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Brauer NR, Kempen AL, Hernandez D, Sintim HO. Non-kinase off-target inhibitory activities of clinically-relevant kinase inhibitors. Eur J Med Chem 2024; 275:116540. [PMID: 38852338 PMCID: PMC11243610 DOI: 10.1016/j.ejmech.2024.116540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024]
Abstract
Protein kinases are responsible for a myriad of cellular functions, such as cell cycle, apoptosis, and proliferation. Because of this, kinases make excellent targets for therapeutics. During the process to identify clinical kinase inhibitor candidates, kinase selectivity profiles of lead inhibitors are typically obtained. Such kinome selectivity screening could identify crucial kinase anti-targets that might contribute to drug toxicity and/or reveal additional kinase targets that potentially contribute to the efficacy of the compound via kinase polypharmacology. In addition to kinome panel screening, practitioners also obtain the inhibition profiles of a few non-kinase targets, such as ion-channels and select GPCR targets to identify compounds that might possess potential liabilities. Often ignored is the possibility that identified kinase inhibitors might also inhibit or bind to the other proteins (greater than 20,000) in the cell that are not kinases, which may be relevant to toxicity or even additional mode of drug action. This review highlights various inhibitors, which have been approved by the FDA or are currently undergoing clinical trials, that also inhibit other non-kinase targets. The binding poses of the drugs in the binding sites of the target kinases and off-targets are analyzed to understand if the same features of the compounds are critical for the polypharmacology.
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Affiliation(s)
- Nickolas R Brauer
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Allison L Kempen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Delmis Hernandez
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Purdue Institute for Drug Discovery, 720 Clinic Drive, West Lafayette, IN, 47907, USA; Purdue Institute for Cancer Research, 201 S. University St., West Lafayette, IN, 47907, USA.
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Yokoyama T, Kusaka K, Mizuguchi M, Nabeshima Y, Fujiwara S. Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin. J Med Chem 2023; 66:15511-15523. [PMID: 37910439 DOI: 10.1021/acs.jmedchem.3c01698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Hereditary ATTR amyloidosis is a disease caused by the deposition of amyloid fibrils formed by mutated transthyretin (TTR), a protein that binds to thyroid hormone in the serum, in the organs. The development of a small molecule that binds to and stabilizes TTR is a promising strategy for the treatment of ATTR amyloidosis. In the present study, we demonstrated that the resveratrol derivatives including pterostilbene available as a dietary supplement inhibit the fibrillization of V30M-TTR to the same extent as the approved drug tafamidis. Furthermore, based on a thermodynamic and X-ray crystallographic analysis, the binding of the resveratrol derivative to TTR was shown to be enthalpy-driven, with the binding enthalpy being acquired by hydrogen bonding to S117. Moreover, direct observation of hydrogen atoms by neutron crystallography provided details of the hydrogen bond network by S117 and emphasized the importance of the CH···π interaction by L110 in the ligand binding.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Katsuhiro Kusaka
- Neutron Industrial Application Promotion Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai 319-1106, Ibaraki, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Satoru Fujiwara
- Institute for Quantum Biology, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai 319-1106, Ibaraki, Japan
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3
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Yokoyama T, Mizuguchi M, Nabeshima Y, Nakagawa Y, Okada T, Toyooka N, Kusaka K. Rafoxanide, a salicylanilide anthelmintic, interacts with human plasma protein transthyretin. FEBS J 2023; 290:5158-5170. [PMID: 37522420 DOI: 10.1111/febs.16915] [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: 03/19/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/01/2023]
Abstract
Transthyretin (TTR) is a carrier protein for thyroid hormone thyroxine (T4 ) in plasma, placental cytosol, and cerebrospinal fluid. While the potential toxicity of small molecules that compete with T4 for binding to TTR should be carefully studied, these small molecules can also serve as anti-ATTR amyloidosis drugs by stabilizing the TTR structure. Here, we demonstrated that rafoxanide, an EU-approved anthelmintic drug for domesticated animals, binds to the T4 -binding site of TTR. An intrinsic fluorescence quenching assay showed that rafoxanide also binds to the thyroid hormone-related proteins, including serum albumin and thyroid hormone receptor β. Rafoxanide strongly inhibited TTR amyloidogenesis in fibrillization assay, but the binding of rafoxanide to TTR was interfered with in human plasma, probably due to interactions with thyroid hormone-related proteins. Protein crystallography provided clues for the optimization of binding affinity and selectivity. Our findings emphasize the importance of considering rafoxanide as both a possible thyroid-disrupting chemical and a lead compound for the development of new ATTR amyloidosis inhibitors.
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Affiliation(s)
| | | | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Japan
| | - Yusuke Nakagawa
- Graduate School of Innovative Life Science, University of Toyama, Japan
| | - Takuya Okada
- Graduate School of Innovative Life Science, University of Toyama, Japan
- Faculty of Engineering, University of Toyama, Japan
| | - Naoki Toyooka
- Graduate School of Innovative Life Science, University of Toyama, Japan
- Faculty of Engineering, University of Toyama, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Japan
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Pant S, Jena NR. Repurposing of antiparasitic drugs against the NS2B-NS3 protease of the Zika virus. J Biomol Struct Dyn 2023:1-13. [PMID: 37747074 DOI: 10.1080/07391102.2023.2255648] [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: 02/23/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
To date, no approved drugs are available to treat the Zika virus (ZIKV) infection. Therefore, it is necessary to urgently identify potential drugs against the ZIKV infection. Here, the repurposing of 30 antiparasitic drugs against the NS2B-NS3 protease of the ZIKV has been carried out by using combined docking and molecular dynamics- (MD) simulations. Based on the docking results, 5 drugs, such as Amodiaquine, Primaquine, Paromomycin, Dichlorophene, and Ivermectin were screened for further analysis by MD simulations and free energy calculations. Among these drugs, Amodiaquine and Dichlorophen are found to produce the most stable complexes and possess relative binding free energies of about -44.3 ± 3.7 kcal/mol and -41.1 ± 5.3 kcal/mol respectively. Therefore, they would act as potent small-molecule inhibitors of the ZIKV protease.However, evaluations of biological and safety activities of these drugs against the ZIKV protease are required before their clinical use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
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5
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Yokoyama T, Kusaka K. Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1. FEBS J 2023; 290:4465-4479. [PMID: 37171222 DOI: 10.1111/febs.16817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/10/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Death-associated protein kinase 1 (DAPK1), a Ca2+/calmodulin-regulated serine/threonine kinase, regulates cell apoptosis and autophagy and has been implicated in the pathogenesis of Alzheimer's disease (AD). Targeting DAPK1 may be a promising approach for treating AD. In our previous study, we found that a natural polyphenol, resveratrol (1), is a moderate DAPK1 inhibitor. In the present study, we investigated the interactions between natural and synthetic derivatives of 1 and DAPK1. Binding assays including intrinsic fluorescence quenching, protein thermal shift and isothermal titration calorimetry indicated that oxyresveratrol (3), a hydroxylated derivative, and pinostilbene (5), a methoxylated derivative, bind to DAPK1 with comparable affinity to 1. The enzymatic assay showed that 3 more effectively inhibits the intrinsic ATPase activity of DAPK1 compared with 1. Crystallographic analysis revealed that the binding modes of the methoxylated derivatives were different from those of 1 and 3, resulting in a unique interaction. Our results suggest that 3 may be helpful in treating AD and provide a clue for the development of promising DAPK1 inhibitors.
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Affiliation(s)
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Japan
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Mizuguchi M, Yokoyama T, Okada T, Nakagawa Y, Fujii K, Nabeshima Y, Toyooka N. Benziodarone and 6-hydroxybenziodarone are potent and selective inhibitors of transthyretin amyloidogenesis. Bioorg Med Chem 2023; 90:117370. [PMID: 37311373 DOI: 10.1016/j.bmc.2023.117370] [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: 04/24/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
Transthyretin amyloidosis is a progressive systemic disorder that is caused by the amyloid deposition of transthyretin in various organs. Stabilization of the native transthyretin is an effective strategy for the treatment of transthyretin amyloidosis. In this study we demonstrate that the clinically used uricosuric agent benziodarone is highly effective to stabilize the tetrameric structure of transthyretin. An acid-induced aggregation assay showed that benziodarone had strong inhibitory activity similar to that of tafamidis, which is currently used as a therapeutic agent for transthyretin amyloidosis. Moreover, a possible metabolite, 6-hydroxybenziodarone, retained the strong amyloid inhibitory activity of benziodarone. An ex vivo competitive binding assay using a fluorogenic probe showed that benziodarone and 6-hydroxybenziodarone were highly potent for selective binding to transthyretin in human plasma. An X-ray crystal structure analysis revealed that the halogenated hydroxyphenyl ring was located at the entrance of the thyroxine binding channel of transthyretin and that the benzofuran ring was located in the inner channel. These studies suggest that benziodarone and 6-hydroxybenziodarone would potentially be effective against transthyretin amyloidosis.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan.
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Yusuke Nakagawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Kanako Fujii
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan; Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
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Mizuguchi M, Nakagawa Y, Inui K, Katayama W, Sawai Y, Shimane A, Kitakami R, Okada T, Nabeshima Y, Yokoyama T, Kanamitsu K, Nakagawa S, Toyooka N. Chlorinated Naringenin Analogues as Potential Inhibitors of Transthyretin Amyloidogenesis. J Med Chem 2022; 65:16218-16233. [PMID: 36472374 DOI: 10.1021/acs.jmedchem.2c00511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Misfolding and aggregation of transthyretin are implicated in the fatal systemic disease known as transthyretin amyloidosis. Here, we report the development of a naringenin derivative bearing two chlorine atoms that will be efficacious for preventing aggregation of transthyretin in the eye. The amyloid inhibitory activity of the naringenin derivative was as strong as that of tafamidis, which is the first therapeutic agent targeting transthyretin in the plasma. X-ray crystal structures of the compounds in complex with transthyretin demonstrated that the naringenin derivative with one chlorine bound to the thyroxine-binding site of transthyretin in the forward mode and that the derivative with two chlorines bound to it in the reverse mode. An ex vivo competitive binding assay showed that naringenin derivatives exhibited more potent binding than tafamidis in the plasma. Furthermore, an in vivo pharmacokinetic study demonstrated that the dichlorinated derivative was significantly delivered to the eye.
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Affiliation(s)
- Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yusuke Nakagawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Japan
| | - Kishin Inui
- Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Wakana Katayama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yurika Sawai
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Ayaka Shimane
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Ryota Kitakami
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Takuya Okada
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Kayoko Kanamitsu
- Drug Discovery Initiative, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinsaku Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Naoki Toyooka
- Faculty of Engineering, University of Toyama, Toyama 930-8555, Japan
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Razzak MA, Cho SJ. Molecular characterization of capsaicin binding interactions with ovalbumin and casein. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mustafa M, Winum JY. The importance of sulfur-containing motifs in drug design and discovery. Expert Opin Drug Discov 2022; 17:501-512. [PMID: 35193437 DOI: 10.1080/17460441.2022.2044783] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Sulfur-containing functional groups are privileged motifs that occur in various pharmacologically effective substances and several natural products. Various functionalities are found with a sulfur atom at diverse oxidation states, as illustrated by thioether, sulfoxide, sulfone, sulfonamide, sulfamate, and sulfamide functions. They are valuable scaffolds in the field of medicinal chemistry and are part of a large array of approved drugs and clinical candidates. AREA COVERED Herein, the authors review the current research on the development of organosulfur-based drug discovery. This article also covers details of their roles in the new lead compounds reported in the literature over the past five years 2017-2021. EXPERT OPINION Given its prominent role in medicinal chemistry and its importance in drug discovery, sulfur has attracted continuing interest and has been used in the design of various valuable compounds that demonstrate a variety of biological and pharmacological feature activities. Overall, sulfur's role in medicinal chemistry continues to grow. However, many sulfur functionalities remain underused in small-molecule drug discovery and deserve special attention in the armamentarium for treating diverse diseases. Research efforts are also still required for the development of a synthetic methodology for direct access to these functions and late-stage functionalization.
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Affiliation(s)
- Muhamad Mustafa
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.,Department of Medicinal Chemistry, Faculty of Pharmacy, Deraya Unuversity, Minia, Egypt
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