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Protein Kinases and Their Inhibitors

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 3735

Special Issue Editors

School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
Interests: medicinal chemistry; autophagy; epigenetics; protein kinase inhibitors; breast cancer; Parkinson’s disease; drug repurposing
Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
Interests: medicinal chemistry; autophagy; neurodegenerative disease; cancer; drug repurposing

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Guest Editor
School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, China
Interests: histone modifications; apoptosis; metabolic reprogramming; targeted drug; DNA damage

Special Issue Information

Dear Colleagues,

Protein kinases (PKs) catalyze the transfer of the γ‑phosphate group of ATP onto a target substrate. A sequence of such phosphorylation events regulates numerous cellular activities, such as proliferation, survival, apoptosis, metabolism, transcription and differentiation. Owing to overexpression and genetic alterations such as mutations and translocations, the dysregulation of protein kinase activity is involved in the pathogenesis of many diseases including autoimmune, cardiovascular, neurodegenerative and inflammatory diseases, as well as a number of malignancies. Accordingly, protein kinases have become one of the most important drug targets over the past two decades. Although substantial progress has been made in the development and discovery of small-molecule protein kinase inhibitors since the FDA approval of imatinib in 2001, this field remains in its early stages. Therefore, we believe that the discovery and optimization of novel small-molecule protein kinase inhibitors will provide more information and experience to related researchers from both the pharmaceutical field and academia.

In this context, it is a great pleasure to invite you to contribute to this thematic Special Issue of Molecules entitled “Protein Kinases and Their Inhibitors”, which will cover the latest research trends and applications in the field. Submissions of reviews and original research papers are highly welcome. Topics of interest include, but are not limited to, the following:

  1. Design and discovery of novel small-molecule protein kinase inhibitors for disease treatment;
  2. Drug repositioning of protein kinase inhibitors.

Dr. Lan Zhang
Dr. Guan Wang
Dr. Dahong Yao
Guest Editors

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Keywords

  • protein kinase
  • inhibitors
  • activators
  • drug design
  • drug discovery
  • structure optimization
  • drug repositioning

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Published Papers (2 papers)

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Research

22 pages, 8170 KiB  
Article
(E)-N-(3-(1-(2-(4-(2,2,2-Trifluoroacetamido)benzoyl)hydrazono)ethyl)phenyl)nicotinamide: A Novel Pyridine Derivative for Inhibiting Vascular Endothelial Growth Factor Receptor-2: Synthesis, Computational, and Anticancer Studies
by Reda G. Yousef, Hazem Elkady, Eslam B. Elkaeed, Ibraheem M. M. Gobaara, Hanan A. Al-ghulikah, Dalal Z. Husein, Ibrahim M. Ibrahim, Ahmed M. Metwaly and Ibrahim H. Eissa
Molecules 2022, 27(22), 7719; https://doi.org/10.3390/molecules27227719 - 9 Nov 2022
Cited by 36 | Viewed by 1791
Abstract
(E)-N-(3-(1-(2-(4-(2,2,2-Trifluoroacetamido)benzoyl)hydrazono)ethyl)phenyl)nicotinamide (compound 10) was designed as an antiangiogenic VEGFR-2 inhibitor with the essential pharmacophoric structural properties to interact with the catalytic pocket of VEGFR-2. The designed derivative was synthesized, and its structure was confirmed through Ms, elemental, 1 [...] Read more.
(E)-N-(3-(1-(2-(4-(2,2,2-Trifluoroacetamido)benzoyl)hydrazono)ethyl)phenyl)nicotinamide (compound 10) was designed as an antiangiogenic VEGFR-2 inhibitor with the essential pharmacophoric structural properties to interact with the catalytic pocket of VEGFR-2. The designed derivative was synthesized, and its structure was confirmed through Ms, elemental, 1H, and 13C spectral data. The potentiality of the designed pyridine derivative to bind with and inhibit the vascular endothelial growth factor receptor-2 (VEGFR-2) enzyme was indicated by molecular docking assessments. In addition, six molecular dynamic (MD) experiments proved its correct binding with VEGFR-2 over 100 ns. Additionally, the molecular mechanics energies, combined with the generalized born and surface area (MM-GBSA) analysis, identified the precise binding with optimum energy. To explore the stability and reactivity of the designed pyridine derivative, density functional theory (DFT) calculations, including electrostatic potential maps and total electron density, were carried out. Additionally, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis demonstrated its general likeness and its safety. The designed compound was synthesized to evaluate its effects against VEGFR-2 protein, cancer, and normal cells. The in vitro results were concordant with the in silico results, because the new pyridine derivative (compound 10) displayed VEGFR-2 inhibition with an IC50 value of 65 nM and displayed potent cytotoxic properties against hepatic (HepG2) and breast (MCF-7) cancer cell lines with IC50 values of 21.00 and 26.10 μM, respectively; additionally, it exhibited high selectivity indices against the normal cell lines (W-38) of 1.55 and 1.25, respectively. The obtained results present compound 10 as a new lead VEGFR-2 inhibitor for further biological investigation and chemical modifications. Full article
(This article belongs to the Special Issue Protein Kinases and Their Inhibitors)
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24 pages, 4177 KiB  
Article
Deactivatable Bisubstrate Inhibitors of Protein Kinases
by Tanel Sõrmus, Darja Lavogina, Erki Enkvist, Asko Uri and Kaido Viht
Molecules 2022, 27(19), 6689; https://doi.org/10.3390/molecules27196689 - 8 Oct 2022
Viewed by 1572
Abstract
Bivalent ligands, including bisubstrate inhibitors, are conjugates of pharmacophores, which simultaneously target two binding sites of the biomolecule. Such structures offer attainable means for the development of compounds whose ability to bind to the biological target could be modulated by an external trigger. [...] Read more.
Bivalent ligands, including bisubstrate inhibitors, are conjugates of pharmacophores, which simultaneously target two binding sites of the biomolecule. Such structures offer attainable means for the development of compounds whose ability to bind to the biological target could be modulated by an external trigger. In the present work, two deactivatable bisubstrate inhibitors of basophilic protein kinases (PKs) were constructed by conjugating the pharmacophores via linkers that could be cleaved in response to external stimuli. The inhibitor ARC-2121 incorporated a photocleavable nitrodibenzofuran-comprising β-amino acid residue in the structure of the linker. The pharmacophores of the other deactivatable inhibitor ARC-2194 were conjugated via reduction-cleavable disulfide bond. The disassembly of the inhibitors was monitored by HPLC-MS. The affinity and inhibitory potency of the inhibitors toward cAMP-dependent PK (PKAcα) were established by an equilibrium competitive displacement assay and enzyme activity assay, respectively. The deactivatable inhibitors possessed remarkably high 1–2-picomolar affinity toward PKAcα. Irradiation of ARC-2121 with 365 nm UV radiation led to reaction products possessing a 30-fold reduced affinity. The chemical reduction of ARC-2194 resulted in the decrease of affinity of over four orders of magnitude. The deactivatable inhibitors of PKs are valuable tools for the temporal inhibition or capture of these pharmacologically important enzymes. Full article
(This article belongs to the Special Issue Protein Kinases and Their Inhibitors)
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