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Vieira TF, Martins FG, Moreira JP, Barbosa T, Sousa SF. In Silico Identification of Possible Inhibitors for Protein Kinase B (PknB) of Mycobacterium tuberculosis. Molecules 2021; 26:molecules26206162. [PMID: 34684743 PMCID: PMC8541300 DOI: 10.3390/molecules26206162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
With tuberculosis still being one of leading causes of death in the world and the emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), researchers have been seeking to find further therapeutic strategies or more specific molecular targets. PknB is one of the 11 Ser/Thr protein kinases of Mtb and is responsible for phosphorylation-mediated signaling, mainly involved in cell wall synthesis, cell division and metabolism. With the amount of structural information available and the great interest in protein kinases, PknB has become an attractive target for drug development. This work describes the optimization and application of an in silico computational protocol to find new PknB inhibitors. This multi-level computational approach combines protein–ligand docking, structure-based virtual screening, molecular dynamics simulations and free energy calculations. The optimized protocol was applied to screen a large dataset containing 129,650 molecules, obtained from the ZINC/FDA-Approved database, Mu.Ta.Lig Virtual Chemotheca and Chimiothèque Nationale. It was observed that the most promising compounds selected occupy the adenine-binding pocket in PknB, and the main interacting residues are Leu17, Val26, Tyr94 and Met155. Only one of the compounds was able to move the active site residues into an open conformation. It was also observed that the P-loop and magnesium position loops change according to the characteristics of the ligand. This protocol led to the identification of six compounds for further experimental testing while also providing additional structural information for the design of more specific and more effective derivatives.
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Affiliation(s)
- Tatiana F. Vieira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Fábio G. Martins
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Joel P. Moreira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Tiago Barbosa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Correspondence:
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Nilkanth VV, Mande SC. Structure-sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis. Proteins 2021; 90:131-141. [PMID: 34329517 DOI: 10.1002/prot.26195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 11/07/2022]
Abstract
Elucidation of signaling events in a pathogen is potentially important to tackle the infection caused by it. Such events mediated by protein phosphorylation play important roles in infection, and therefore, to predict the phosphosites and substrates of the serine/threonine protein kinases, we have developed a Machine learning-based approach for Mycobacterium tuberculosis serine/threonine protein kinases using kinase-peptide structure-sequence data. This approach utilizes features derived from kinase three-dimensional-structure environment and known phosphosite sequences to generate support vector machine (SVM)-based kinase-specific predictions of phosphosites of serine/threonine protein kinases (STPKs) with no or scarce data of their substrates. SVM outperformed the four machine learning algorithms we tried (random forest, logistic regression, SVM, and k-nearest neighbors) with an area under the curve receiver-operating characteristic value of 0.88 on the independent testing dataset and a 10-fold cross-validation accuracy of ~81.6% for the final model. Our predicted phosphosites of M. tuberculosis STPKs form a useful resource for experimental biologists enabling elucidation of STPK mediated posttranslational regulation of important cellular processes.
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Affiliation(s)
- Vipul V Nilkanth
- National Centre for Cell Science, S.P. Pune University Campus, Pune, India
| | - Shekhar C Mande
- Council of Scientific and Industrial Research, New Delhi, India
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Olotu FA, Soliman ME. Probing the Highly Disparate Dual Inhibitory Mechanisms of Novel Quinazoline Derivatives against Mycobacterium tuberculosis Protein Kinases A and B. Molecules 2020; 25:E4247. [PMID: 32947886 PMCID: PMC7571077 DOI: 10.3390/molecules25184247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) serine/threonine (Ser/Thr) Protein kinases A (PknA) and B (PknB) have been identified as highly attractive targets for overcoming drug resistant tuberculosis. A recent lead series optimization study yielded compound 33 which exhibited potencies ~1000 times higher than compound 57. This huge discrepancy left us curious to investigate the mechanistic 'dual' (in)activities of the compound using computational methods, as carried out in this study. Findings revealed that 33 stabilized the PknA and B conformations and reduced their structural activities relative to 57. Optimal stability of 33 in the hydrophobic pockets further induced systemic alterations at the P-loops, catalytic loops, helix Cs and DFG motifs of PknA and B. Comparatively, 57 was more surface-bound with highly unstable motions. Furthermore, 33 demonstrated similar binding patterns in PknA and B, involving conserved residues of their binding pockets. Both π and hydrogen interactions played crucial roles in the binding of 33, which altogether culminated in high ΔGs for both proteins. On the contrary, the binding of 57 was characterized by unfavorable interactions with possible repulsive effects on its optimal dual binding to both proteins, as evidenced by the relatively lowered ΔGs. These findings would significantly contribute to the rational structure-based design of novel and highly selective dual inhibitors of Mtb PknA and B.
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Affiliation(s)
| | - Mahmoud E. Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa;
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Lipa P, Vinardell JM, Janczarek M. Transcriptomic Studies Reveal that the Rhizobium leguminosarum Serine/Threonine Protein Phosphatase PssZ has a Role in the Synthesis of Cell-Surface Components, Nutrient Utilization, and Other Cellular Processes. Int J Mol Sci 2019; 20:ijms20122905. [PMID: 31197117 PMCID: PMC6628131 DOI: 10.3390/ijms20122905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023] Open
Abstract
Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing symbiotic associations with clover plants (Trifolium spp.). Surface polysaccharides, transport systems, and extracellular components synthesized by this bacterium are required for both the adaptation to changing environmental conditions and successful infection of host plant roots. The pssZ gene located in the Pss-I region, which is involved in the synthesis of extracellular polysaccharide, encodes a protein belonging to the group of serine/threonine protein phosphatases. In this study, a comparative transcriptomic analysis of R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt297 carrying a pssZ mutation was performed. RNA-Seq data identified a large number of genes differentially expressed in these two backgrounds. Transcriptome profiling of the pssZ mutant revealed a role of the PssZ protein in several cellular processes, including cell signalling, transcription regulation, synthesis of cell-surface polysaccharides and components, and bacterial metabolism. In addition, we show that inactivation of pssZ affects the rhizobial ability to grow in the presence of different sugars and at various temperatures, as well as the production of different surface polysaccharides. In conclusion, our results identified a set of genes whose expression was affected by PssZ and confirmed the important role of this protein in the rhizobial regulatory network.
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Affiliation(s)
- Paulina Lipa
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - José-María Vinardell
- Department of Microbiology, Faculty of Biology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain.
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
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Beekmann K, de Haan LHJ, Actis-Goretta L, van Bladeren PJ, Rietjens IMCM. Effect of Glucuronidation on the Potential of Kaempferol to Inhibit Serine/Threonine Protein Kinases. J Agric Food Chem 2016; 64:1256-1263. [PMID: 26808477 DOI: 10.1021/acs.jafc.5b05456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To study the effect of metabolic conjugation of flavonoids on the potential to inhibit protein kinase activity, the inhibitory effects of the dietary flavonol kaempferol and its major plasma conjugate kaempferol-3-O-glucuronide on protein kinases were studied. To this end, the inhibition of the phosphorylation activity of recombinant protein kinase A (PKA) and of cell lysate from the hepatocellular carcinoma cell line HepG2 on 141 putative serine/threonine phosphorylation sites derived from human proteins was assessed. Glucuronidation reduced the inhibitory potency of kaempferol on the phosphorylation activity of PKA and HepG2 lysate on average about 16 and 3.5 times, respectively, but did not appear to affect the target selectivity for kinases present in the lysate. The data demonstrate that, upon glucuronidation, kaempferol retains part of its intrinsic kinase inhibition potential, which implies that K3G does not necessarily need to be deconjugated to the aglycone for a potential inhibitory effect on protein kinases.
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Affiliation(s)
- Karsten Beekmann
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
| | - Lucas Actis-Goretta
- Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, Case Postale 44, 1000 Lausanne 26, Switzerland
| | - Peter J van Bladeren
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
- Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, Case Postale 44, 1000 Lausanne 26, Switzerland
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
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Rawat SJ, Chernoff J. Regulation of mammalian Ste20 (Mst) kinases. Trends Biochem Sci 2015; 40:149-56. [PMID: 25665457 DOI: 10.1016/j.tibs.2015.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/31/2014] [Accepted: 01/06/2015] [Indexed: 12/23/2022]
Abstract
Initially identified as mammalian homologs to yeast Ste20 kinases, the mammalian sterile twenty-like (Mst) 1/2 kinases have been widely investigated subsequent to their rediscovery as key components of the Hippo tumor suppressor pathway in flies. To date, our understanding of Mst substrates and downstream signaling outstrips our knowledge of how these enzymes are controlled by upstream signals. While much remains to be discovered regarding the mechanisms of Mst regulation, it is clear that Mst1 kinase activity is governed at least in part by its state of dimerization, including self-association and also heterodimerization with various other signaling partners. Here we review the basic architecture of Mst signaling and function and discuss recent advances in our understanding of how these important kinases are regulated.
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Affiliation(s)
- Sonali J Rawat
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA; Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jonathan Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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Yunta C, Martinez-Ripoll M, Albert A. SnRK2.6/OST1 from Arabidopsis thaliana: cloning, expression, purification, crystallization and preliminary X-ray analysis of K50N and D160A mutants. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:364-8. [PMID: 21393844 PMCID: PMC3053164 DOI: 10.1107/s1744309110053807] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 12/22/2010] [Indexed: 11/10/2022]
Abstract
The SnRK2.6 (SNF1-related kinase 2.6) gene from Arabidopsis thaliana encodes the serine/threonine protein kinase SnRK2.6/OST1 (OPEN STOMATA 1). It plays a central role in the drought-tolerance mechanism. OST1 is in fact the main positive effector in the hydric stress response. The SnRK2.6 gene was cloned into the pGEX4T1 plasmid, mutated and expressed in Escherichia coli, allowing purification to homogeneity in two chromatographic steps. Various OST1 mutants yielded crystals using vapour-diffusion techniques, but only one mutant showed a good diffraction pattern. Its crystals diffracted to 2.8 Å resolution and belonged to space group P222(1), with unit-cell parameters a=77.7, b=99.4, c=108.4 Å. A promising molecular-replacement solution was found using the structure of the kinase domain of the yeast AMP-activated protein kinase SNF1 (PDB entry 3hyh) as the search model.
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Affiliation(s)
- Cristina Yunta
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
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Bekker O, Alekseeva M, Osolodkin D, Palyulin V, Elizarov S, Zefirov N, Danilenko V. New Test System for Serine/Threonine Protein Kinase Inhibitors Screening: E. coli APHVIII/Pk25 design. Acta Naturae 2010; 2:110-21. [PMID: 22649658 PMCID: PMC3347566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
An efficient test system for serine/threonine protein kinase inhibitors screening has been developed based on theE. coliprotein system APHVIII/Pk25. Phosphorylation of aminoglycoside phosphotransferase VIII (APHVIII) by protein kinases enhances resistance of the bacterial cell to aminoglycoside antibiotics, e.g. kanamycin. Addition of protein kinase inhibitors prevents phosphorylation and increases cell sensitivity to kanamycin. We have obtained modifications of APHVIII in which phosphorylatable Ser146 was encompassed into the canonical autophosphorylation sequence ofStreptomyces coelicolorPk25 protein kinase. Mutant and wild-typeaphVIII were cloned intoE. coliwith the catalytic domain ofpk25. As a result of the expression of these genes, accumulation of corresponding proteins was clearly observed. Extracted from bacterial lysates, Pk25 demonstrated its ability to autophosphorylate. It was shown that variants ofE. colicontaining bothaphVIIIand рк25were more resistant to kanamycin than those carrying onlyaphVIII. Protein kinase inhibitors of the indolylmaleimide class actively inhibited Pk25 and reduced cell resistance to kanamycin. Modeling of APHVIII and Pk25 3D structures showed that pSer146 is an analog of phosphoserine in the ribose pocket of protein kinase A. Pk25 conformation was similar to that of РknB ofMycobacterium tuberculosis. Potential indolylmaleimide inhibitors were docked into the ATP-binding pocket of Pk25. The designed test system can be used for the primary selection of ATP-competitive small molecule protein kinase inhibitors.
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Affiliation(s)
- O.B. Bekker
- Vavilov Institute of General Genetics, Russian Academy of Sciences
| | - M.G. Alekseeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences
| | - D.I. Osolodkin
- Lomonosov Moscow State University, Department of Chemistry
| | - V.A. Palyulin
- Lomonosov Moscow State University, Department of Chemistry
| | - S.M. Elizarov
- Bach Institute of Biochemistry, Russian Academy of Sciences
| | - N.S. Zefirov
- Lomonosov Moscow State University, Department of Chemistry
| | - V.N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences
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