review can act as a cynosure for guiding discovery, design, and development of selective and non-toxic LRRK2 inhibitors. Although, there might be challenges in developing effective LRRK2 inhibitors, the opportunity to successfully develop novel therapeutics targeting LRRK2 against PD has never been greater.
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Affiliation(s)
- Anurag Tk Baidya
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi 221005, UP, India
| | - Sonam Deshwal
- Department of Biochemistry, Panjab University, Chandigarh 160014, India
| | - Bhanuranjan Das
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi 221005, UP, India
| | - Alen T Mathew
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi 221005, UP, India
| | - Bharti Devi
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi 221005, UP, India
| | - Rajat Sandhir
- Department of Biochemistry, Panjab University, Chandigarh 160014, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi 221005, UP, India.
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7
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Kattar SD, Gulati A, Margrey KA, Keylor MH, Ardolino M, Yan X, Johnson R, Palte RL, McMinn SE, Nogle L, Su J, Xiao D, Piesvaux J, Lee S, Hegde LG, Woodhouse JD, Faltus R, Moy LY, Xiong T, Ciaccio PJ, Pearson K, Patel M, Otte KM, Leyns CEG, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Discovery of MK-1468: A Potent, Kinome-Selective, Brain-Penetrant Amidoisoquinoline LRRK2 Inhibitor for the Potential Treatment of Parkinson's Disease. J Med Chem 2023; 66:14912-14927. [PMID: 37861679 DOI: 10.1021/acs.jmedchem.3c01486] [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: 10/21/2023]
Abstract
Genetic mutation of the leucine-rich repeat kinase 2 (LRRK2) protein has been associated with Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder that is devoid of efficacious disease-modifying therapies. Herein, we describe the invention of an amidoisoquinoline (IQ)-derived LRRK2 inhibitor lead chemical series. Knowledge-, structure-, and property-based drug design in concert with rigorous application of in silico calculations and presynthesis predictions enabled the prioritization of molecules with favorable CNS "drug-like" physicochemical properties. This resulted in the discovery of compound 8, which was profiled extensively before human ether-a-go-go (hERG) ion channel inhibition halted its progression. Strategic reduction of lipophilicity and basicity resulted in attenuation of hERG ion channel inhibition while maintaining a favorable CNS efflux transporter profile. Further structure- and property-based optimizations resulted in the discovery of preclinical candidate MK-1468. This exquisitely selective LRRK2 inhibitor has a projected human dose of 48 mg BID and a preclinical safety profile that supported advancement toward GLP toxicology studies.
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Affiliation(s)
- Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dong Xiao
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Susi Lee
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kara Pearson
- Merck & Co., Inc., 770 Sumneytown Pike., West Point, Pennsylvania 19486, United States
| | - Mayankbhai Patel
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cheryl E G Leyns
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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8
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Tan S, Wang J, Gao P, Xie G, Zhang Q, Liu H, Yao X. Unveiling the Selectivity Mechanism of Type-I LRRK2 Inhibitors by Computational Methods: Insights from Binding Thermodynamics and Kinetics Simulation. ACS Chem Neurosci 2023; 14:3472-3486. [PMID: 37647597 DOI: 10.1021/acschemneuro.3c00338] [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] [Indexed: 09/01/2023] Open
Abstract
Understanding the selectivity mechanisms of inhibitors toward highly similar proteins is very important in new drug discovery. Developing highly selective targeting of leucine-rich repeat kinase 2 (LRRK2) kinases for the treatment of Parkinson's disease (PD) is challenging because of the similarity of the kinase ATP binding pocket. During the development of LRRK2 inhibitors, off-target effects on other kinases, especially TTK and JAK2 kinases, have been observed. As a result, significant time and resources have been devoted to improving the selectivity for the LRRK2 target. DNL201 is an LRRK2 kinase inhibitor entering phase I clinical studies. The experiments have shown that DNL201 significantly inhibits LRRK2 kinase activity, with >167-fold selectivity over JAK2 and TTK kinases. However, the potential mechanisms of inhibitor preferential binding to LRRK2 kinase are still not well elucidated. In this work, to reveal the underlying general selectivity mechanism, we carried out several computational methods and comprehensive analyses from both the binding thermodynamics and kinetics on two representative LRRK2 inhibitors (DNL201 and GNE7915) to LRRK2. Our results suggest that the structural and kinetic differences between the proteins may play a key role in determining the activity of the selective small-molecule inhibitor. The selectivity mechanisms proposed in this work could be helpful for the rational design of novel selective LRRK2 kinase inhibitors against PD.
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Affiliation(s)
- Shuoyan Tan
- College of Chemistry and Chemical Engineering, Lanzhou University, 730000 Lanzhou, Gansu, China
| | - Jun Wang
- Ping An Healthcare Technology, 100000 Beijing, China
| | - Peng Gao
- Ping An Healthcare Technology, 100000 Beijing, China
| | - Guotong Xie
- Ping An Healthcare Technology, 100000 Beijing, China
| | - Qianqian Zhang
- Faculty of Applied Science, Macao Polytechnic University, 999078 Macao SAR, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, 999078 Macao SAR, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, 730000 Lanzhou, Gansu, China
- Faculty of Applied Science, Macao Polytechnic University, 999078 Macao SAR, China
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9
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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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10
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Weng JH, Ma W, Wu J, Sharma PK, Silletti S, McCammon JA, Taylor S. Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors. ACS Chem Biol 2023; 18:810-821. [PMID: 37043829 PMCID: PMC10127209 DOI: 10.1021/acschembio.2c00868] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023]
Abstract
Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinson's disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. In this study, we combined enhanced sampling simulations with HDX-MS to characterize the inhibitor-induced dynamic changes and the allosteric communications within the C-terminal domains of LRRK2, LRRK2RCKW. We find that the binding of MLi-2 (a type I kinase inhibitor) stabilizes a closed kinase conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKW structure. In contrast, the binding of Rebastinib (a type II kinase inhibitor) stabilizes an open kinase conformation, which promotes a more extended LRRK2RCKW structure. By probing the distinct effects of the type I and type II inhibitors, key interdomain interactions are found to regulate the communication between the kinase domain and the GTPase domain. The intermediate states revealed in our simulations facilitate the efforts toward in silico design of allosteric modulators that control LRRK2 conformations and potentially mediate the oligomeric states of LRRK2 and its interactions with other proteins.
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Affiliation(s)
- Jui-Hung Weng
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Wen Ma
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Jian Wu
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Pallavi Kaila Sharma
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Steve Silletti
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Susan Taylor
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
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11
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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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12
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Candito DA, Simov V, Gulati A, Kattar S, Chau RW, Lapointe BT, Methot JL, DeMong DE, Graham TH, Kurukulasuriya R, Keylor MH, Tong L, Morriello GJ, Acton JJ, Pio B, Liu W, Scott JD, Ardolino MJ, Martinot TA, Maddess ML, Yan X, Gunaydin H, Palte RL, McMinn SE, Nogle L, Yu H, Minnihan EC, Lesburg CA, Liu P, Su J, Hegde LG, Moy LY, Woodhouse JD, Faltus R, Xiong T, Ciaccio P, Piesvaux JA, Otte KM, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Neelamkavil S, Wood HB, Fuller PH, Ellis JM. Discovery and Optimization of Potent, Selective, and Brain-Penetrant 1-Heteroaryl-1 H-Indazole LRRK2 Kinase Inhibitors for the Treatment of Parkinson's Disease. J Med Chem 2022; 65:16801-16817. [PMID: 36475697 DOI: 10.1021/acs.jmedchem.2c01605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of leucine-rich repeat kinase 2 (LRRK2) kinase activity represents a genetically supported, chemically tractable, and potentially disease-modifying mechanism to treat Parkinson's disease. Herein, we describe the optimization of a novel series of potent, selective, central nervous system (CNS)-penetrant 1-heteroaryl-1H-indazole type I (ATP competitive) LRRK2 inhibitors. Type I ATP-competitive kinase physicochemical properties were integrated with CNS drug-like properties through a combination of structure-based drug design and parallel medicinal chemistry enabled by sp3-sp2 cross-coupling technologies. This resulted in the discovery of a unique sp3-rich spirocarbonitrile motif that imparted extraordinary potency, pharmacokinetics, and favorable CNS drug-like properties. The lead compound, 25, demonstrated exceptional on-target potency in human peripheral blood mononuclear cells, excellent off-target kinase selectivity, and good brain exposure in rat, culminating in a low projected human dose and a pre-clinical safety profile that warranted advancement toward pre-clinical candidate enabling studies.
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Affiliation(s)
- David A Candito
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Solomon Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ryan W Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Blair T Lapointe
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Joey L Methot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Duane E DeMong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Thomas H Graham
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ravi Kurukulasuriya
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ling Tong
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Weiguo Liu
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Jack D Scott
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Theodore A Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew L Maddess
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hakan Gunaydin
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hongshi Yu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ellen C Minnihan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Paul Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jennifer A Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - J Michael Ellis
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
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13
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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: 0] [Impact Index Per Article: 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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14
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Discovery of azaspirocyclic 1H-3,4,5-Trisubstitued pyrazoles as novel G2019S-LRRK2 selective kinase inhibitors. Eur J Med Chem 2022; 242:114693. [PMID: 36049274 DOI: 10.1016/j.ejmech.2022.114693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/22/2022]
Abstract
Mutations in the Leucine Rich Repeat Protein Kinase 2 gene (LRRK2) are genetic predispositions for Parkinson's Disease, of which the G2019S (GS) missense mutation is the most common. GS-LRRK2 has a hyperactive kinase, and although numerous drug discovery programs have targeted the LRRK2 kinase, few have reached clinical trials. We recently reported on the discovery of a novel LRRK2 kinase inhibitor chemotype, 1H-pyrazole biaryl sulfonamides. Although both potent and selective GS-LRRK2 inhibitors, 1H-pyrazole biaryl sulfonamides are incapable of crossing the blood-brain barrier. Retaining the core 1H-pyrazole and focusing our efforts on a phenylsulfonamide bioisosteric replacement, we report the discovery and preliminary development of azaspirocyclic 1H-3,4,5-trisubstituted pyrazoles as potent and selective (>2000-fold) GS-LRRK2 kinase inhibitors capable of entering rodent brain. The compounds disclosed here present an excellent starting point for the development of more brain penetrant compounds.
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15
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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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16
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17
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Leśniak RK, Nichols RJ, Schonemann M, Zhao J, Gajera CR, Lam G, Nguyen KC, Langston JW, Smith M, Montine TJ. Discovery of 1 H-Pyrazole Biaryl Sulfonamides as Novel G2019S-LRRK2 Kinase Inhibitors. ACS Med Chem Lett 2022; 13:981-988. [DOI: 10.1021/acsmedchemlett.2c00116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Robert K. Leśniak
- Medicinal Chemistry Knowledge Center, Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - R. Jeremy Nichols
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Marcus Schonemann
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Jing Zhao
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Chandresh R. Gajera
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Grace Lam
- Departments of Medicine and Microbiology and Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Khanh C. Nguyen
- Departments of Medicine and Microbiology and Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - J. William Langston
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
- Department of Neurology and Neuroscience, Stanford University, 300 Pasteur Drive, Stanford, California 94304, United States
| | - Mark Smith
- Medicinal Chemistry Knowledge Center, Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Thomas J. Montine
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, United States
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18
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Singh RK, Soliman A, Guaitoli G, Störmer E, von Zweydorf F, Dal Maso T, Oun A, Van Rillaer L, Schmidt SH, Chatterjee D, David JA, Pardon E, Schwartz TU, Knapp S, Kennedy EJ, Steyaert J, Herberg FW, Kortholt A, Gloeckner CJ, Versées W. Nanobodies as allosteric modulators of Parkinson's disease-associated LRRK2. Proc Natl Acad Sci U S A 2022; 119:e2112712119. [PMID: 35217606 PMCID: PMC8892280 DOI: 10.1073/pnas.2112712119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Mutations in the gene coding for leucine-rich repeat kinase 2 (LRRK2) are a leading cause of the inherited form of Parkinson's disease (PD), while LRRK2 overactivation is also associated with the more common idiopathic form of PD. LRRK2 is a large multidomain protein, including a GTPase as well as a Ser/Thr protein kinase domain. Common, disease-causing mutations increase LRRK2 kinase activity, presenting LRRK2 as an attractive target for drug discovery. Currently, drug development has mainly focused on ATP-competitive kinase inhibitors. Here, we report the identification and characterization of a variety of nanobodies that bind to different LRRK2 domains and inhibit or activate LRRK2 in cells and in in vitro. Importantly, nanobodies were identified that inhibit LRRK2 kinase activity while binding to a site that is topographically distinct from the active site and thus act through an allosteric inhibitory mechanism that does not involve binding to the ATP pocket or even to the kinase domain. Moreover, while certain nanobodies completely inhibit the LRRK2 kinase activity, we also identified nanobodies that specifically inhibit the phosphorylation of Rab protein substrates. Finally, in contrast to current type I kinase inhibitors, the studied kinase-inhibitory nanobodies did not induce LRRK2 microtubule association. These comprehensively characterized nanobodies represent versatile tools to study the LRRK2 function and mechanism and can pave the way toward novel diagnostic and therapeutic strategies for PD.
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Affiliation(s)
- Ranjan K Singh
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Ahmed Soliman
- Department of Cell Biochemistry, University of Groningen, 9747AG Groningen, The Netherlands
| | | | - Eliza Störmer
- Department of Biochemistry, Institute for Biology, University of Kassel, 34132 Kassel, Germany
| | | | - Thomas Dal Maso
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Asmaa Oun
- Department of Cell Biochemistry, University of Groningen, 9747AG Groningen, The Netherlands
- Groningen Research Institute of Pharmacy, Molecular Pharmacology XB10, 9700AD Groningen, The Netherlands
| | - Laura Van Rillaer
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sven H Schmidt
- Department of Biochemistry, Institute for Biology, University of Kassel, 34132 Kassel, Germany
| | - Deep Chatterjee
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua A David
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Els Pardon
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, 34132 Kassel, Germany
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747AG Groningen, The Netherlands
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, D-72076 Tübingen, Germany
- Core Facility for Medical Bioanalytics, Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Wim Versées
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium;
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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19
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Charoensutthivarakul S, Thomas SE, Curran A, Brown KP, Belardinelli JM, Whitehouse AJ, Acebrón-García-de-Eulate M, Sangan J, Gramani SG, Jackson M, Mendes V, Floto RA, Blundell TL, Coyne AG, Abell C. Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach. ACS Infect Dis 2022; 8:296-309. [PMID: 35037462 PMCID: PMC7614835 DOI: 10.1021/acsinfecdis.1c00432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mycobacterium abscessus (Mab) has emerged as a challenging threat to individuals with cystic fibrosis. Infections caused by this pathogen are often impossible to treat due to the intrinsic antibiotic resistance leading to lung malfunction and eventually death. Therefore, there is an urgent need to develop new drugs against novel targets in Mab to overcome drug resistance and subsequent treatment failure. In this study, SAICAR synthetase (PurC) from Mab was identified as a promising target for novel antibiotics. An in-house fragment library screen and a high-throughput X-ray crystallographic screen of diverse fragment libraries were explored to provide crucial starting points for fragment elaboration. A series of compounds developed from fragment growing and merging strategies, guided by crystallographic information and careful hit-to-lead optimization, have achieved potent nanomolar binding affinity against the enzyme. Some compounds also show a promising inhibitory effect against Mab and Mtb. This work utilizes a fragment-based design and demonstrates for the first time the potential to develop inhibitors against PurC from Mab.
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Affiliation(s)
- Sitthivut Charoensutthivarakul
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Amy Curran
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Andrew J Whitehouse
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jaspar Sangan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Subramanian G Gramani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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20
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Bata N, Chaikuad A, Bakas NA, Limpert AS, Lambert LJ, Sheffler DJ, Berger LM, Liu G, Yuan C, Wang L, Peng Y, Dong J, Celeridad M, Layng F, Knapp S, Cosford NDP. Inhibitors of the Hippo Pathway Kinases STK3/MST2 and STK4/MST1 Have Utility for the Treatment of Acute Myeloid Leukemia. J Med Chem 2022; 65:1352-1369. [PMID: 34807584 PMCID: PMC10149138 DOI: 10.1021/acs.jmedchem.1c00804] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Serine/threonine-protein kinases 3 and 4 (STK3 and STK4, respectively) are key components of the Hippo signaling pathway, which regulates cell proliferation and death and provides a potential therapeutic target for acute myeloid leukemia (AML). Herein, we report the structure-based design of a series of pyrrolopyrimidine derivatives as STK3 and STK4 inhibitors. In an initial screen, the compounds exhibited low nanomolar potency against both STK3 and STK4. Crystallization of compound 6 with STK4 revealed two-point hinge binding in the ATP-binding pocket. Further characterization and analysis demonstrated that compound 20 (SBP-3264) specifically inhibited the Hippo signaling pathway in cultured mammalian cells and possessed favorable pharmacokinetic and pharmacodynamic properties in mice. We show that genetic knockdown and pharmacological inhibition of STK3 and STK4 suppress the proliferation of AML cells in vitro. Thus, SBP-3264 is a valuable chemical probe for understanding the roles of STK3 and STK4 in AML and is a promising candidate for further advancement as a potential therapy.
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Affiliation(s)
- Nicole Bata
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Apirat Chaikuad
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Nicole A Bakas
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Allison S Limpert
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lester J Lambert
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Douglas J Sheffler
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lena M Berger
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Guoxiong Liu
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Cunxiang Yuan
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Li Wang
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Yi Peng
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Jing Dong
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Maria Celeridad
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabiana Layng
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Stefan Knapp
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Translational cancer network DKTK site Frankfurt/Mainz and Frankfurt Cancer Institute (FCI), Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Nicholas D P Cosford
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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21
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Keylor MH, Gulati A, Kattar SD, Johnson RE, Chau RW, Margrey KA, Ardolino MJ, Zarate C, Poremba KE, Simov V, Morriello GJ, Acton JJ, Pio B, Yan X, Palte RL, McMinn SE, Nogle L, Lesburg CA, Adpressa D, Lin S, Neelamkavil S, Liu P, Su J, Hegde LG, Woodhouse JD, Faltus R, Xiong T, Ciaccio PJ, Piesvaux J, Otte KM, Wood HB, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Structure-Guided Discovery of Aminoquinazolines as Brain-Penetrant and Selective LRRK2 Inhibitors. J Med Chem 2021; 65:838-856. [PMID: 34967623 DOI: 10.1021/acs.jmedchem.1c01968] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The leucine-rich repeat kinase 2 (LRRK2) protein has been genetically and functionally linked to Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder whose current therapies are limited in scope and efficacy. In this report, we describe a rigorous hit-to-lead optimization campaign supported by structural enablement, which culminated in the discovery of brain-penetrant, candidate-quality molecules as represented by compounds 22 and 24. These compounds exhibit remarkable selectivity against the kinome and offer good oral bioavailability and low projected human doses. Furthermore, they showcase the implementation of stereochemical design elements that serve to enable a potency- and selectivity-enhancing increase in polarity and hydrogen bond donor (HBD) count while maintaining a central nervous system-friendly profile typified by low levels of transporter-mediated efflux and encouraging brain penetration in preclinical models.
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Affiliation(s)
- Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca E Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan W Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cayetana Zarate
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kelsey E Poremba
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Donovon Adpressa
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Shishi Lin
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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22
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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: 9] [Impact Index Per Article: 3.0] [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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23
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Foloppe N, Chen IJ. The reorganization energy of compounds upon binding to proteins, from dynamic and solvated bound and unbound states. Bioorg Med Chem 2021; 51:116464. [PMID: 34798378 DOI: 10.1016/j.bmc.2021.116464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 11/30/2022]
Abstract
The intramolecular reorganization energy (ΔEReorg) of compounds upon binding to proteins is a component of the binding free energy, which has long received particular attention, for fundamental and practical reasons. Understanding ΔEReorg would benefit the science of molecular recognition and drug design. For instance, the tolerable strain energy of compounds upon binding has been elusive. Prior studies found some large ΔEReorg values (e.g. > 10 kcal/mol), received with skepticism since they imply excessive opposition to binding. Indeed, estimating ΔEReorg is technically difficult. Typically, ΔEReorg has been approached by taking two energy-minimized conformers representing the bound and unbound states, and subtracting their conformational energy. This is a drastic oversimplification, liable to conformational collapse of the unbound conformer. Instead, the present work applies extensive molecular dynamics (MD) and the modern OPLS3 force-field to simulate compounds bound and unbound states, in explicit solvent under physically relevant conditions. The thermalized unbound compounds populate multiple conformations, not reducible to one or a few energy-minimized conformers. The intramolecular energies in the bound and unbound states were averaged over pertinent conformational ensembles, and the reorganization enthalpy upon binding (ΔHReorg) deduced by subtraction. This was applied to 76 systems, including 43 approved drugs, carefully selected for i) the quality of the bioactive X-ray structures and ii) the diversity of the chemotypes, their properties and protein targets. It yielded comparatively low ΔHReorg values (median = 1.4 kcal/mol, mean = 3.0 kcal/mol). A new finding is the observation of negative ΔHReorg values. Indeed, reorganization energies do not have to oppose binding, e.g. when intramolecular interactions stabilize preferentially the bound state. Conversely, even with competing water molecules, intramolecular interactions can occur predominantly in the unbound compound, and be replaced by intermolecular counterparts upon protein binding. Such disruption of intramolecular interactions upon binding gives rise to occasional larger ΔHReorg values. Such counterintuitive larger ΔHReorg values may be rationalized as a redistribution of interactions upon binding, qualitatively compatible with binding.
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Affiliation(s)
- Nicolas Foloppe
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
| | - I-Jen Chen
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
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24
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Wojewska DN, Kortholt A. LRRK2 Targeting Strategies as Potential Treatment of Parkinson's Disease. Biomolecules 2021; 11:1101. [PMID: 34439767 PMCID: PMC8392603 DOI: 10.3390/biom11081101] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Parkinson's Disease (PD) affects millions of people worldwide with no cure to halt the progress of the disease. Leucine-rich repeat kinase 2 (LRRK2) is the most common genetic cause of PD and, as such, LRRK2 inhibitors are promising therapeutic agents. In the last decade, great progress in the LRRK2 field has been made. This review provides a comprehensive overview of the current state of the art, presenting recent developments and challenges in developing LRRK2 inhibitors, and discussing extensively the potential targeting strategies from the protein perspective. As currently there are three LRRK2-targeting agents in clinical trials, more developments are predicted in the upcoming years.
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Affiliation(s)
- Dominika Natalia Wojewska
- Faculty of Science and Engineering, University of Groningen, Nijenborg 7, 9747AG Groningen, The Netherlands;
| | - Arjan Kortholt
- Faculty of Science and Engineering, University of Groningen, Nijenborg 7, 9747AG Groningen, The Netherlands;
- YETEM-Innovative Technologies Application and Research Center, Suleyman Demirel University, 32260 Isparta, Turkey
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25
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Malykhin RS, Sukhorukov AY. Nucleophilic Halogenation of Heterocyclic
N
‐Oxides: Recent Progress and a Practical Guide. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Roman S. Malykhin
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences Leninsky prospect, 47 Moscow 119991 Russia
- M. V. Lomonosov Moscow State University Department of Chemistry Leninskie gory, 1, str. 3 Moscow 119991 Russian Federation
| | - Alexey Yu. Sukhorukov
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences Leninsky prospect, 47 Moscow 119991 Russia
- Plekhanov Russian University of Economics Stremyanny per. 36 Moscow 117997 Russia
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26
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Williamson DS, Smith GP, Mikkelsen GK, Jensen T, Acheson-Dossang P, Badolo L, Bedford ST, Chell V, Chen IJ, Dokurno P, Hentzer M, Newland S, Ray SC, Shaw T, Surgenor AE, Terry L, Wang Y, Christensen KV. Design and Synthesis of Pyrrolo[2,3- d]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate. J Med Chem 2021; 64:10312-10332. [PMID: 34184879 DOI: 10.1021/acs.jmedchem.1c00720] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inhibitors of leucine-rich repeat kinase 2 (LRRK2) and mutants, such as G2019S, have potential utility in Parkinson's disease treatment. Fragment hit-derived pyrrolo[2,3-d]pyrimidines underwent optimization using X-ray structures of LRRK2 kinase domain surrogates, based on checkpoint kinase 1 (CHK1) and a CHK1 10-point mutant. (2R)-2-Methylpyrrolidin-1-yl derivative 18 (LRRK2 G2019S cKi 0.7 nM, LE 0.66) was identified, with increased potency consistent with an X-ray structure of 18/CHK1 10-pt. mutant showing the 2-methyl substituent proximal to Ala147 (Ala2016 in LRRK2). Further structure-guided elaboration of 18 gave the 2-[(1,3-dimethyl-1H-pyrazol-4-yl)amino] derivative 32. Optimization of 32 afforded diastereomeric oxolan-3-yl derivatives 44 and 45, which demonstrated a favorable in vitro PK profile, although they displayed species disconnects in the in vivo PK profile, and a propensity for P-gp- and/or BCRP-mediated efflux in a mouse model. Compounds 44 and 45 demonstrated high potency and exquisite selectivity for LRRK2 and utility as chemical probes for the study of LRRK2 inhibition.
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Affiliation(s)
| | | | | | | | | | | | - Simon T Bedford
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Victoria Chell
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - I-Jen Chen
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Pawel Dokurno
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | | | - Samantha Newland
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Stuart C Ray
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Terry Shaw
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Allan E Surgenor
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Lindsey Terry
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Yikang Wang
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
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27
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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A 2021; 118:2100844118. [PMID: 34088839 PMCID: PMC8201809 DOI: 10.1073/pnas.2100844118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To explore how pathogenic mutations of the multidomain leucine-rich repeat kinase 2 (LRRK2) hijack its finely tuned activation process and drive Parkinson's disease (PD), we used a multitiered approach. Most mutations mimic Rab-mediated activation by "unleashing" kinase activity, and many, like the kinase inhibitor MLi-2, trap LRRK2 onto microtubules. Here we mimic activation by simply deleting the inhibitory N-terminal domains and then characterize conformational changes induced by MLi-2 and PD mutations. After confirming that LRRK2RCKW retains full kinase activity, we used hydrogen-deuterium exchange mass spectrometry to capture breathing dynamics in the presence and absence of MLi-2. Solvent-accessible regions throughout the entire protein are reduced by MLi-2 binding. With molecular dynamics simulations, we created a dynamic portrait of LRRK2RCKW and demonstrate the consequences of kinase domain mutations. Although all domains contribute to regulating kinase activity, the kinase domain, driven by the DYGψ motif, is the allosteric hub that drives LRRK2 regulation.
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28
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Gulati A, Yeung CS, Lapointe B, Kattar SD, Gunaydin H, Scott JD, Childers KK, Methot JL, Simov V, Kurukulasuriya R, Pio B, Morriello GJ, Liu P, Tang H, Neelamkavil S, Wood HB, Rada VL, Ardolino MJ, Yan XC, Palte R, Otte K, Faltus R, Woodhouse J, Hegde LG, Ciaccio P, Minnihan EC, DiMauro EF, Fell MJ, Fuller PH, Ellis JM. Optimization of brain-penetrant picolinamide derived leucine-rich repeat kinase 2 (LRRK2) inhibitors. RSC Med Chem 2021; 12:1164-1173. [PMID: 34355182 DOI: 10.1039/d1md00097g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
The discovery of potent, kinome selective, brain penetrant LRRK2 inhibitors is the focus of extensive research seeking new, disease-modifying treatments for Parkinson's disease (PD). Herein, we describe the discovery and evolution of a picolinamide-derived lead series. Our initial optimization efforts aimed at improving the potency and CLK2 off-target selectivity of compound 1 by modifying the heteroaryl C-H hinge and linker regions. This resulted in compound 12 which advanced deep into our research operating plan (ROP) before heteroaryl aniline metabolite 14 was characterized as Ames mutagenic, halting its progression. Strategic modifications to our ROP were made to enable early de-risking of putative aniline metabolites or hydrolysis products for mutagenicity in Ames. This led to the discovery of 3,5-diaminopyridine 15 and 4,6-diaminopyrimidine 16 as low risk for mutagenicity (defined by a 3-strain Ames negative result). Analysis of key matched molecular pairs 17 and 18 led to the prioritization of the 3,5-diaminopyridine sub-series for further optimization due to enhanced rodent brain penetration. These efforts culminated in the discovery of ethyl trifluoromethyl pyrazole 23 with excellent LRRK2 potency and expanded selectivity versus off-target CLK2.
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Affiliation(s)
- Anmol Gulati
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Charles S Yeung
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Blair Lapointe
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Solomon D Kattar
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Hakan Gunaydin
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Jack D Scott
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Kaleen K Childers
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Joey L Methot
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Vladimir Simov
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Ravi Kurukulasuriya
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Barbara Pio
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Greg J Morriello
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Ping Liu
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Haiqun Tang
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | | | - Harold B Wood
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Vanessa L Rada
- Merck & Co., Inc. 770 Sumneytown Pike West Point Pennsylvania 19486 USA
| | - Michael J Ardolino
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Xin Cindy Yan
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Rachel Palte
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Karin Otte
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Robert Faltus
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Janice Woodhouse
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Laxminarayan G Hegde
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Paul Ciaccio
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Ellen C Minnihan
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Erin F DiMauro
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Matthew J Fell
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Peter H Fuller
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - J Michael Ellis
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
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29
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Wang H, Qin Z, Yan A. Classification models and SAR analysis on CysLT1 receptor antagonists using machine learning algorithms. Mol Divers 2021; 25:1597-1616. [PMID: 33534023 DOI: 10.1007/s11030-020-10165-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/27/2020] [Indexed: 12/21/2022]
Abstract
Cysteinyl leukotrienes 1 (CysLT1) receptor is a promising drug target for rhinitis or other allergic diseases. In our study, we built classification models to predict bioactivities of CysLT1 receptor antagonists. We built a dataset with 503 CysLT1 receptor antagonists which were divided into two groups: highly active molecules (IC50 < 1000 nM) and weakly active molecules (IC50 ≥ 1000 nM). The molecules were characterized by several descriptors including CORINA descriptors, MACCS fingerprints, Morgan fingerprint and molecular SMILES. For CORINA descriptors and two types of fingerprints, we used the random forests (RF) and deep neural networks (DNN) to build models. For molecular SMILES, we used recurrent neural networks (RNN) with the self-attention to build models. The accuracies of test sets for all models reached 85%, and the accuracy of the best model (Model 2C) was 93%. In addition, we made structure-activity relationship (SAR) analyses on CysLT1 receptor antagonists, which were based on the output from the random forest models and RNN model. It was found that highly active antagonists usually contained the common substructures such as tetrazoles, indoles and quinolines. These substructures may improve the bioactivity of the CysLT1 receptor antagonists.
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Affiliation(s)
- Hongzhao Wang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, University of Chemical Technology, Beijing, People's Republic of China
| | - Zijian Qin
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, University of Chemical Technology, Beijing, People's Republic of China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, University of Chemical Technology, Beijing, People's Republic of China.
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30
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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31
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Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD. Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. Cell Chem Biol 2020; 27:1229-1240.e4. [PMID: 32755567 PMCID: PMC8053042 DOI: 10.1016/j.chembiol.2020.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/27/2022]
Abstract
Doublecortin-like kinase 1 (DCLK1) is critical for neurogenesis, but overexpression is also observed in multiple cancers and is associated with poor prognosis. Nevertheless, the function of DCLK1 in cancer, especially the context-dependent functions, are poorly understood. We present a "toolkit" that includes the DCLK1 inhibitor DCLK1-IN-1, a complementary DCLK1-IN-1-resistant mutation G532A, and kinase dead mutants D511N and D533N, which can be used to investigate signaling pathways regulated by DCLK1. Using a cancer cell line engineered to be DCLK1 dependent for growth and cell migration, we show that this toolkit can be used to discover associations between DCLK1 kinase activity and biological processes. In particular, we show an association between DCLK1 and RNA processing, including the identification of CDK11 as a potential substrate of DCLK1 using phosphoproteomics.
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Affiliation(s)
- Yan Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Lianbo Li
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Wayne Harshbarger
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Sudershan Gondi
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth D Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA; Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
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32
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The In Situ Structure of Parkinson's Disease-Linked LRRK2. Cell 2020; 182:1508-1518.e16. [PMID: 32783917 DOI: 10.1016/j.cell.2020.08.004] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of familial Parkinson's disease. LRRK2 is a multi-domain protein containing a kinase and GTPase. Using correlative light and electron microscopy, in situ cryo-electron tomography, and subtomogram analysis, we reveal a 14-Å structure of LRRK2 bearing a pathogenic mutation that oligomerizes as a right-handed double helix around microtubules, which are left-handed. Using integrative modeling, we determine the architecture of LRRK2, showing that the GTPase and kinase are in close proximity, with the GTPase closer to the microtubule surface, whereas the kinase is exposed to the cytoplasm. We identify two oligomerization interfaces mediated by non-catalytic domains. Mutation of one of these abolishes LRRK2 microtubule-association. Our work demonstrates the power of cryo-electron tomography to generate models of previously unsolved structures in their cellular environment.
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Manschwetus JT, Wallbott M, Fachinger A, Obergruber C, Pautz S, Bertinetti D, Schmidt SH, Herberg FW. Binding of the Human 14-3-3 Isoforms to Distinct Sites in the Leucine-Rich Repeat Kinase 2. Front Neurosci 2020; 14:302. [PMID: 32317922 PMCID: PMC7155755 DOI: 10.3389/fnins.2020.00302] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Proteins of the 14-3-3 family are well known modulators of the leucine-rich repeat kinase 2 (LRRK2) regulating kinase activity, cellular localization, and ubiquitylation. Although binding between those proteins has been investigated, a comparative study of all human 14-3-3 isoforms interacting with LRRK2 is lacking so far. In a comprehensive approach, we quantitatively analyzed the interaction between the seven human 14-3-3 isoforms and LRRK2-derived peptides covering both, reported and putative 14-3-3 binding sites. We observed that phosphorylation is an absolute prerequisite for 14-3-3 binding and generated binding patterns of 14-3-3 isoforms to interact with peptides derived from the N-terminal phosphorylation cluster (S910 and S935), the Roc domain (S1444) and the C-terminus. The tested 14-3-3 binding sites in LRRK2 preferentially were recognized by the isoforms γ and η, whereas the isoforms ϵ and especially σ showed the weakest or no binding. Interestingly, the possible pathogenic mutation Q930R in LRRK2 drastically increases binding affinity to a peptide encompassing pS935. We then identified the autophosphorylation site T2524 as a so far not described 14-3-3 binding site at the very C-terminus of LRRK2. Binding affinities of all seven 14-3-3 isoforms were quantified for all three binding regions with pS1444 displaying the highest affinity of all measured singly phosphorylated peptides. The strongest binding was detected for the combined phosphosites S910 and S935, suggesting that avidity effects are important for high affinity interaction between 14-3-3 proteins and LRRK2.
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Affiliation(s)
| | | | | | | | | | | | | | - Friedrich W. Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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34
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Ramonet D, Dietz GPH. Novel Cell-Based Assay for Identification of LRRK2 Inhibitors Using Its Aberrant Regulation of a Pluripotency Gene. SLAS DISCOVERY 2019; 25:104-112. [PMID: 31373835 DOI: 10.1177/2472555219864086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2), such as the G2019S mutation, are the most common cause of familial Parkinson's disease (PD). The G2019S mutation impairs neurite outgrowth. We hypothesized that those effects could be related to an altered expression of pluripotency genes, which may provide a readout for a screening assay based on LRRK2 function. Here, we show that the G2019S mutation mediates a sustained aberrant upregulation of the transcription factors Nanog and Oct4 that in wild-type are downregulated after differentiation. The aberrant regulation of Nanog can be concentration dependently reversed by LRRK2 tool inhibitors. Building on this knowledge, we developed an assay for the identification and assessment of compounds that inhibit the aberrant pathophysiological activity of mutant LRRK2. Furthermore, the aberrant neural pluripotency is consistent with Parkinson's pathophysiology and with the epidemiological association between the G2019S genotype and cancer risk.
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Affiliation(s)
- David Ramonet
- Department Neurodegeneration, H. Lundbeck A/S, Valby, Denmark.,Centre for Molecular Medicine Norway, Oslo University, Oslo, Norway
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35
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Thorpe JH, Edgar EV, Smith KJ, Lewell XQ, Rella M, White GV, Polyakova O, Nassau P, Walker AL, Holmes DS, Pearce AC, Wang Y, Liddle J, Hovnanian A. Evaluation of a crystallographic surrogate for kallikrein 5 in the discovery of novel inhibitors for Netherton syndrome. Acta Crystallogr F Struct Biol Commun 2019; 75:385-391. [PMID: 31045568 PMCID: PMC6497096 DOI: 10.1107/s2053230x19003169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 11/10/2022] Open
Abstract
The inhibition of kallikrein 5 (KLK5) has been identified as a potential strategy for treatment of the genetic skin disorder Netherton syndrome, in which loss-of-function mutations in the SPINK5 gene lead to down-regulation of the endogenous inhibitor LEKTI-1 and profound skin-barrier defects with severe allergic manifestations. To aid in the development of a medicine for this target, an X-ray crystallographic system was developed to facilitate fragment-guided chemistry and knowledge-based drug-discovery approaches. Here, the development of a surrogate crystallographic system in place of KLK5, which proved to be challenging to crystallize, is described. The biochemical robustness of the crystallographic surrogate and the suitability of the system for the study of small nonpeptidic fragments and lead-like molecules are demonstrated.
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Affiliation(s)
- James H. Thorpe
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Emma V. Edgar
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Kathrine J. Smith
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Xiao Q. Lewell
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Monika Rella
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Gemma V. White
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Oxana Polyakova
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Pamela Nassau
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Ann L. Walker
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Duncan S. Holmes
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Andrew C. Pearce
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Yichen Wang
- INSERM UMR1163 Laboratory of Genetic Skin Diseases, Imagine Institute and Université Paris Descartes–Sorbonne Paris Cité, Paris, France
| | - John Liddle
- GlaxoSmithKline, Medicinal Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Alain Hovnanian
- INSERM UMR1163 Laboratory of Genetic Skin Diseases, Imagine Institute and Université Paris Descartes–Sorbonne Paris Cité, Paris, France
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36
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Shi Y, Mader M. Brain penetrant kinase inhibitors: Learning from kinase neuroscience discovery. Bioorg Med Chem Lett 2018; 28:1981-1991. [PMID: 29752185 DOI: 10.1016/j.bmcl.2018.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/06/2023]
Abstract
A recent review of kinase inhibitors in clinical trials for brain cancer noted differences in the properties of these compounds relative to the mean property parameters associated with drugs marketed for CNS-associated conditions. However, many of these kinase drugs arose from opportunistic observations of brain activity, rather than design or flow schemes focused on optimizing CNS penetration. Thus, this digest examines kinase inhibitors that have been developed specifically for neurodegenerative indications such as Alzheimer's or Parkinson's disease, and considers design, flow scheme, and the physicochemical properties associated with compounds that have demonstrated brain penetrance.
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Affiliation(s)
- Yuan Shi
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Mary Mader
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.
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37
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Rui Q, Ni H, Li D, Gao R, Chen G. The Role of LRRK2 in Neurodegeneration of Parkinson Disease. Curr Neuropharmacol 2018; 16:1348-1357. [PMID: 29473513 PMCID: PMC6251048 DOI: 10.2174/1570159x16666180222165418] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/17/2017] [Accepted: 02/22/2018] [Indexed: 01/19/2023] Open
Abstract
The leucine-rich repeat kinase 2 (LRRK2) gene and α-synuclein gene (SNCA) are the key influencing factors of Parkinson's disease (PD). It is reported that dysfunction of LRRK2 may influence the accumulation of α-synuclein and its pathology to alter cellular functions and signaling pathways by the kinase activation of LRRK2. The accumulation of α-synuclein is one of the main stimulants of microglial activation. Microglia are macrophages that reside in the brain, and activation of microglia is believed to contribute to neuroinflammation and neuronal death in PD. Therefore, clarifying the complex relationship among LRRK2, α-synuclein and microglials could offer targeted clinical therapies for PD. Here, we provide an updated review focused on the discussion of the evidence supporting some of the key mechanisms that are important for LRRK2-dependent neurodegeneration in PD.
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Affiliation(s)
| | | | | | - Rong Gao
- Address correspondence to this author at the Department of Neurosurgery, The First People’s Hospital of Zhangjiagang City, No.68 Jiyang Western Road, Suzhou, P.R. China; Tel: +86-18921962599; E-mail:
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