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Asquith CRM, Temme L, East MP, Laitinen T, Pickett J, Kwarcinski FE, Sinha P, Wells CI, Johnson GL, Zutshi R, Drewry DH. Identification of 4-anilino-quin(az)oline as a cell active Protein Kinase Novel 3 (PKN3) inhibitor chemotype. ChemMedChem 2022; 17:e202200161. [PMID: 35403825 DOI: 10.1002/cmdc.202200161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/08/2022]
Abstract
Deep annotation of a library of 4-anilinoquinolines led to the identification of 7-iodo- N -(3,4,5-trimethoxyphenyl)quinolin-4-amine 16 as a potent inhibitor (IC 50 = 14 nM) of Protein Kinase Novel 3 (PKN3) with micromolar activity in cells. Compound 16 is a potential tool compound to study the cell biology of PKN3 and its role in pancreatic and prostate cancer and T-cell acute lymphoblastic leukemia. These 4-anilinoquinolines may also be useful tools to uncover the therapeutic potential of PKN3 inhibition in a broad range of diseases.
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Affiliation(s)
| | - Louisa Temme
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
| | - Michael P East
- University of North Carolina at Chapel Hill, Department of Pharmacology, School of Medicine, UNITED STATES
| | - Tuomo Laitinen
- University of Eastern Finland Faculty of Health Sciences: Ita-Suomen yliopisto Terveystieteiden tiedekunta, School of Pharmacy, FINLAND
| | - Julie Pickett
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
| | - Frank E Kwarcinski
- Luceome Biotechnologies, LLC, Luceome Biotechnologies, LLC, UNITED STATES
| | - Parvathi Sinha
- Luceome Biotechnologies, LLC, Luceome Biotechnologies, LLC, UNITED STATES
| | - Carrow I Wells
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
| | - Gary L Johnson
- University of North Carolina at Chapel Hill, Department of Pharmacology, School of Medicine,, UNITED STATES
| | - Reena Zutshi
- Luceome Biotechnologies, LLC, Luceome Biotechnologies, LLC,, UNITED STATES
| | - David H Drewry
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
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2
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Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding? Biochem Soc Trans 2022; 50:633-648. [PMID: 35226061 PMCID: PMC9022976 DOI: 10.1042/bst20210837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
In recent years, protein kinases have been one of the most pursued drug targets. These determined efforts have resulted in ever increasing numbers of small-molecule kinase inhibitors reaching to the market, offering novel treatment options for patients with distinct diseases. One essential component related to the activation and normal functionality of a protein kinase is the regulatory spine (R-spine). The R-spine is formed of four conserved residues named as RS1–RS4. One of these residues, RS3, located in the C-terminal part of αC-helix, is usually accessible for the inhibitors from the ATP-binding cavity as its side chain is lining the hydrophobic back pocket in many protein kinases. Although the role of RS3 has been well acknowledged in protein kinase function, this residue has not been actively considered in inhibitor design, even though many small-molecule kinase inhibitors display interactions to this residue. In this minireview, we will cover the current knowledge of RS3, its relationship with the gatekeeper, and the role of RS3 in kinase inhibitor interactions. Finally, we comment on the future perspectives how this residue could be utilized in the kinase inhibitor design.
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3
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Andac CA, Çakmak O, Ökten S, Çağlar-Andac S, Işıldak İ. In-silico Pharmacokinetic and Affinity Studies of Piperazine/Morpholine Substituted Quinolines in Complex with GAK as Promising Anti-HCV Agent. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s273741652150054x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Piperazine/morpholine derivatives of quinoline substituted at positions C-3, C-6 and C-8 has been previously prepared by SNAr reactions of 3,6,8-tribromoquinoline (1) under microwave or conventional heating reaction conditions. In this study, we evaluated binding interactions between the piperazine/morpholine substituted quinolines and its highly-likely receptor, Cyclin G associated kinase (GAK) involved in hepatitis C virus (HCV) entry into host cells, via docking, molecular dynamics (MD), thermodynamic and pharmacokinetics computations in order to select a possible lead compound, which may be used for lead-optimization in our future studies to develop novel drug candidates against HCV infections. 372 nsec MD simulations followed by MM-PBSA thermodynamic computations revealed that compound 23 ([Formula: see text]= 0.08[Formula: see text]nM) possesses the greatest potential to inhibit GAK. Pharmacokinetics computations suggest that compound 23 is a drug-like molecule as it conforms to the Lipinski filter. We determined that compound 23 could be a lead-like molecule for peripheric and cerebral HCV infections.
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Affiliation(s)
- Cenk A. Andac
- Department of Pharmaceutical Chemistry, School of Pharmacy, Istinye University, Zeytinburnu, İstanbul 34010, Turkey
- Department of Medical Pharmacology, School of Medicine, Yeditepe University, İstanbul 34755, Turkey
| | - Osman Çakmak
- Department of Gastronomy, Faculty of Arts and Design, İstanbul Rumeli University, Silivri, İstanbul 34570, Turkey
| | - Salih Ökten
- Department of Mathematic and Science Education, Division of Science Education, Faculty of Education, Kırıkkale University, Yahşihan, Kırıkkale 71450, Turkey
| | - Sena Çağlar-Andac
- Department of Analytical Chemistry, Faculty of Pharmacy, Istanbul University, Fatih, İstanbul 34116, Turkey
| | - İbrahim Işıldak
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, Davutpaşa, Istanbul 34210, Turkey
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4
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Abourehab MAS, Alqahtani AM, Youssif BGM, Gouda AM. Globally Approved EGFR Inhibitors: Insights into Their Syntheses, Target Kinases, Biological Activities, Receptor Interactions, and Metabolism. Molecules 2021; 26:6677. [PMID: 34771085 PMCID: PMC8587155 DOI: 10.3390/molecules26216677] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
Targeting the EGFR with small-molecule inhibitors is a confirmed valid strategy in cancer therapy. Since the FDA approval of the first EGFR-TKI, erlotinib, great efforts have been devoted to the discovery of new potent inhibitors. Until now, fourteen EGFR small-molecule inhibitors have been globally approved for the treatment of different types of cancers. Although these drugs showed high efficacy in cancer therapy, EGFR mutations have emerged as a big challenge for these drugs. In this review, we focus on the EGFR small-molecule inhibitors that have been approved for clinical uses in cancer therapy. These drugs are classified based on their chemical structures, target kinases, and pharmacological uses. The synthetic routes of these drugs are also discussed. The crystal structures of these drugs with their target kinases are also summarized and their bonding modes and interactions are visualized. Based on their binding interactions with the EGFR, these drugs are also classified into reversible and irreversible inhibitors. The cytotoxicity of these drugs against different types of cancer cell lines is also summarized. In addition, the proposed metabolic pathways and metabolites of the fourteen drugs are discussed, with a primary focus on the active and reactive metabolites. Taken together, this review highlights the syntheses, target kinases, crystal structures, binding interactions, cytotoxicity, and metabolism of the fourteen globally approved EGFR inhibitors. These data should greatly help in the design of new EGFR inhibitors.
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Affiliation(s)
- Mohammed A. S. Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Alaa M. Alqahtani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Bahaa G. M. Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt;
| | - Ahmed M. Gouda
- Department of Medicinal Chemistry, Faculty of pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
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5
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Gil C, Ginex T, Maestro I, Nozal V, Barrado-Gil L, Cuesta-Geijo MÁ, Urquiza J, Ramírez D, Alonso C, Campillo NE, Martinez A. COVID-19: Drug Targets and Potential Treatments. J Med Chem 2020; 63:12359-12386. [PMID: 32511912 PMCID: PMC7323060 DOI: 10.1021/acs.jmedchem.0c00606] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Currently, humans are immersed in a pandemic caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which threatens public health worldwide. To date, no drug or vaccine has been approved to treat the severe disease caused by this coronavirus, COVID-19. In this paper, we will focus on the main virus-based and host-based targets that can guide efforts in medicinal chemistry to discover new drugs for this devastating disease. In principle, all CoV enzymes and proteins involved in viral replication and the control of host cellular machineries are potentially druggable targets in the search for therapeutic options for SARS-CoV-2. This Perspective provides an overview of the main targets from a structural point of view, together with reported therapeutic compounds with activity against SARS-CoV-2 and/or other CoVs. Also, the role of innate immune response to coronavirus infection and the related therapeutic options will be presented.
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Affiliation(s)
- Carmen Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Tiziana Ginex
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Inés Maestro
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Vanesa Nozal
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Lucía Barrado-Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Ángel Cuesta-Geijo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Urquiza
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas,
Universidad Autónoma de Chile,
Llano Subercaseaux 2801- piso 6, 7500912 Santiago,
Chile
| | - Covadonga Alonso
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - Nuria E. Campillo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
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6
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Asquith CRM, Tizzard GJ, Bennett JM, Wells CI, Elkins JM, Willson TM, Poso A, Laitinen T. Targeting the Water Network in Cyclin G‐Associated Kinase (GAK) with 4‐Anilino‐quin(az)oline Inhibitors. ChemMedChem 2020; 15:1200-1215. [DOI: 10.1002/cmdc.202000150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Christopher R. M. Asquith
- Department of Pharmacology, School of MedicineUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Graham J. Tizzard
- UK National Crystallography Service, School of ChemistryUniversity of Southampton Southampton SO17 1BJ UK
| | - James M. Bennett
- Structural Genomics Consortium and Target Discovery Institute Nuffield Department of Clinical MedicineUniversity of Oxford Old Road Campus Research Building Oxford OX3 7DQ UK)
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Jonathan M. Elkins
- Structural Genomics Consortium and Target Discovery Institute Nuffield Department of Clinical MedicineUniversity of Oxford Old Road Campus Research Building Oxford OX3 7DQ UK)
- Structural Genomics ConsortiumUniversidade Estadual de Campinas – UNICAMP Campinas São Paulo 13083-886 Brazil
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Antti Poso
- School of Pharmacy, Faculty of Health SciencesUniversity of Eastern Finland 70211 Kuopio Finland
- University Hospital Tübingen Department of Internal Medicine VIIIUniversity of Tübingen 72076 Tübingen Germany
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health SciencesUniversity of Eastern Finland 70211 Kuopio Finland
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7
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Asquith CRM, Laitinen T, Bennett JM, Wells CI, Elkins JM, Zuercher WJ, Tizzard GJ, Poso A. Design and Analysis of the 4-Anilinoquin(az)oline Kinase Inhibition Profiles of GAK/SLK/STK10 Using Quantitative Structure-Activity Relationships. ChemMedChem 2019; 15:26-49. [PMID: 31675459 DOI: 10.1002/cmdc.201900521] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Indexed: 01/01/2023]
Abstract
The 4-anilinoquinoline and 4-anilinoquinazoline ring systems have been the focus of significant efforts in prior kinase drug discovery programs, which have led to approved medicines. Broad kinome profiles of these compounds have now been assessed with the advent of advanced screening technologies. These ring systems, while originally designed for specific targets including epidermal growth factor receptor (EGFR), but actually display a number of potent collateral kinase targets, some of which have been associated with negative clinical outcomes. We have designed and synthesized a series of 4-anilinoquin(az)olines in order to better understand the structure-activity relationships of three main collateral kinase targets of quin(az)oline-based kinase inhibitors: cyclin G associated kinase (GAK), STE20-like serine/threonine-protein kinase (SLK) and serine/threonine-protein kinase 10 (STK10). This was achieved through a series of quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites and extensive small-molecule X-ray structural analysis.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - James M Bennett
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M Elkins
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.,Structural Genomics Consortium, Universidade Estadual de Campinas-UNICAMP, Campinas, São Paulo, 13083-886 (Brazil)
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland.,University Hospital Tübingen, Deparment of Internal Medicine VIII, University of Tübingen, 72076, Tübingen, Germany
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8
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Towards the Development of an In vivo Chemical Probe for Cyclin G Associated Kinase (GAK). Molecules 2019; 24:molecules24224016. [PMID: 31698822 PMCID: PMC6891286 DOI: 10.3390/molecules24224016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 12/15/2022] Open
Abstract
SGC-GAK-1 (1) is a potent, selective, cell-active chemical probe for cyclin G-associated kinase (GAK). However, 1 was rapidly metabolized in mouse liver microsomes by cytochrome P450-mediated oxidation, displaying rapid clearance in liver microsomes and in mice, which limited its utility in in vivo studies. Chemical modifications of 1 that improved metabolic stability, generally resulted in decreased GAK potency. The best analog in terms of GAK activity in cells was 6-bromo-N-(1H-indazol-6-yl)quinolin-4-amine (35) (IC50 = 1.4 μM), showing improved stability in liver microsomes while still maintaining a narrow spectrum activity across the kinome. As an alternative to scaffold modifications we also explored the use of the broad-spectrum cytochrome P450 inhibitor 1-aminobenzotriazole (ABT) to decrease intrinsic clearance of aminoquinoline GAK inhibitors. Taken together, these approaches point towards the development of an in vivo chemical probe for the dark kinase GAK.
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9
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Lv G, Yin CL. A new heterocyclic compound initiates ROS accumulation and cause apoptotic cell death in human bone cancer cells. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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