1
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Latosińska M, Latosińska JN. Serine/Threonine Protein Kinases as Attractive Targets for Anti-Cancer Drugs-An Innovative Approach to Ligand Tuning Using Combined Quantum Chemical Calculations, Molecular Docking, Molecular Dynamic Simulations, and Network-like Similarity Graphs. Molecules 2024; 29:3199. [PMID: 38999151 PMCID: PMC11243552 DOI: 10.3390/molecules29133199] [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: 06/01/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Serine/threonine protein kinases (CK2, PIM-1, RIO1) are constitutively active, highly conserved, pleiotropic, and multifunctional kinases, which control several signaling pathways and regulate many cellular functions, such as cell activity, survival, proliferation, and apoptosis. Over the past decades, they have gained increasing attention as potential therapeutic targets, ranging from various cancers and neurological, inflammation, and autoimmune disorders to viral diseases, including COVID-19. Despite the accumulation of a vast amount of experimental data, there is still no "recipe" that would facilitate the search for new effective kinase inhibitors. The aim of our study was to develop an effective screening method that would be useful for this purpose. A combination of Density Functional Theory calculations and molecular docking, supplemented with newly developed quantitative methods for the comparison of the binding modes, provided deep insight into the set of desirable properties responsible for their inhibition. The mathematical metrics helped assess the distance between the binding modes, while heatmaps revealed the locations in the ligand that should be modified according to binding site requirements. The Structure-Binding Affinity Index and Structural-Binding Affinity Landscape proposed in this paper helped to measure the extent to which binding affinity is gained or lost in response to a relatively small change in the ligand's structure. The combination of the physico-chemical profile with the aforementioned factors enabled the identification of both "dead" and "promising" search directions. Tests carried out on experimental data have validated and demonstrated the high efficiency of the proposed innovative approach. Our method for quantifying differences between the ligands and their binding capabilities holds promise for guiding future research on new anti-cancer agents.
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Affiliation(s)
- Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-814 Poznań, Poland
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2
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Al-Qadhi MA, Yahya TAA, El-Nassan HB. Recent Advances in the Discovery of CK2 Inhibitors. ACS OMEGA 2024; 9:20702-20719. [PMID: 38764653 PMCID: PMC11097362 DOI: 10.1021/acsomega.3c10478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
CK2 is a vital enzyme that phosphorylates a large number of substrates and thereby controls many processes in the body. Its upregulation was reported in many cancer types. Inhibitors of CK2 might have anticancer activity, and two compounds are currently under clinical trials. However, both compounds are ATP-competitive inhibitors that may have off-target side effects. The development of allosteric and dual inhibitors can overcome this drawback. These inhibitors showed higher selectivity and specificity for the CK2 enzyme compared to the ATP-competitive inhibitors. The present review summarizes the efforts exerted in the last five years in the design of CK2 inhibitors.
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Affiliation(s)
- Mustafa A. Al-Qadhi
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a, Yemen
| | - Tawfeek A. A. Yahya
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Sana’a University, 18084 Sana’a,Yemen
| | - Hala B. El-Nassan
- Pharmaceutical
Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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3
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Delaveris CS, Kong S, Glasgow J, Loudermilk RP, Kirkemo LL, Zhao F, Salangsang F, Phojanakong P, Camara Serrano JA, Steri V, Wells JA. Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585970. [PMID: 38562834 PMCID: PMC10983885 DOI: 10.1101/2024.03.20.585970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
New epitopes for immune recognition provide the basis of anticancer immunity. Due to the high concentration of extracellular adenosine triphosphate in the tumor microenvironment, we hypothesized that extracellular kinases (ectokinases) could have dysregulated activity and introduce aberrant phosphorylation sites on cell surface proteins. We engineered a cell-tethered version of the extracellular kinase CK2α, demonstrated it was active on cells under tumor-relevant conditions, and profiled its substrate scope using a chemoproteomic workflow. We then demonstrated that mice developed polyreactive antisera in response to syngeneic tumor cells that had been subjected to surface hyperphosphorylation with CK2α. Interestingly, these mice developed B cell and CD4+ T cell responses in response to these antigens but failed to develop a CD8+ T cell response. This work provides a workflow for probing the extracellular phosphoproteome and demonstrates that extracellular phosphoproteins are immunogenic even in a syngeneic system.
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Affiliation(s)
- Corleone S Delaveris
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Sophie Kong
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Rita P Loudermilk
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Lisa L Kirkemo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Fangzhu Zhao
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - Fernando Salangsang
- Preclinical Therapeutics Core, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, 94158, USA
| | - Paul Phojanakong
- Preclinical Therapeutics Core, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, 94158, USA
| | - Juan Antonio Camara Serrano
- Preclinical Therapeutics Core, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, 94158, USA
| | - Veronica Steri
- Preclinical Therapeutics Core, Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California, 94158, USA
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4
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Yadav S, Ahamad S, Gupta D, Mathur P. Lead optimization, pharmacophore development and scaffold design of protein kinase CK2 inhibitors as potential COVID-19 therapeutics. J Biomol Struct Dyn 2023; 41:1811-1827. [PMID: 35014595 DOI: 10.1080/07391102.2021.2024449] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Therapeutic agents being designed against COVID-19 have targeted either the virus directly or the host cellular machinery. A particularly attractive host target is the ubiquitous and constitutively active serine-threonine kinase, Protein kinase CK2 (CK2). CK2 enhances viral protein synthesis by inhibiting the sequestration of host translational machinery as stress granules and assists in viral egression via association with the N-protein at filopodial protrusions of the infected cell. CK2 inhibitors such as Silmitasertib have been proposed as possible therapeutic candidates in COVID-19 infections. The present study aims to optimize Silmitasertib, develop pharmacophore models and design unique scaffolds to modulate CK2. The lead optimization phase involved the generation of compounds structurally similar to Silmitasertib via bioisostere replacement followed by a multi-stage docking approach to identify drug-like candidates. Molecular dynamics (MD) simulations were performed for two promising candidates (ZINC-43206125 and PC-57664175) to estimate their binding stability and interaction. Top scoring candidates from the lead optimization phase were utilized to build ligand-based pharmacophore models. These models were then merged with structure-based pharmacophores (e-pharmacophores) to build a hybrid hypothesis. This hybrid hypothesis was validated against a decoy set and used to screen a diverse kinase inhibitors library to identify favored chemical features in the retrieved actives. These chemical features include; an anion, an aromatic ring and an H-bond acceptor. Based on the knowledge of these features; de-novo scaffold design was carried out which identified phenindiones, carboxylated steroids, macrocycles and peptides as novel scaffolds with the potential to modulate CK2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Siddharth Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puniti Mathur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
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5
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Zhang H, Modenutti C, Nekkanti YPK, Denis M, Bermejo IA, Lefèbre J, Che K, Kim D, Kagelmacher M, Kurzbach D, Nazaré M, Rademacher C. Identification of the Allosteric Binding Site for Thiazolopyrimidine on the C-Type Lectin Langerin. ACS Chem Biol 2022; 17:2728-2733. [PMID: 36153965 PMCID: PMC9594047 DOI: 10.1021/acschembio.2c00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Langerin is a mammalian C-type lectin expressed on Langerhans cells in the skin. As an innate immune cell receptor, Langerin is involved in coordinating innate and adaptive immune responses against various incoming threats. We have previously reported a series of thiazolopyrimidines as murine Langerin ligands. Prompted by the observation that its human homologue exhibits different binding specificities for these small molecules, we report here our investigations to define their exact binding site. By using structural comparison and molecular dynamics simulations, we showed that the nonconserved short loops have a high degree of conformational flexibility between the human and murine homologues. Sequence analysis and mutational studies indicated that a pair of residues are essential for the recognition of the thiazolopyrimidines. Taking solvent paramagnetic relaxation enhancement NMR studies together with a series of peptides occupying the same site, we could define the cleft between the short and long loops as the allosteric binding site for these aromatic heterocycles.
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Affiliation(s)
- Hengxi Zhang
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Biology, Chemistry, and Pharmacy, Freie
Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo), University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - Carlos Modenutti
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Departamento
de Química Biológica, Facultad
de Ciencias Exactas y Naturales, C1428EHA Buenos Aires, Argentina,Instituto
de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, C1428EHA Buenos
Aires, Argentina
| | - Yelha Phani Kumar Nekkanti
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany,Berlin
Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Maxime Denis
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Iris A. Bermejo
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jonathan Lefèbre
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo), University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - Kateryna Che
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria,Doctoral
School in Chemistry (DoSChem), University
of Vienna, Währingerstr. 42, 1090 Vienna, Austria
| | - Dongyoon Kim
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marten Kagelmacher
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Biology, Chemistry, and Pharmacy, Freie
Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Marc Nazaré
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany,Berlin
Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Christoph Rademacher
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Biology, Chemistry, and Pharmacy, Freie
Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,
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6
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Ni D, Chai Z, Wang Y, Li M, Yu Z, Liu Y, Lu S, Zhang J. Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Duan Ni
- College of Pharmacy Ningxia Medical University Yinchuan China
- The Charles Perkins Centre University of Sydney Sydney New South Wales Australia
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital Second Military Medical University Shanghai China
| | - Ying Wang
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Mingyu Li
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
| | | | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Shaoyong Lu
- College of Pharmacy Ningxia Medical University Yinchuan China
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jian Zhang
- College of Pharmacy Ningxia Medical University Yinchuan China
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai China
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
- School of Pharmaceutical Sciences Zhengzhou University Zhengzhou China
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7
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Wang P, Sun GB, Dou GX, Wang BQ. Long non-coding RNA B3GALT5-AS1 contributes to the progression of gastric cancer via interacting with CSNK2A1. Exp Ther Med 2021; 22:927. [PMID: 34306196 PMCID: PMC8281446 DOI: 10.3892/etm.2021.10359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer is a type of cancer that is characterized by high morbidity and mortality rates. Long non-coding RNA (lncRNA) β-1,3-galactosyltransferase 5-AS1 (B3GALT5-AS1) was previously found to be highly expressed in the serum of patients with gastric cancer. However, the regulatory effects of B3GALT5-AS1 in gastric cancer remain poorly understood. The present study aimed to investigate the effects of B3GALT5-AS1 in gastric cancer cell lines. The expression levels of B3GALT5-AS1 were determined in different gastric cancer cell lines (AGS, HGC-27 and MKN-45) using reverse transcription-quantitative PCR. The potential interaction between B3GALT5-AS1 and casein kinase 2 a1 (CSNK2A1) was evaluated using an RNA binding protein immunoprecipitation and RNA pull down assays. Western blot analysis was performed to measure protein expression levels. Cell Counting Kit-8 assay was utilized to determine cell viability, whilst cell invasion and migration were assessed using Transwell and wound healing assays, respectively. Apoptotic cells were evaluated using TUNEL assays. The results showed that B3GALT5-AS1 expression was upregulated in MKN-45 cells compared with the control group. In addition, B3GALT5-AS1 could bind to CSNK2A1 to regulate its expression. B3GALT5-AS1 knockdown attenuated cell viability, invasion and migration, whilst promoting cell apoptosis. These effects were partly reversed by CSNK2A1 overexpression. Overall, results of the present study revealed that interference with B3GALT5-AS1 impeded gastric cancer cell migration and invasion whilst promoting apoptosis by regulating CSNK2A1 expression. These findings suggested that B3GALT5-AS1 and CSNK2A1 may serve a tumorigenic role in the progression of gastric cancer and serve as therapeutic targets for this type of cancer.
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Affiliation(s)
- Ping Wang
- Center of Digestive Endoscopy, Tianjin Fifth Central Hospital, Tianjin 300451, P.R. China
| | - Guang-Bin Sun
- Center of Digestive Endoscopy, Tianjin Fifth Central Hospital, Tianjin 300451, P.R. China
| | - Guang-Xian Dou
- Center of Digestive Endoscopy, Tianjin Fifth Central Hospital, Tianjin 300451, P.R. China
| | - Bai-Qing Wang
- Center of Digestive Endoscopy, Tianjin Fifth Central Hospital, Tianjin 300451, P.R. China
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8
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Silva-Pavez E, Tapia JC. Protein Kinase CK2 in Cancer Energetics. Front Oncol 2020; 10:893. [PMID: 32626654 PMCID: PMC7315807 DOI: 10.3389/fonc.2020.00893] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
Protein kinase CK2 (formerly known as casein kinase 2) is abnormally elevated in many cancers. This may increase tumor aggressiveness through CK2-dependent phosphorylation of key proteins in several signaling pathways. In this work, we have compiled evidence from the literature to suggest that CK2 also modulates a metabolic switch characteristic of cancer cells that enhances resistance to death, due to either drugs or to a microenvironment deficient in oxygen or nutrients. Concurrently, CK2 may help to preserve mitochondrial activity in a PTEN-dependent manner. PTEN, widely recognized as a tumor suppressor, is another CK2 substrate in the PI3K/Akt signaling pathway that promotes cancer viability and aerobic glycolysis. Given that CK2 can regulate Akt as well as two of its main effectors, namely mTORC1 and β-catenin, we comprehensively describe how CK2 may modulate cancer energetics by regulating expression of key targets and downstream processes, such as HIF-1 and autophagy, respectively. Thus, the specific inhibition of CK2 may lead to a catastrophic death of cancer cells, which could become a feasible therapeutic strategy to beat this devastating disease. In fact, ATP-competitive inhibitors, synthetic peptides and antisense oligonucleotides have been designed as CK2 inhibitors, some of them used in preclinical models of cancer, of which TBB and silmitasertib are widely known. We will finish by discussing a hypothetical scenario in which cancer cells are "addicted" to CK2; i.e., in which many proteins that regulate signaling pathways and metabolism-linked processes are highly dependent on this kinase.
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Affiliation(s)
- Eduardo Silva-Pavez
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Julio C Tapia
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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9
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He H, Liu B, Luo H, Zhang T, Jiang J. Big data and artificial intelligence discover novel drugs targeting proteins without 3D structure and overcome the undruggable targets. Stroke Vasc Neurol 2020; 5:381-387. [PMID: 33376199 PMCID: PMC7804061 DOI: 10.1136/svn-2019-000323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 12/27/2022] Open
Abstract
The discovery of targeted drugs heavily relies on three-dimensional (3D) structures of target proteins. When the 3D structure of a protein target is unknown, it is very difficult to design its corresponding targeted drugs. Although the 3D structures of some proteins (the so-called undruggable targets) are known, their targeted drugs are still absent. As increasing crystal/cryogenic
electron microscopy structures are deposited in Protein Data Bank, it is much more possible to discover the targeted drugs. Moreover, it is also highly probable to turn previous undruggable targets into druggable ones when we identify their hidden allosteric sites. In this review, we focus on the currently available advanced methods for the discovery of novel compounds targeting proteins without 3D structure and how to turn undruggable targets into druggable ones.
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Affiliation(s)
- Huiqin He
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Benquan Liu
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Hongyi Luo
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Tingting Zhang
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Jingwei Jiang
- Institute of Pharmacologic Science, China Pharmaceutical University, Nanjing, China
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10
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Chen X, Li C, Wang D, Chen Y, Zhang N. Recent Advances in the Discovery of CK2 Allosteric Inhibitors: From Traditional Screening to Structure-Based Design. Molecules 2020; 25:molecules25040870. [PMID: 32079098 PMCID: PMC7070378 DOI: 10.3390/molecules25040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Protein kinase (CK2) has emerged as an attractive cancer therapeutic target and recent efforts have been made to develop its inhibitors. However, the development of selective inhibitors remains challenging because of the highly conserved ATP-binding pocket (orthosteric site) of kinase family. As an alternative strategy, allosteric inhibitors, by targeting the much more diversified allosteric site relative to the conserved ATP-binding site, achieve better pharmacological advantages than orthosteric inhibitors. Traditional serendipitous screening and structure-based design are robust tools for the discovery of CK2 allosteric inhibitors. In this review, we summarize the recent advances in the identification of CK2 allosteric inhibitors. Firstly, we briefly present the CK2 allosteric sites. Then, the allosteric inhibitors targeting the well-elucidated allosteric sites (α/β interface, αD pocket and interface between the Glycine-rich loop and αC-helix) are highlighted in the discovery process and possible binding modes with the allosteric sites are described. This study is expected to provide valuable clues for the design of CK2 allosteric inhibitors.
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Affiliation(s)
- Xiaolan Chen
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; (D.W.); (Y.C.)
- Correspondence: (X.C.); (N.Z.); Tel.: +86-0523-86158081 (X.C.)
| | - Chunqiong Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China;
| | - Dada Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; (D.W.); (Y.C.)
| | - Yu Chen
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China; (D.W.); (Y.C.)
| | - Na Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China;
- Correspondence: (X.C.); (N.Z.); Tel.: +86-0523-86158081 (X.C.)
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11
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Li C, Zhang X, Zhang N, Zhou Y, Sun G, Zhao L, Zhong R. Identification and Biological Evaluation of CK2 Allosteric Fragments through Structure-Based Virtual Screening. Molecules 2020; 25:molecules25010237. [PMID: 31935979 PMCID: PMC6983002 DOI: 10.3390/molecules25010237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/19/2022] Open
Abstract
Casein kinase II (CK2) is considered as an attractive cancer therapeutic target, and recent efforts have been made to develop its ATP-competitive inhibitors. However, achieving selectivity with respect to related kinases remains challenging due to the highly conserved ATP-binding pocket of kinases. Allosteric inhibitors, by targeting the much more diversified allosteric site relative to the highly conserved ATP-binding pocket, might be a promising strategy with the enhanced selectivity and reduced toxicity than ATP-competitive inhibitors. The previous studies have highlighted the traditional serendipitousity of discovering allosteric inhibitors owing to the complicate allosteric modulation. In this current study, we identified the novel allosteric inhibitors of CK2α by combing structure-based virtual screening and biological evaluation methods. The structure-based pharmacophore model was built based on the crystal structure of CK2α-compound 15 complex. The ChemBridge fragment library was searched by evaluating the fit values of these molecules with the optimized pharmacophore model, as well as the binding affinity of the CK2α-ligand complexes predicted by Alloscore web server. Six hits forming the holistic interaction mechanism with the αD pocket were retained after pharmacophore- and Alloscore-based screening for biological test. Compound 3 was found to be the most potent non-ATP competitive CK2α inhibitor (IC50 = 13.0 μM) with the anti-proliferative activity on A549 cancer cells (IC50 = 23.1 μM). Our results provide new clues for further development of CK2 allosteric inhibitors as anti-cancer hits.
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Affiliation(s)
- Chunqiong Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Xuewen Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Na Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
- Correspondence: ; Tel.: +86-10-67392001
| | - Yue Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China;
| | - Guohui Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
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12
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Huang M, Song K, Liu X, Lu S, Shen Q, Wang R, Gao J, Hong Y, Li Q, Ni D, Xu J, Chen G, Zhang J. AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Res 2019; 46:W451-W458. [PMID: 29757429 PMCID: PMC6030990 DOI: 10.1093/nar/gky374] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/28/2018] [Indexed: 01/07/2023] Open
Abstract
Allostery tweaks innumerable biological processes and plays a fundamental role in human disease and drug discovery. Exploration of allostery has thus been regarded as a crucial requirement for research on biological mechanisms and the development of novel therapeutics. Here, based on our previously developed allosteric data and methods, we present an interactive platform called AlloFinder that identifies potential endogenous or exogenous allosteric modulators and their involvement in human allosterome. AlloFinder automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator-protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome. This web server exhibits prominent performance in the reemergence of allosteric metabolites and exogenous allosteric modulators in known allosteric proteins. Specifically, AlloFinder enables identification of allosteric metabolites for metabolic enzymes and screening of potential allosteric compounds for disease-related targets. Significantly, the feasibility of AlloFinder to discover allosteric modulators was tested in a real case of signal transduction and activation of transcription 3 (STAT3) and validated by mutagenesis and functional experiments. Collectively, AlloFinder is expected to contribute to exploration of the mechanisms of allosteric regulation between metabolites and metabolic enzymes, and to accelerate allosteric drug discovery. The AlloFinder web server is freely available to all users at http://mdl.shsmu.edu.cn/ALF/.
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Affiliation(s)
- Min Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Kun Song
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Xinyi Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Qiancheng Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Renxiao Wang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingze Gao
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Yuanyuan Hong
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Qian Li
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Jianrong Xu
- Department of Pharmacology, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Guoqiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
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13
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Lu S, Shen Q, Zhang J. Allosteric Methods and Their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms. Acc Chem Res 2019; 52:492-500. [PMID: 30688063 DOI: 10.1021/acs.accounts.8b00570] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Allostery, or allosteric regulation, is the phenomenon in which protein functional activity is altered by the binding of an effector at an allosteric site that is topographically distinct from the orthosteric, active site. As one of the most direct and efficient ways to regulate protein function, allostery has played a fundamental role in innumerable biological processes of all living organisms, including enzyme catalysis, signal transduction, cell metabolism, and gene transcription. It is thus considered as "the second secret of life". The abnormality of allosteric communication networks between allosteric and orthosteric sites is associated with the pathogenesis of human diseases. Allosteric modulators, by attaching to structurally diverse allosteric sites, offer the potential for differential selectivity and improved safety compared with orthosteric drugs that bind to conserved orthosteric sites. Harnessing allostery has thus been regarded as a novel strategy for drug discovery. Despite much progress having been made in the repertoire of allostery since the turn of the millennium, the identification of allosteric drugs for therapeutic targets and the elucidation of allosteric mechanisms still present substantial challenges. These challenges are derived from the difficulties in the identification of allosteric sites and mutations, the assessment of allosteric protein-modulator interactions, the screening of allosteric modulators, and the elucidation of allosteric mechanisms in biological systems. To address these issues, we have developed a panel of allosteric services for specific allosteric applications over the past decade, including (i) the creation of the Allosteric Database, with the aim of providing comprehensive allosteric information such as allosteric proteins, modulators, sites, pathways, etc., (ii) the construction of the ASBench benchmark of high-quality allosteric sites for the development of computational methods for predicting allosteric sites, (iii) the development of Allosite and AllositePro for the prediction of the location of allosteric sites in proteins, (iv) the development of the Alloscore scoring function for the evaluation of allosteric protein-modulator interactions, (v) the development of Allosterome for evolutionary analysis of query allosteric sites/modulators within the human proteome, (vi) the development of AlloDriver for the prediction of allosteric mutagenesis, and (vii) the development of AlloFinder for the virtual screening of allosteric modulators and the investigation of allosteric mechanisms. Importantly, we have validated computationally predicted allosteric sites, mutations, and modulators in the real cases of sirtuin 6, casein kinase 2α, phosphodiesterase 10A, and signal transduction and activation of transcription 3. Furthermore, our developed allosteric methods have been widely exploited by other users around the world for allosteric research. Therefore, these allosteric services are expected to expedite the discovery of allosteric drugs and the investigation of allosteric mechanisms.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Qiancheng Shen
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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14
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Tang S, Zhang N, Zhou Y, Cortopassi WA, Jacobson MP, Zhao LJ, Zhong RG. Structure-based Discovery of Novel CK2α-Binding Cyclic Peptides with Anti-cancer Activity. Mol Inform 2018; 38:e1800089. [PMID: 30307134 DOI: 10.1002/minf.201800089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022]
Abstract
Protein kinase CK2 is considered as an emerging target in cancer therapy, and recent efforts have been made to develop its ATP-competitive inhibitors, but achieving selectivity with respect to related kinases remains challenging because of the highly conserved ATP-binding pocket of kinases. Non-ATP competitive inhibitors might solve this challenge; one such strategy is to identify compounds that target the CK2α/CK2β interface as CK2 holoenzyme antagonists. Here we improved the binding affinity to CK2α and cell-based anti-cancer activity of a CK2β-derived cyclic peptide (Pc) by combining structure-based computational design with experimental evaluation. By analyzing molecular dynamics simulations of Pc bound to CK2α, a series of Pc-derived peptides was rationally designed and synthesized to evaluate their binding affinity to CK2α, as well as anti-proliferative and pro-apoptotic effects against HepG2 cancer cell line. One amino acid substitutions on Pc, I192F, exhibited over 10-fold improvement in the predicted binding affinity to CK2α when compared to Pc, and a cell-permeable version, I192F-Tat, also demonstrated more potent anti-proliferative and pro-apoptotic effects against HepG2 compared to Pc. A second modification of Pc, H193W, also led to more potent cell-based activity, despite having weaker binding affinity (∼5×) to CK2α. The discovery of the I192F and H193W peptides provides new insights for further optimization of CK2 antagonist candidates as anti-cancer leads.
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Affiliation(s)
- Shan Tang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Na Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Yue Zhou
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94143, United States
| | - Li-Jiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Ru-Gang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
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15
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Lu G, Tandang-Silvas MR, Dawson AC, Dawson TJ, Groppe JC. Hypoxia-selective allosteric destabilization of activin receptor-like kinases: A potential therapeutic avenue for prophylaxis of heterotopic ossification. Bone 2018; 112:71-89. [PMID: 29626545 PMCID: PMC9851731 DOI: 10.1016/j.bone.2018.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/21/2023]
Abstract
Heterotopic ossification (HO), the pathological extraskeletal formation of bone, can arise from blast injuries, severe burns, orthopedic procedures and gain-of-function mutations in a component of the bone morphogenetic protein (BMP) signaling pathway, the ACVR1/ALK2 receptor serine-threonine (protein) kinase, causative of Fibrodysplasia Ossificans Progressiva (FOP). All three ALKs (-2, -3, -6) that play roles in bone morphogenesis contribute to trauma-induced HO, hence are well-validated pharmacological targets. That said, development of inhibitors, typically competitors of ATP binding, is inherently difficult due to the conserved nature of the active site of the 500+ human protein kinases. Since these enzymes are regulated via inherent plasticity, pharmacological chaperone-like drugs binding to another (allosteric) site could hypothetically modulate kinase conformation and activity. To test for such a mechanism, a surface pocket of ALK2 kinase formed largely by a key allosteric substructure was targeted by supercomputer docking of drug-like compounds from a virtual library. Subsequently, the effects of docked hits were further screened in vitro with purified recombinant kinase protein. A family of compounds with terminal hydrogen-bonding acceptor groups was identified that significantly destabilized the protein, inhibiting activity. Destabilization was pH-dependent, putatively mediated by ionization of a histidine within the allosteric substructure with decreasing pH. In vivo, nonnative proteins are degraded by proteolysis in the proteasome complex, or cellular trashcan, allowing for the emergence of therapeutics that inhibit through degradation of over-active proteins implicated in the pathology of diseases and disorders. Because HO is triggered by soft-tissue trauma and ensuing hypoxia, dependency of ALK destabilization on hypoxic pH imparts selective efficacy on the allosteric inhibitors, providing potential for safe prophylactic use.
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Affiliation(s)
- Guorong Lu
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX 75246, United States
| | - Mary R Tandang-Silvas
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX 75246, United States
| | - Alyssa C Dawson
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX 75246, United States
| | - Trenton J Dawson
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX 75246, United States
| | - Jay C Groppe
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX 75246, United States.
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16
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Insights into the Impact of Linker Flexibility and Fragment Ionization on the Design of CK2 Allosteric Inhibitors: Comparative Molecular Dynamics Simulation Studies. Int J Mol Sci 2018; 19:ijms19010111. [PMID: 29301250 PMCID: PMC5796060 DOI: 10.3390/ijms19010111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 11/17/2022] Open
Abstract
Protein kinase is a novel therapeutic target for human diseases. The off-target and side effects of ATP-competitive inhibitors preclude them from the clinically relevant drugs. The compounds targeting the druggable allosteric sites outside the highly conversed ATP binding pocket have been identified as promising alternatives to overcome current barriers of ATP-competitive inhibitors. By simultaneously interacting with the αD region (new allosteric site) and sub-ATP binding pocket, the attractive compound CAM4066 was named as allosteric inhibitor of CK2α. It has been demonstrated that the rigid linker and non-ionizable substituted fragment resulted in significant decreased inhibitory activities of compounds. The molecular dynamics simulations and energy analysis revealed that the appropriate coupling between the linker and pharmacophore fragments were essential for binding of CAM4066 with CK2α. The lower flexible linker of compound 21 lost the capability of coupling fragments A and B to αD region and positive area, respectively, whereas the methyl benzoate of fragment B induced the re-orientated Pre-CAM4066 with the inappropriate polar interactions. Most importantly, the match between the optimized linker and pharmacophore fragments is the challenging work of fragment-linking based drug design. These results provide rational clues to further structural modification and development of highly potent allosteric inhibitors of CK2.
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