1
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Suriya U, Mahalapbutr P, Geronikaki A, Kartsev V, Zubenko A, Divaeva L, Chekrisheva V, Petrou A, Oopkaew L, Somngam P, Choowongkomon K, Rungrotmongkol T. Discovery of furopyridine-based compounds as novel inhibitors of Janus kinase 2: In silico and in vitro studies. Int J Biol Macromol 2024; 260:129308. [PMID: 38218283 DOI: 10.1016/j.ijbiomac.2024.129308] [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: 09/01/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
Abstract
Janus kinase 2 (JAK2), one of the JAK isoforms participating in a JAK/STAT signaling cascade, has been considered a potential clinical target owing to its critical role in physiological processes involved in cell growth, survival, development, and differentiation of various cell types, especially immune and hematopoietic cells. Substantial studies have proven that the inhibition of this target could disrupt the JAK/STAT pathway and provide therapeutic outcomes for cancer, immune disorders, inflammation, and COVID-19. Herein, we performed docking-based virtual screening of 63 in-house furopyridine-based compounds and verified the first-round screened compounds by in vitro enzyme- and cell-based assays. By shedding light on the integration of both in silico and in vitro methods, we could elucidate two promising compounds. PD19 showed cytotoxic effects on human erythroblast cell lines (TF-1 and HEL) with IC50 values of 57.27 and 27.28 μM, respectively, while PD12 exhibited a cytotoxic effect on TF-1 with an IC50 value of 83.47 μM by suppressing JAK2/STAT5 autophosphorylation. In addition, all screened compounds were predicted to meet drug-like criteria based on Lipinski's rule of five, and none of the extreme toxicity features were found. Molecular dynamic simulations revealed that PD12 and PD19 could form stable complexes with JAK2 in an aqueous environment, and the van der Waals interactions were the main force driving the complex formation. Besides, all compounds sufficiently interacted with surrounding amino acids in all crucial regions, including glycine, catalytic, and activation loops. Altogether, PD12 and PD19 identified here could potentially be developed as novel therapeutic inhibitors disrupting the JAK/STAT pathway.
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Affiliation(s)
- Utid Suriya
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khan Kaen 40002, Thailand.
| | - Athina Geronikaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | | | - Alexsander Zubenko
- North-Caucasian Zonal Research Veterinary Institute, 346406 Novocherkassk, Russia
| | - Liudmila Divaeva
- Institute of Physical and Organic Chemistry, Southern Federal University, Rostov-on-Don, 344090, Russia
| | - Victoria Chekrisheva
- North-Caucasian Zonal Research Veterinary Institute, 346406 Novocherkassk, Russia
| | - Anthi Petrou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Lipika Oopkaew
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Phitchakorn Somngam
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand; Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
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2
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García-Ortegón M, Simm GNC, Tripp AJ, Hernández-Lobato JM, Bender A, Bacallado S. DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. J Chem Inf Model 2022; 62:3486-3502. [PMID: 35849793 PMCID: PMC9364321 DOI: 10.1021/acs.jcim.1c01334] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 01/05/2023]
Abstract
The field of machine learning for drug discovery is witnessing an explosion of novel methods. These methods are often benchmarked on simple physicochemical properties such as solubility or general druglikeness, which can be readily computed. However, these properties are poor representatives of objective functions in drug design, mainly because they do not depend on the candidate compound's interaction with the target. By contrast, molecular docking is a widely applied method in drug discovery to estimate binding affinities. However, docking studies require a significant amount of domain knowledge to set up correctly, which hampers adoption. Here, we present dockstring, a bundle for meaningful and robust comparison of ML models using docking scores. dockstring consists of three components: (1) an open-source Python package for straightforward computation of docking scores, (2) an extensive dataset of docking scores and poses of more than 260,000 molecules for 58 medically relevant targets, and (3) a set of pharmaceutically relevant benchmark tasks such as virtual screening or de novo design of selective kinase inhibitors. The Python package implements a robust ligand and target preparation protocol that allows nonexperts to obtain meaningful docking scores. Our dataset is the first to include docking poses, as well as the first of its size that is a full matrix, thus facilitating experiments in multiobjective optimization and transfer learning. Overall, our results indicate that docking scores are a more realistic evaluation objective than simple physicochemical properties, yielding benchmark tasks that are more challenging and more closely related to real problems in drug discovery.
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Affiliation(s)
- Miguel García-Ortegón
- Statistical
Laboratory, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Rd., Cambridge CB3 0WB, United Kingdom
| | - Gregor N. C. Simm
- Department
of Engineering, University of Cambridge, Trumpington St., Cambridge CB2 1PZ, United Kingdom
| | - Austin J. Tripp
- Department
of Engineering, University of Cambridge, Trumpington St., Cambridge CB2 1PZ, United Kingdom
| | | | - Andreas Bender
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Rd., Cambridge CB2 1EW, United Kingdom
| | - Sergio Bacallado
- Statistical
Laboratory, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Rd., Cambridge CB3 0WB, United Kingdom
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3
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Rakshit A, Dhara HN, Sahoo AK, Alam T, Patel BK. Pd(II)-Catalyzed Synthesis of Furo[2,3- b]pyridines from β-Ketodinitriles and Alkynes via Cyclization and N-H/C Annulation. Org Lett 2022; 24:3741-3746. [PMID: 35584095 DOI: 10.1021/acs.orglett.2c01472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A Pd(II)-catalyzed synthesis of furopyridines has been developed from β-ketodinitriles and alkynes via an unusual N-H/C annulation. The participation of both the nitrile groups and the concurrent construction of furan and pyridine rings through the formation of C-C, C═C, C-O, C-N, and C═N bonds are the important features. The synthetic applicability is further demonstrated through a series of postsynthetic alterations.
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Affiliation(s)
- Amitava Rakshit
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati 781039, India
| | - Hirendra Nath Dhara
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati 781039, India
| | - Ashish Kumar Sahoo
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati 781039, India
| | - Tipu Alam
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati 781039, India
| | - Bhisma K Patel
- Department of Chemistry, Indian Institute of Technology Guwahati, North Guwahati 781039, India
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4
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Elkamhawy A, Ali EMH, Lee K. New horizons in drug discovery of lymphocyte-specific protein tyrosine kinase (Lck) inhibitors: a decade review (2011-2021) focussing on structure-activity relationship (SAR) and docking insights. J Enzyme Inhib Med Chem 2021; 36:1574-1602. [PMID: 34233563 PMCID: PMC8274522 DOI: 10.1080/14756366.2021.1937143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lymphocyte-specific protein tyrosine kinase (Lck), a non-receptor Src family kinase, has a vital role in various cellular processes such as cell cycle control, cell adhesion, motility, proliferation, and differentiation. Lck is reported as a key factor regulating the functions of T-cell including the initiation of TCR signalling, T-cell development, in addition to T-cell homeostasis. Alteration in expression and activity of Lck results in numerous disorders such as cancer, asthma, diabetes, rheumatoid arthritis, atherosclerosis, and neuronal diseases. Accordingly, Lck has emerged as a novel target against different diseases. Herein, we amass the research efforts in literature and pharmaceutical patents during the last decade to develop new Lck inhibitors. Additionally, structure-activity relationship studies (SAR) and docking models of these new inhibitors within the active site of Lck were demonstrated offering deep insights into their different binding modes in a step towards the identification of more potent, selective, and safe Lck inhibitors.
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Affiliation(s)
- Ahmed Elkamhawy
- College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea.,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Eslam M H Ali
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Republic of Korea.,University of Science & Technology (UST), Daejeon, Republic of Korea.,Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
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5
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Discovery of New Pyrazolopyridine, Furopyridine, and Pyridine Derivatives as CDK2 Inhibitors: Design, Synthesis, Docking Studies, and Anti-Proliferative Activity. Molecules 2021; 26:molecules26133923. [PMID: 34206976 PMCID: PMC8272136 DOI: 10.3390/molecules26133923] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
New pyridine, pyrazoloyridine, and furopyridine derivatives substituted with naphthyl and thienyl moieties were designed and synthesized starting from 6-(naphthalen-2-yl)-2-oxo-4-(thiophen-2-yl)-1,2-dihydropyridine-3-carbonitrile (1). The chloro, methoxy, cholroacetoxy, imidazolyl, azide, and arylamino derivatives were prepared to obtain the pyridine-−C2 functionalized derivatives. The derived pyrazolpyridine-N-glycosides were synthesized via heterocyclization of the C2-thioxopyridine derivative followed by glycosylation using glucose and galactose. The furopyridine derivative 14 and the tricyclic pyrido[3′,2′:4,5]furo[3,2-d]pyrimidine 15 were prepared via heterocyclization of the ester derivative followed by a reaction with formamide. The newly synthesized compounds were evaluated for their ability to in vitro inhibit the CDK2 enzyme. In addition, the cytotoxicity of the compounds was tested against four different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549). The CDK2/cyclin A2 enzyme inhibitory results revealed that pyridone 1, 2-chloro-6-(naphthalen-2-yl)-4-(thiophen-2-yl)nicotinonitrile (4), 6-(naphthalen-2-yl)-4-(thiophen-2-yl)-1H-pyrazolo[3,4-b]pyridin-3-amine (8), S-(3-cyano-6-(naphthaen-2-yl)-4-(thiophen-2-yl)pyridin-2-yl) 2-chloroethanethioate (11), and ethyl 3-amino-6-(naphthalen-2-yl)-4-(thiophen-2-yl)furo[2,3-b]pyridine-2-carboxylate (14) are among the most active inhibitors with IC50 values of 0.57, 0.24, 0.65, 0.50, and 0.93 µM, respectively, compared to roscovitine (IC50 0.394 μM). Most compounds showed significant inhibition on different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549) with IC50 ranges of 31.3–49.0, 19.3–55.5, 22.7–44.8, and 36.8–70.7 μM, respectively compared to doxorubicin (IC50 40.0, 64.8, 24.7 and 58.1 µM, respectively). Furthermore, a molecular docking study suggests that most of the target compounds have a similar binding mode as a reference compound in the active site of the CDK2 enzyme. The structural requirements controlling the CDK2 inhibitory activity were determined through the generation of a statistically significant 2D-QSAR model.
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6
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O’Byrne SN, Eduful BJ, Willson TM, Drewry DH. Concise, gram-scale synthesis of furo[2,3- b]pyridines with functional handles for chemoselective cross-coupling. Tetrahedron Lett 2020; 61:152353. [PMID: 33012852 PMCID: PMC7526865 DOI: 10.1016/j.tetlet.2020.152353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A concise 4-step synthesis of furo[2,3-b]pyridines, with handles in the 3- and 5-positions for palladium mediated cross-coupling reactions, is described. The synthetic route has been optimized, with only one step requiring purification by column chromatography. The route is amenable to scale-up, and was successfully executed on a multi-gram scale. Furopyridines are of growing interest in medicinal chemistry, and this route should enable easy access to the core for structure-activity relationship (SAR) studies.
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Affiliation(s)
- Sean N. O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin J. Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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7
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Guterres H, Im W. Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:2189-2198. [PMID: 32227880 DOI: 10.1021/acs.jcim.0c00057] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structure-based virtual screening relies on classical scoring functions that often fail to reliably discriminate binders from nonbinders. In this work, we present a high-throughput protein-ligand complex molecular dynamics (MD) simulation that uses the output from AutoDock Vina to improve docking results in distinguishing active from decoy ligands in a directory of useful decoy-enhanced (DUD-E) dataset. MD trajectories are processed by evaluating ligand-binding stability using root-mean-square deviations. We select 56 protein targets (of 7 different protein classes) and 560 ligands (280 actives, 280 decoys) and show 22% improvement in ROC AUC (area under the curve, receiver operating characteristics curve), from an initial value of 0.68 (AutoDock Vina) to a final value of 0.83. The MD simulation demonstrates a robust performance across all seven different protein classes. In addition, some predicted ligand-binding modes are moderately refined during MD simulations. These results systematically validate the reliability of a physics-based approach to evaluate protein-ligand binding interactions.
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Affiliation(s)
- Hugo Guterres
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.,School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
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8
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Matouš P, Kadaník M, Timoracký M, Kuneš J, Maříková J, Růžička A, Kočovský P, Pour M. Nucleophile-assisted cyclization of β-propargylamino acrylic compounds catalyzed by gold( i): a rapid construction of multisubstituted tetrahydropyridines and their fused derivatives. Org Chem Front 2020. [DOI: 10.1039/d0qo00653j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A variety of medicinally important multisubstituted tetrahydropyridines, 4-aryl piperidines, isoquinolines and fused pyridines were prepared in 1–3 step sequences via nucleophile-assisted Au(i)-catalyzed cyclizations of easily available azaenynes.
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Affiliation(s)
- Petr Matouš
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
| | - Michal Kadaník
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
| | - Marek Timoracký
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
| | - Jiří Kuneš
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
| | - Jana Maříková
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry
- University of Pardubice
- Faculty of Chemical Technology
- 532 10 Pardubice
- Czech Republic
| | - Pavel Kočovský
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
| | - Milan Pour
- Department of Organic and Bioorganic Chemistry
- Charles University
- Faculty of Pharmacy in Hradec Králové
- Hradec Králové 500 05
- Czech Republic
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9
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Sirakanyan SN, Hakobyan EK, Hovakimyan AA. Synthesis of New Furo[2,3-b]pyridine and Furo[3,2-d]pyrimidine Derivatives. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1070428019090136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Santhosh Kumar G, Poornachandra Y, Kumar Gunda S, Ratnakar Reddy K, Mohmed J, Shaik K, Ganesh Kumar C, Narsaiah B. Synthesis of novel hetero ring fused pyridine derivatives; Their anticancer activity, CoMFA and CoMSIA studies. Bioorg Med Chem Lett 2018; 28:2328-2337. [DOI: 10.1016/j.bmcl.2018.04.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 02/02/2023]
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11
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Wang D, Shen M, Wang Y, Hu J, Zhao J, Yu P. Access to Furo[2,3‐
b
]pyridines by Transition‐Metal‐Free Intramolecular Cyclization of C3‐substituted Pyridine
N
‐oxides. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong Wang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Meng Shen
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Yuxi Wang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Jianyong Hu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Junjie Zhao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Peng Yu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
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12
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Wales TE, Hochrein JM, Morgan CR, Emert-Sedlak LA, Smithgall TE, Engen JR. Subtle Dynamic Changes Accompany Hck Activation by HIV-1 Nef and are Reversed by an Antiretroviral Kinase Inhibitor. Biochemistry 2015; 54:6382-91. [PMID: 26440750 PMCID: PMC4615603 DOI: 10.1021/acs.biochem.5b00875] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The HIV-1 virulence factor Nef interacts with the macrophage Src-family kinase Hck, resulting in constitutive kinase activation that contributes to viral replication and immune escape. Previous chemical library screens identified the diphenylfuranopyrimdine kinase inhibitor DFP-4AB, which selectively inhibits Nef-dependent Hck activity in biochemical assays and potently blocks HIV replication in vitro. In the present study, hydrogen exchange mass spectrometry (HX MS) was used to study conformational changes in downregulated Hck that result from Nef binding, as well as the impact of DFP-4AB on these changes. Remarkably, interaction with Nef induced only subtle changes in deuterium uptake by Hck, with the most significant changes in the N-lobe of the kinase domain adjacent to the docking site for Nef on the SH3 domain. No changes in hydrogen exchange were observed in the Hck SH2 domain or C-terminal tail, indicating that this regulatory interaction is unaffected by Nef binding. When HX MS was performed in the presence of DFP-4AB, the effect of Nef on Hck N-lobe dynamics was completely reversed. These results show that constitutive activation of Hck by HIV-1 Nef requires only modest changes to the conformational dynamics of the overall kinase structure. DFP-4AB reverses these effects, consistent with its activity against this Nef-induced signaling event in HIV-infected cells.
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Affiliation(s)
- Thomas E. Wales
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - James M. Hochrein
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Christopher R. Morgan
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
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13
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Sirakanyan SN, Hovakimyan AA, Noravyan AS. Synthesis, transformations and biological properties of furo[2,3-b]pyridines. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Lawrence HR, Mahajan K, Luo Y, Zhang D, Tindall N, Huseyin M, Gevariya H, Kazi S, Ozcan S, Mahajan NP, Lawrence NJ. Development of novel ACK1/TNK2 inhibitors using a fragment-based approach. J Med Chem 2015; 58:2746-63. [PMID: 25699576 DOI: 10.1021/jm501929n] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The tyrosine kinase ACK1, a critical signal transducer regulating survival of hormone-refractory cancers, is an important therapeutic target, for which there are no selective inhibitors in clinical trials to date. This work reports the discovery of novel and potent inhibitors for ACK1 tyrosine kinase (also known as TNK2) using an innovative fragment-based approach. Focused libraries were designed and synthesized by selecting fragments from reported ACK inhibitors to create hybrid structures in a mix and match process. The hybrid library was screened by enzyme-linked immunosorbent assay-based kinase inhibition and (33)P HotSpot assays. Systematic structure-activity relationship studies led to the identification of compound (R)-9b, which shows potent in vitro (IC50 = 56 nM, n = 3, (33)P HotSpot assay) and in vivo (IC50 < 2 μM, human cancer cell lines) ACK1 inhibition. Both (R)-9b and (S)-9b were stable in human plasma and displayed a long half-life (t(1/2) > 6 h).
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Affiliation(s)
- Harshani R Lawrence
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Kiran Mahajan
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | | | | | | | | | | | | | | | - Nupam P Mahajan
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Nicholas J Lawrence
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
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15
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Jasselin-Hinschberger A, Comoy C, Chartoire A, Fort Y. Elaboration of Furopyridine Scaffolds. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403412] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Palladium-Catalyzed sp2 C–N Bond Forming Reactions: Recent Developments and Applications. TOP ORGANOMETAL CHEM 2012. [DOI: 10.1007/3418_2012_56] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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17
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Abstract
INTRODUCTION because of their important roles in disease and excellent 'druggability', kinases have become the second largest drug target family. The great success of the BCR-ABL inhibitor imatinib in treating chronic myelogenous leukemia illustrates the high potential of kinase inhibitor (KI) therapeutics, but also unveils a major limitation: the development of drug resistance. This is a significant concern as KIs reach large patient populations for an expanding array of indications. AREAS COVERED we provide an up-to-date understanding of the mechanisms through which KIs function and through which cells can become KI-resistant. We review current and future approaches to overcome KI resistance, focusing on currently approved KIs and KIs in clinical trials. We then discuss approaches to improve KI efficacy and overcome drug resistance and novel approaches to develop less drug resistance-prone KI therapeutics. EXPERT OPINION although drug resistance is a concern for current KI therapeutics, recent progress in our understanding of the underlying mechanisms and promising technological advances may overcome this limitation and provide powerful new therapeutics.
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Affiliation(s)
- Rina Barouch-Bentov
- Stanford University School of Medicine, Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford, California 94305, USA
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Martin MW, Machacek MR. Update on lymphocyte specific kinase inhibitors: a patent survey. Expert Opin Ther Pat 2010; 20:1573-93. [PMID: 20831362 DOI: 10.1517/13543776.2010.517749] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
IMPORTANCE OF THE FIELD Lck (p56(lck) or lymphocyte specific kinase) is a cytoplasmic tyrosine kinase of the Src family expressed in T cells and natural killer (NK) cells. Genetic evidence from knockout mice and human mutations demonstrates that Lck kinase activity is critical for T cell receptor (TCR)-mediated signaling, leading to normal T-cell development and activation. Selective inhibition of Lck is expected to offer a new therapy for the treatment of T-cell-mediated autoimmune and inflammatory disorders and/or organ transplant rejection. AREAS COVERED IN THIS REVIEW This review covers the patents, patent applications and associated publications for small molecule kinase inhibitors of Lck since 2005 and attempts to place them in context from a structural point of view. WHAT THE READER WILL GAIN Readers will gain an overview of the structural classes and binding modes of Lck inhibitors, the major players in this area and an insight into the current state of the field. TAKE HOME MESSAGE The search for a potent and orally active inhibitor of Lck has been an intense area of research for a number of years. Despite tremendous efforts, the identification of a highly selective and potent Lck inhibitor suitable for use as an immunosuppressive agent remains elusive.
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Affiliation(s)
- Matthew W Martin
- Amgen, Inc., Department of Medicinal Chemistry, Cambridge, Massachusetts 02142, USA.
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Anisimov VM, Bugaenko VL. QM/QM docking method based on the variational finite localized molecular orbital approximation. J Comput Chem 2009; 30:784-98. [DOI: 10.1002/jcc.21100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bhagwat SS. Kinase inhibitors for the treatment of inflammatory and autoimmune disorders. Purinergic Signal 2008; 5:107-15. [PMID: 18568424 PMCID: PMC2721774 DOI: 10.1007/s11302-008-9117-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 05/13/2008] [Indexed: 12/03/2022] Open
Abstract
Drugs targeting inhibition of kinases for the treatment of inflammation and autoimmune disorders have become a major focus in the pharmaceutical and biotech industry. Multiple kinases from different pathways have been the targets of interest in this endeavor. This review describes some of the recent developments in the search for inhibitors of IKK2, Syk, Lck, and JAK3 kinases. It is anticipated that some of these compounds or newer inhibitors of these kinases will be approved for the treatment of rheumatoid arthritis, psoriasis, organ transplantation, and other autoimmune diseases.
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Affiliation(s)
- Shripad S Bhagwat
- Ambit Biosciences, 4215 Sorrento Valley Boulevard, San Diego, CA, 92121, USA,
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Hynes J, Wu H, Pitt S, Shen DR, Zhang R, Schieven GL, Gillooly KM, Shuster DJ, Taylor TL, Yang X, McIntyre KW, McKinnon M, Zhang H, Marathe PH, Doweyko AM, Kish K, Kiefer SE, Sack JS, Newitt JA, Barrish JC, Dodd J, Leftheris K. The discovery of (R)-2-(sec-butylamino)-N-(2-methyl-5-(methylcarbamoyl)phenyl) thiazole-5-carboxamide (BMS-640994)-A potent and efficacious p38alpha MAP kinase inhibitor. Bioorg Med Chem Lett 2008; 18:1762-7. [PMID: 18313298 DOI: 10.1016/j.bmcl.2008.02.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 02/11/2008] [Accepted: 02/13/2008] [Indexed: 12/01/2022]
Abstract
A novel structural class of p38alpha MAP kinase inhibitors has been identified via iterative SAR studies of a focused deck screen hit. Optimization of the lead series generated 6e, BMS-640994, a potent and selective p38alpha inhibitor that is orally efficacious in rodent models of acute and chronic inflammation.
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Affiliation(s)
- John Hynes
- Bristol-Myers Squibb, Princeton, NJ 08543-4000, USA.
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Martin MW, Newcomb J, Nunes JJ, Boucher C, Chai L, Epstein LF, Faust T, Flores S, Gallant P, Gore A, Gu Y, Hsieh F, Huang X, Kim JL, Middleton S, Morgenstern K, Oliveira-dos-Santos A, Patel VF, Powers D, Rose P, Tudor Y, Turci SM, Welcher AA, Zack D, Zhao H, Zhu L, Zhu X, Ghiron C, Ermann M, Johnston D, Saluste CGP. Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity. J Med Chem 2008; 51:1637-48. [PMID: 18278858 DOI: 10.1021/jm701095m] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lck, or lymphocyte specific kinase, is a cytoplasmic tyrosine kinase of the Src family expressed in T-cells and NK cells. Genetic evidence from knockout mice and human mutations demonstrates that Lck kinase activity is critical for T-cell receptor-mediated signaling, leading to normal T-cell development and activation. A small molecule inhibitor of Lck is expected to be useful in the treatment of T-cell-mediated autoimmune and inflammatory disorders and/or organ transplant rejection. In this paper, we describe the structure-guided design, synthesis, structure-activity relationships, and pharmacological characterization of 2-amino-6-phenylpyrimido[5',4':5,6]pyrimido[1,2- a]benzimidazol-5(6 H)-ones, a new class of compounds that are potent inhibitors of Lck. The most promising compound of this series, 6-(2,6-dimethylphenyl)-2-((4-(4-methyl-1-piperazinyl)phenyl)amino)pyrimido[5',4':5,6]pyrimido-[1,2- a]benzimidazol-5(6 H)-one ( 25), exhibits potent inhibition of Lck kinase activity. This activity translates into inhibition of in vitro cell-based assays and in vivo models of T-cell activation and arthritis, respectively.
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Affiliation(s)
- Matthew W Martin
- Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Cambridge, MA 02139, USA.
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Erratum to “Discovery of 4-amino-5,6-biaryl-furo[2,3-d]pyrimidines as inhibitors of Lck: Development of an expedient and divergent synthetic route and preliminary SAR” [Bioorg. Med. Chem. Lett. 17 (2007) 2305–2309]. Bioorg Med Chem Lett 2007. [DOI: 10.1016/j.bmcl.2007.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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DiMauro EF, Newcomb J, Nunes JJ, Bemis JE, Boucher C, Buchanan JL, Buckner WH, Cheng A, Faust T, Hsieh F, Huang X, Lee JH, Marshall TL, Martin MW, McGowan DC, Schneider S, Turci SM, White RD, Zhu X. Discovery of 4-amino-5,6-biaryl-furo[2,3-d]pyrimidines as inhibitors of Lck: development of an expedient and divergent synthetic route and preliminary SAR. Bioorg Med Chem Lett 2007; 17:2305-9. [PMID: 17280833 DOI: 10.1016/j.bmcl.2007.01.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 01/12/2007] [Accepted: 01/18/2007] [Indexed: 10/23/2022]
Abstract
4-Amino-5,6-biaryl-furo[2,3-d]pyrimidines were identified as potent non-selective inhibitors of Lck. A novel, divergent, and practical synthetic route was developed to access derivatives from bifunctional intermediates. Lead optimization was guided by X-ray crystallographic data, and preliminary SAR led to the identification of compounds with improved cellular potency and selectivity.
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Affiliation(s)
- Erin F DiMauro
- Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Building 1000, Cambridge, MA 02139, USA.
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