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LIM Kinases, Promising but Reluctant Therapeutic Targets: Chemistry and Preclinical Validation In Vivo. Cells 2022; 11:cells11132090. [PMID: 35805176 PMCID: PMC9265711 DOI: 10.3390/cells11132090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
LIM Kinases are important actors in the regulation of cytoskeleton dynamics by controlling microtubule and actin filament turnover. The signaling pathways involving LIM kinases for actin filament remodeling are well established. They are downstream effectors of small G proteins of the Rho-GTPases family and have become promising targets for the treatment of several major diseases because of their position at the lower end of these signaling cascades. Cofilin, which depolymerizes actin filaments, is the best-known substrate of these enzymes. The phosphorylation of cofilin to its inactive form by LIM kinases avoids actin filament depolymerization. The balance between phosphorylated and non-phosphorylated cofilin is thought to play an important role in tumor cell invasion and metastasis. Since 2006, many small molecules have been developed for LIMK inhibition, and in this review article, we will discuss the structure–activity relationships of the few inhibitor families that have been tested in vivo on different pathological models.
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Ariawan D, Au C, Paric E, Fath T, Ke YD, Kassiou M, van Eersel J, Ittner LM. The Nature of Diamino Linker and Halogen Bonding Define Selectivity of Pyrrolopyrimidine-Based LIMK1 Inhibitors. Front Chem 2021; 9:781213. [PMID: 34966720 PMCID: PMC8711653 DOI: 10.3389/fchem.2021.781213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022] Open
Abstract
The LIM-domain kinase (LIMK) family consists of two isoforms, LIMK1 and LIMK2, which are highly homologous, making selective inhibitor development challenging. LIMK regulates dynamics of the actin cytoskeleton, thereby impacting many cellular functions including cell morphology and motility. Here, we designed and synthesised analogues of a known pyrrolopyrimidine LIMK inhibitor with moderate selectivity for LIMK1 over LIMK2 to gain insights into which features contribute to both activity and selectivity. We incorporated a different stereochemistry around a cyclohexyl central moiety to achieve better selectivity for different LIMK isoforms. Inhibitory activity was assessed by kinase assays, and biological effects in cells were determined using an in vitro wound closure assay. Interestingly, a slight change in stereochemistry alters LIMK isoform selectivity. Finally, a docking study was performed to predict how the new compounds interact with the target.
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Affiliation(s)
- Daryl Ariawan
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Carol Au
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Esmeralda Paric
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Thomas Fath
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Yazi D Ke
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, Darlington, NSW, Australia
| | - Janet van Eersel
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lars M Ittner
- Dementia Research Centre, Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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Zhong W, Zhao L, Yang Z, Yu-Chian Chen C. Graph convolutional network approach to investigate potential selective Limk1 inhibitors. J Mol Graph Model 2021; 107:107965. [PMID: 34167067 DOI: 10.1016/j.jmgm.2021.107965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022]
Abstract
Since the Limk1 is a promising drug target and few inhibitors with good Limk1/ROCK2 selectivity have been reported, discovering potential and selective Limk1 inhibitors with novel scaffolds is becoming an urgent need to develop new treatments for the related diseases. Here, we utilized molecular docking to screen potential compounds of Limk1 from Traditional Chinese Medicine (TCM) database. Meanwhile, we performed a three-dimensional graph convolutional network (3DGCN), based on 3D molecular graph, to predict the inhibitory activity of Limk1 and ROCK2. Compared with the baseline models (RF, GCN and Weave), the 3DGCN achieved higher accuracy and the averaged RMSE values on test sets for Limk1 and ROCK2 were 0.721 and 0.852 respectively. In 3DGCN, above 80% of the test-set molecules from both two datasets were predicted within absolute error of 1.0 and the feature visualization suggested that it could automatically learn relevant structure features including 3D molecular information from a specific task for prediction. Furthermore, molecular dynamics (MD) simulations within 100 ns were employed to verify the stability of ligand-protein complexes and reveal the binding modes of the potential selective lead compounds of Limk1. Finally, integrating docking results, the predicted values by the 3DGCN and the MD analysis, we found that 7549 and 2007_15649 might be the potential and selective inhibitors for Limk1 receptor.
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Affiliation(s)
- Weihe Zhong
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University, Shenzhen, Guangdong, 510275, China; School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
| | - Lu Zhao
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University, Shenzhen, Guangdong, 510275, China; Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Ziduo Yang
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
| | - Calvin Yu-Chian Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University, Shenzhen, Guangdong, 510275, China; Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan; Department of Bioinformatics and Medical Engineering, Asia University, Taichung, 41354, Taiwan.
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Yin Y, Sun Y, Zhao L, Pan J, Feng Y. Computer-aided discovery of phenylpyrazole based amides as potent S6K1 inhibitors. RSC Med Chem 2020; 11:583-590. [PMID: 33479660 DOI: 10.1039/c9md00537d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/04/2020] [Indexed: 12/16/2022] Open
Abstract
Ribosomal protein S6 kinase beta-1 (S6K1) is an attractive therapeutic target. In this study, computational analysis of five thiophene urea-based S6K1 inhibitors was performed. Molecular docking showed that the five compounds formed hydrogen bonds with residues Glu173 and Leu175 of S6K1 and hydrophobic interactions with residues Val105, Leu97 and Met225, and these interactions were key elements for the inhibitory potency of the compounds. Binding free energy (ΔG bind) decomposition analysis showed that Leu97, Glu173, Val 105, Leu175, Leu97 and Met225 contribute the most to ΔG bind. Based on the computer results, phenylpyrazole based amides (D1-D3) were designed and synthesized. Biological evaluation revealed that D2 exhibited 15.9 nM S6K1 inhibition, medium microsomal stability and desirable bioavailability.
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Affiliation(s)
- Yan Yin
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Hai Quan Rd. , Shanghai , 201418 , P. R. China .
| | - Yuxing Sun
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Hai Quan Rd. , Shanghai , 201418 , P. R. China .
| | - Lianhua Zhao
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Hai Quan Rd. , Shanghai , 201418 , P. R. China .
| | - Jinpeng Pan
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Hai Quan Rd. , Shanghai , 201418 , P. R. China .
| | - Yangbo Feng
- Medicinal Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , USA.,Reaction Biology Corporation , Malvern , PA 19355 , USA
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Saroj, Patel OP, Rangan K, Kumar A. Metal-free synthesis of pyridin-2-yl ureas from 2-aminopyridinium salts. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.07.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Discovery of (S)-6-methoxy-chroman-3-carboxylic acid (4-pyridin-4-yl-phenyl)-amide as potent and isoform selective ROCK2 inhibitors. Bioorg Med Chem 2019; 27:1382-1390. [DOI: 10.1016/j.bmc.2019.02.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 01/22/2023]
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Patel OPS, Dhiman S, Khan S, Shinde VN, Jaspal S, Srivathsa MR, Jha PN, Kumar A. A straightforward TBHP-mediated synthesis of 2-amidobenzoic acids from 2-arylindoles and their antimicrobial activity. Org Biomol Chem 2019; 17:5962-5970. [DOI: 10.1039/c9ob00797k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of 2-amidobenzoic acids has been achieved through TBHP-mediated oxidative ring opening of 2-arylindoles. The synthesized compounds have been evaluated for their antimicrobial activity.
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Affiliation(s)
| | - Shiv Dhiman
- Department of Chemistry
- BITS Pilani
- Pilani Campus
- India
| | - Shahid Khan
- Department of Biological Sciences
- BITS Pilani
- Pilani Campus
- India
| | | | - Sonam Jaspal
- Department of Chemistry
- BITS Pilani
- Pilani Campus
- India
| | | | - Prabhat N. Jha
- Department of Biological Sciences
- BITS Pilani
- Pilani Campus
- India
| | - Anil Kumar
- Department of Chemistry
- BITS Pilani
- Pilani Campus
- India
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Meng F, Yin Y, Lu C, Duan Y, Zhu Y, Huang C, Zhou Y, Xu X, Wu F. Design, synthesis, and in vitro evaluation of epigoitrin derivatives as neuraminidase inhibitors. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2245-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lu C, Yin Y, Meng F, Dun Y, Pei K, Wang C, Xu X, Wu F. Discovery of (E)-1-amino-4-phenylbut-3-en-2-ol derivatives as novel neuraminidase inhibitors. Bioorg Med Chem Lett 2018; 28:2003-2007. [PMID: 29748050 DOI: 10.1016/j.bmcl.2018.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/25/2018] [Accepted: 05/02/2018] [Indexed: 11/19/2022]
Abstract
Neuraminidase has been considered as an important target for designing agents against influenza viruses. In a discovery of anti-influenza agents with epigoitrin as the initial lead compound, a series of 1-amino-2-alkanols were synthesized and biologically evaluated. The in vitro evaluation indicated that (E)-1-amino-4-phenylbut-3-en-2-ol (C1) had better inhibitory activities than 2-amino-1-arylethan-1-ol derivatives. To our surprise, sulfonation of C1 with 4-methoxybenzenesulfonyl chloride afforded more active inhibitor II with up to 6.4 μM IC50 value against neuraminidase. Furthermore, docking of inhibitor II into the active site of NA found that the H atoms in both NH2 and OH groups of inhibitor II were the key factors for potency. Molecular docking research did not explained very well the observed structure-activity relationship (SAR) from amino acid residue level, but also aided the discovery of (E)-1-amino-4-phenylbut-3-en-2-ol derivatives as novel and potent NA inhibitors.
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Affiliation(s)
- Cheng Lu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
| | - Yan Yin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China.
| | - Fanli Meng
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
| | - Yongbin Dun
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
| | - Keke Pei
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
| | - Chenlu Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
| | - Xu Xu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
| | - Fanhong Wu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 100 Hai Quan Rd., Shanghai, China
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Manetti F. Recent advances in the rational design and development of LIM kinase inhibitors are not enough to enter clinical trials. Eur J Med Chem 2018; 155:445-458. [PMID: 29908439 DOI: 10.1016/j.ejmech.2018.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022]
Abstract
LIM kinases are involved in various pathophysiological processes that depend on actin organization. Alteration of microtubule dynamics by LIMK dysregulation is in fact related to tumor progression and metastasis, viral infection, and ocular diseases, such as glaucoma. As a consequence, many efforts have been done in recent years to rationally design small molecules able to inhibit LIMK activity selectively, without affecting other kinases. As a result, compounds optimized in terms of binding affinity and pharmacokinetic parameters have been discovered, that however failed to access clinical trials. In this review, a comprehensive survey of recent LIMK inhibitors is reported, together with SAR considerations and optimization processes.
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Affiliation(s)
- Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), via A. Moro 2, I-53100 Siena, Italy.
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Ozay O, Yildirim M, Ozay H. Synthesis, structural characterization, and anion interactions of new triazole-linked urea derivative fully substituted cyclotriphosphazene compounds. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2016.1237950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ozgur Ozay
- Department of Chemistry and Chemical Processing Technologies, Lapseki Vocational School, Canakkale Onsekiz Mart University, Canakkale/Lapseki, Turkey
| | - Mehmet Yildirim
- Department of Materials Science and Engineering, Faculty of Engineering, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Hava Ozay
- Department of Chemistry, Inorganic Chemistry Laboratory, Faculty of Science and Arts, Canakkale Onsekiz Mart University, Canakkale, Turkey
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Li D, Song H, Wu T, Xie D, Hu J, Zhao J, Fang L. MiR-138-5p targeting LIMK1 suppresses breast cancer cell proliferation and motility. RSC Adv 2017. [DOI: 10.1039/c7ra09042k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Breast cancer is the most frequently diagnosed female cancer.
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Affiliation(s)
- Dengfeng Li
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
| | - Hongming Song
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
| | - Tianqi Wu
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
| | - Dan Xie
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
| | - Jiashu Hu
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
| | - Junyong Zhao
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
| | - Lin Fang
- Department of Thyroid and Breast
- General Surgery
- Shanghai Tenth People's Hospital
- Tongji University School of Medicine
- Shanghai 200072
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Tsai YF, Yang SC, Hwang TL. Formyl peptide receptor modulators: a patent review and potential applications for inflammatory diseases (2012-2015). Expert Opin Ther Pat 2016; 26:1139-1156. [PMID: 27454150 DOI: 10.1080/13543776.2016.1216546] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The activation of leukocytes and the subsequent immune cascade play an essential role in sterile and infectious inflammation. Dysregulation of these immune responses or excess leukocyte activation can induce tissue damage, organ dysfunction and mortality. Formyl peptide receptors (FPRs) are functionally diverse pattern recognition receptors responsible for recognizing different endogenous damage-associated molecular patterns or exogenous pathogen-associated molecular patterns. FPRs mediate leukocyte activation during inflammation. FPR1 antagonists and FPR2 agonists have demonstrated significant anti-inflammatory effects based on in vitro and in vivo studies. An increasing number of synthesized compounds targeting FPRs, especially potential FPR1 antagonists and FPR2 agonists, have been disclosed in patents. Areas covered: This article summarizes the current pharmacology patents related to FPR family modulators and their therapeutic indications based on a review of patent applications disclosed between 2012 and 2015. Expert opinion: In this review, FPR1 modulators comprise β-1,3-glucan synthase inhibitors containing an FPR ligand moiety, template-fixed peptidomimetics, cyclosporin H, and dipeptide derivatives. FPR2 modulators include phenylurea, bridged spiro[2.4]heptane ester, naphthalene, aminotriazole, polycyclic pyrrolidine-2,5-dione, imidazolidine-2,4-dione, (2-ureidoacetamido)alkyl, amide, oxazolyl-methylether, oxazole, thiazole, and crystalline potassium salt derivatives. These compounds have potential applications for human conditions such as inflammatory lung diseases, ischemia-reperfusion injury, sepsis, inflammatory bowel disease, and wound healing. FPRs are emerging as important targets for treating leukocyte-dominant inflammation.
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Affiliation(s)
- Yung-Fong Tsai
- a Graduate Institute of Natural Products, School of Traditional Medicine, College of Medicine , Chang Gung University , Taoyuan , Taiwan.,b Graduate Institute of Clinical Medical Sciences, College of Medicine , Chang Gung University , Taoyuan , Taiwan.,c Department of Anesthesiology , Chang Gung Memorial Hospital , Taoyuan , Taiwan
| | - Shun-Chin Yang
- d Department of Anesthesiology , Taipei Veterans General Hospital and National Yang-Ming University , Taipei , Taiwan.,e Division of Natural Products, Graduate Institute of Biomedical Sciences, College of Medicine , Chang Gung University , Taoyuan , Taiwan
| | - Tsong-Long Hwang
- a Graduate Institute of Natural Products, School of Traditional Medicine, College of Medicine , Chang Gung University , Taoyuan , Taiwan.,c Department of Anesthesiology , Chang Gung Memorial Hospital , Taoyuan , Taiwan.,e Division of Natural Products, Graduate Institute of Biomedical Sciences, College of Medicine , Chang Gung University , Taoyuan , Taiwan.,f Chinese Herbal Medicine Research Team, Healthy Aging Research Centre , Chang Gung University , Taoyuan , Taiwan.,g Research Center for Industry of Human Ecology and Graduate Institute of Health Industry Technology , Chang Gung University of Science and Technology , Taoyuan , Taiwan
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Synthesis and Biological Evaluation of Gem-Difluoromethylenated Statin Derivatives as Highly Potent HMG-CoA Reductase Inhibitors. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201600180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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