Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors Article First Online: 26 October 2018 Abstract
In the last decades, human protein kinases (PKs) have been relevant as targets in the development of novel therapies against many diseases, but the study of
Mycobacterium tuberculosis PKs (MTPKs) involved in tuberculosis pathogenesis began much later and has not yet reached an advanced stage of development. To increase knowledge of these enzymes, in this work we studied the structural features of MTPKs, with focus on their ATP-binding sites and their interactions with inhibitors. PknA, PknB, and PknG are the most studied MTPKs, which were previously crystallized; ATP-competitive inhibitors have been designed against them in the last decade. In the current work, reported PknA, PknB, and PknG inhibitors were extracted from literature and their orientations inside the ATP-binding site were proposed by using docking method. With this information, interaction fingerprints were elaborated, which reveal the more relevant residues for establishing chemical interactions with inhibitors. The non-crystallized MTPKs PknD, PknF, PknH, PknJ, PknK, and PknL were also studied; their three-dimensional structural models were developed by using homology modeling. The main characteristics of MTPK ATP-binding sites (the non-crystallized and crystallized MTPKs, including PknE and PknI) were accounted; schemes of the main polar and nonpolar groups inside their ATP-binding sites were constructed, which are suitable for a major understanding of these proteins as antituberculotic targets. These schemes could be used for establishing comparisons between MTPKs and human PKs in order to increase selectivity of MTPK inhibitors. As a key tool for guiding medicinal chemists interested in the design of novel MTPK inhibitors, our work provides a map of the structural elements relevant for the design of more selective ATP-competitive MTPK inhibitors. Keywords Mycobacterium tuberculosis protein kinases Protein kinases selectivity Molecular docking Interaction fingerprings Electronic supplementary material
The online version of this article (
) contains supplementary material, which is available to authorized users. https://doi.org/10.1007/s10822-018-0173-3 Notes Acknowledgements
Thanks to the funds of FONDECYT postdoctoral project N
0 3150035 (AMB and JC). JC also acknowledges funds of FONDECYT Regular N 0 1170718. CNR also acknowledges funds of FONDECYT postdoctoral project N0 3170434. References
Hallows KR, Alzamora R, Li H et al (2009) AMP-activated protein kinase inhibits alkaline pH- and PKA-induced apical vacuolar H+-ATPase accumulation in epididymal clear cells. Am J Physiol Cell Physiol 296:C672–C681.
https://doi.org/10.1152/ajpcell.00004.2009 CrossRef Google Scholar
Nesher R, Anteby E, Yedovizky M et al (2002) Beta-cell protein kinases and the dynamics of the insulin response to glucose. Diabetes 51(Suppl 1):S68–S73
CrossRef Google Scholar
Salminen A, Kaarniranta K, Haapasalo A et al (2011) AMP-activated protein kinase: a potential player in Alzheimer’s disease. J Neurochem 118:460–474.
https://doi.org/10.1111/j.1471-4159.2011.07331.x CrossRef Google Scholar
Kotlyarov A, Neininger A, Schubert C et al (1999) MAPKAP kinase 2 is essential for LPS-induced TNF-alpha biosynthesis. Nat Cell Biol 1:94–97.
https://doi.org/10.1038/10061 CrossRef Google Scholar
Av-Gay Y, Davies J (1997) Components of eukaryotic-like protein signaling pathways in
. Microb Comp Genomics 2:63–73.
https://doi.org/10.1089/omi.1.1997.2.63 CrossRef Google Scholar
Cole ST, Brosch R, Parkhill J et al (1998) Deciphering the biology of
from the complete genome sequence. Nature 393:537–544.
https://doi.org/10.1038/31159 CrossRef Google Scholar
Prisic S, Husson RN (2014)
serine/threonine protein kinases. Microbiol Spectr.
https://doi.org/10.1128/microbiolspec.MGM2-0006-2013 CrossRef Google Scholar
Chow K, Ng D, Stokes R, Johnson P (1994) Protein tyrosine phosphorylation in
. FEMS Microbiol Lett 124:203–207
CrossRef Google Scholar
Av-Gay Y, Everett M (2000) The eukaryotic-like Ser/Thr protein kinases of
. Trends Microbiol 8:238–244
CrossRef Google Scholar
Zuccotto F, Ardini E, Casale E, Angiolini M (2010) Through the “Gatekeeper Door”: exploiting the active kinase conformation. J Med Chem 53:2681–2694.
https://doi.org/10.1021/jm901443h CrossRef Google Scholar
Chakraborti PK, Matange N, Nandicoori VK et al (2011) Signalling mechanisms in Mycobacteria. Tuberc Edinb Scotl 91:432–440.
https://doi.org/10.1016/j.tube.2011.04.005 CrossRef Google Scholar
Khan S, Nagarajan SN, Parikh A et al (2010) Phosphorylation of enoyl-acyl carrier protein reductase InhA impacts mycobacterial growth and survival. J Biol Chem 285:37860–37871.
https://doi.org/10.1074/jbc.M110.143131 CrossRef Google Scholar
Greenstein AE, MacGurn JA, Baer CE et al (2007) M. tuberculosis Ser/Thr protein kinase D phosphorylates an anti-anti-sigma factor homolog. PLoS Pathog 3:e49.
https://doi.org/10.1371/journal.ppat.0030049 CrossRef Google Scholar
Pérez J, Garcia R, Bach H et al (2006)
transporter MmpL7 is a potential substrate for kinase PknD. Biochem Biophys Res Commun 348:6–12.
https://doi.org/10.1016/j.bbrc.2006.06.164 CrossRef Google Scholar
Jayakumar D, Jacobs WR, Narayanan S (2008) Protein kinase E of
has a role in the nitric oxide stress response and apoptosis in a human macrophage model of infection. Cell Microbiol 10:365–374.
https://doi.org/10.1111/j.1462-5822.2007.01049.x CrossRef Google Scholar
Molle V, Soulat D, Jault J-M et al (2004) Two FHA domains on an ABC transporter, Rv1747, mediate its phosphorylation by PknF, a Ser/Thr protein kinase from
. FEMS Microbiol Lett 234:215–223.
https://doi.org/10.1016/j.femsle.2004.03.033 CrossRef Google Scholar
Deol P, Vohra R, Saini AK et al (2005) Role of Mycobacterium tuberculosis Ser/Thr kinase PknF: implications in glucose transport and cell division. J Bacteriol 187:3415–3420.
https://doi.org/10.1128/JB.187.10.3415-3420.2005 CrossRef Google Scholar
Walburger A, Koul A, Ferrari G et al (2004) Protein kinase G from pathogenic mycobacteria promotes survival within macrophages. Science 304:1800–1804.
https://doi.org/10.1126/science.1099384 CrossRef Google Scholar
O’Hare HM, Durán R, Cerveñansky C et al (2008) Regulation of glutamate metabolism by protein kinases in mycobacteria. Mol Microbiol 70:1408–1423.
https://doi.org/10.1111/j.1365-2958.2008.06489.x CrossRef Google Scholar
Rieck B, Degiacomi G, Zimmermann M et al (2017) PknG senses amino acid availability to control metabolism and virulence of
. PLoS Pathog 13:e1006399.
https://doi.org/10.1371/journal.ppat.1006399 CrossRef Google Scholar
Gómez-Velasco A, Bach H, Rana AK et al (2013) Disruption of the serine/threonine protein kinase H affects phthiocerol dimycocerosates synthesis in
. Microbiol Read Engl 159:726–736.
https://doi.org/10.1099/mic.0.062067-0 CrossRef Google Scholar
Sharma K, Chandra H, Gupta PK et al (2004) PknH, a transmembrane Hank’s type serine/threonine kinase from
is differentially expressed under stress conditions. FEMS Microbiol Lett 233:107–113.
https://doi.org/10.1016/j.femsle.2004.01.045 CrossRef Google Scholar
Gopalaswamy R, Narayanan S, Chen B et al (2009) The serine/threonine protein kinase PknI controls the growth of
upon infection. FEMS Microbiol Lett 295:23–29.
https://doi.org/10.1111/j.1574-6968.2009.01570.x CrossRef Google Scholar
Venkatesan A, Palaniyandi K, Sharma D et al (2016) Functional characterization of PknI-Rv2159c interaction in redox homeostasis of
. Front Microbiol 7:1654.
https://doi.org/10.3389/fmicb.2016.01654 CrossRef Google Scholar
Singh DK, Singh PK, Tiwari S et al (2014) Phosphorylation of pyruvate kinase A by protein kinase J leads to the altered growth and differential rate of intracellular survival of mycobacteria. Appl Microbiol Biotechnol 98:10065–10076.
https://doi.org/10.1007/s00253-014-5859-4 CrossRef Google Scholar
Kumar P, Kumar D, Parikh A et al (2009) The Mycobacterium tuberculosis protein kinase K modulates activation of transcription from the promoter of mycobacterial monooxygenase operon through phosphorylation of the transcriptional regulator VirS. J Biol Chem 284:11090–11099.
https://doi.org/10.1074/jbc.M808705200 CrossRef Google Scholar
Canova MJ, Veyron-Churlet R, Zanella-Cleon I et al (2008) The
serine/threonine kinase PknL phosphorylates Rv2175c: mass spectrometric profiling of the activation loop phosphorylation sites and their role in the recruitment of Rv2175c. Proteomics 8:521–533.
https://doi.org/10.1002/pmic.200700442 CrossRef Google Scholar
Sipos A, Pató J, Székely R et al (2015) Lead selection and characterization of antitubercular compounds using the nested chemical library. Tuberc Edinb Scotl 95(Suppl 1):S200–S206.
https://doi.org/10.1016/j.tube.2015.02.028 CrossRef Google Scholar
Székely R, Wáczek F, Szabadkai I et al (2008) A novel drug discovery concept for tuberculosis: inhibition of bacterial and host cell signalling. Immunol Lett 116:225–231.
https://doi.org/10.1016/j.imlet.2007.12.005 CrossRef Google Scholar
Lougheed KEA, Osborne SA, Saxty B et al (2011) Effective inhibitors of the essential kinase PknB and their potential as anti-mycobacterial agents. Tuberc Edinb Scotl 91:277–286.
https://doi.org/10.1016/j.tube.2011.03.005 CrossRef Google Scholar
Chapman TM, Bouloc N, Buxton RS et al (2012) Substituted aminopyrimidine protein kinase B (PknB) inhibitors show activity against
. Bioorg Med Chem Lett 22:3349–3353.
https://doi.org/10.1016/j.bmcl.2012.02.107 CrossRef Google Scholar
Pató J, Kéri G, Örfi L et al (2009) Novel therapeutic targets for the treatment of mycobacterial infections and compounds useful therefor. U.S. Patent US20090298842
Wang T, Bemis G, Hanzelka B et al (2017) Mtb PKNA/PKNB dual inhibition provides selectivity advantages for inhibitor design to minimize host kinase interactions. ACS Med Chem Lett 8:1224–1229.
https://doi.org/10.1021/acsmedchemlett.7b00239 CrossRef Google Scholar
Lee Y-V, Choi SB, Wahab HA, Choong YS (2017) Active site flexibility of
isocitrate lyase in dimer form. J Chem Inf Model 57:2351–2357.
https://doi.org/10.1021/acs.jcim.7b00265 CrossRef Google Scholar
Perryman AL, Yu W, Wang X et al (2015) A virtual screen discovers novel, fragment-sized inhibitors of
InhA. J Chem Inf Model 55:645–659.
https://doi.org/10.1021/ci500672v CrossRef Google Scholar
Espinoza-Moraga M, Njuguna NM, Mugumbate G et al (2013) In silico comparison of antimycobacterial natural products with known antituberculosis drugs. J Chem Inf Model 53:649–660.
https://doi.org/10.1021/ci300467b CrossRef Google Scholar
Silva JRA, Roitberg AE, Alves CN (2014) Catalytic mechanism of L,D-transpeptidase 2 from
described by a computational approach: insights for the design of new antibiotics drugs. J Chem Inf Model 54:2402–2410.
https://doi.org/10.1021/ci5003069 CrossRef Google Scholar
Riadi G, Caballero J (2014) Easy Identification of residues involved on structural differences between nonphosphorylated and phosphorylated CDK2ï£¿Cyclin A complexes using two-dimensional networks. Mol Inform 33:151–162.
https://doi.org/10.1002/minf.201300100 CrossRef Google Scholar
Khuntawee W, Rungrotmongkol T, Hannongbua S (2012) Molecular dynamic behavior and binding affinity of flavonoid analogues to the cyclin dependent kinase 6/cyclin D complex. J Chem Inf Model 52:76–83.
https://doi.org/10.1021/ci200304v CrossRef Google Scholar
Mena-Ulecia K, Vergara-Jaque A, Poblete H et al (2014) Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA. PLoS ONE 9:e109639.
https://doi.org/10.1371/journal.pone.0109639 CrossRef Google Scholar
Mena-Ulecia K, Gonzalez-Norambuena F, Vergara-Jaque A et al (2018) Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: free energy perturbation (FEP) calculations. J Comput Chem.
https://doi.org/10.1002/jcc.25176 CrossRef Google Scholar
Alzate-Morales J, Caballero J (2010) Computational study of the interactions between guanine derivatives and cyclin-dependent kinase 2 (CDK2) by CoMFA and QM/MM. J Chem Inf Model 50:110–122.
https://doi.org/10.1021/ci900302z CrossRef Google Scholar
Alzate-Morales JH, Vergara-Jaque A, Caballero J (2010) Computational study on the interaction of N1 substituted pyrazole derivatives with B-Raf kinase: an unusual water wire hydrogen-bond network and novel interactions at the entrance of the active site. J Chem Inf Model 50:1101–1112.
https://doi.org/10.1021/ci100049h CrossRef Google Scholar
Caballero J, Zilocchi S, Tiznado W et al (2011) Binding studies and quantitative structure-activity relationship of 3-amino-1H-indazoles as inhibitors of GSK3β. Chem Biol Drug Des 78:631–641.
https://doi.org/10.1111/j.1747-0285.2011.01186.x CrossRef Google Scholar
Caballero J, Alzate-Morales JH, Vergara-Jaque A (2011) Investigation of the differences in activity between hydroxycycloalkyl N1 substituted pyrazole derivatives as inhibitors of B-Raf kinase by using docking, molecular dynamics, QM/MM, and fragment-based de novo design: study of binding mode of diastereomer compounds. J Chem Inf Model 51:2920–2931.
https://doi.org/10.1021/ci200306w CrossRef Google Scholar
Caballero J, Alzate-Morales JH (2012) Molecular dynamics of protein kinase-inhibitor complexes: a valid structural information. Curr Pharm Des 18:2946–2963
CrossRef Google Scholar
Caballero J, Muñoz C, Alzate-Morales JH et al (2012) Synthesis, in silico, in vitro, and in vivo investigation of 5-[
C]methoxy-substituted sunitinib, a tyrosine kinase inhibitor of VEGFR-2. Eur J Med Chem 58:272–280.
https://doi.org/10.1016/j.ejmech.2012.10.020 CrossRef Google Scholar
Munoz C, Adasme F, Alzate-Morales JH et al (2012) Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations. J Mol Graph Model 32:39–48.
https://doi.org/10.1016/j.jmgm.2011.10.005 CrossRef Google Scholar
Quesada-Romero L, Caballero J (2014) Docking and quantitative structure–activity relationship of oxadiazole derivates as inhibitors of GSK3beta. Mol Divers 18:149–159.
https://doi.org/10.1007/s11030-013-9483-5 CrossRef Google Scholar
Quesada-Romero L, Mena-Ulecia K, Tiznado W, Caballero J (2014) Insights into the interactions between maleimide derivates and GSK3β combining molecular docking and QSAR. PLoS ONE 9:e102212.
https://doi.org/10.1371/journal.pone.0102212 CrossRef Google Scholar
Adasme-Carreño F, Muñoz-Gutierrez C, Caballero J, Alzate-Morales J (2014) Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case. Phys Chem Chem Phys 16:14047–14058.
https://doi.org/10.1039/C4CP01378F CrossRef Google Scholar
Navarro-Retamal C, Caballero J (2016) Flavonoids as CDK1 inhibitors: insights in their binding orientations and structure-activity relationship. PLoS ONE 11:e0161111.
https://doi.org/10.1371/journal.pone.0161111 CrossRef Google Scholar
Navarro-Retamal C, Caballero J (2018) Molecular modeling of tau proline-directed protein kinase (PDPK) inhibitors. In: Computational modeling of drugs against Alzheimer’s disease. Humana Press, New York, pp 305–345
CrossRef Google Scholar
Gay LM, Ng H-L, Alber T (2006) A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from
. J Mol Biol 360:409–420.
https://doi.org/10.1016/j.jmb.2006.05.015 CrossRef Google Scholar
Lisa M-N, Wagner T, Alexandre M et al (2017) The crystal structure of PknI from
shows an inactive, pseudokinase-like conformation. FEBS J 284:602–614.
https://doi.org/10.1111/febs.14003 CrossRef Google Scholar
Yan Q, Jiang D, Qian L et al (2017) Structural insight into the activation of PknI kinase from
via dimerization of the extracellular sensor domain. Structure 25:1286–1294.e4.
https://doi.org/10.1016/j.str.2017.06.010 CrossRef Google Scholar
Ravala SK, Singh S, Yadav GS et al (2015) Evidence that phosphorylation of threonine in the GT motif triggers activation of PknA, a eukaryotic-type serine/threonine kinase from
. FEBS J 282:1419–1431.
https://doi.org/10.1111/febs.13230 CrossRef Google Scholar
Mieczkowski C, Iavarone AT, Alber T (2008) Auto-activation mechanism of the
PknB receptor Ser/Thr kinase. EMBO J 27:3186–3197.
https://doi.org/10.1038/emboj.2008.236 CrossRef Google Scholar
Young TA, Delagoutte B, Endrizzi JA et al (2003) Structure of
PknB supports a universal activation mechanism for Ser/Thr protein kinases. Nat Struct Biol 10:168–174.
https://doi.org/10.1038/nsb897 CrossRef Google Scholar
Wehenkel A, Fernandez P, Bellinzoni M et al (2006) The structure of PknB in complex with mitoxantrone, an ATP-competitive inhibitor, suggests a mode of protein kinase regulation in mycobacteria. FEBS Lett 580:3018–3022.
https://doi.org/10.1016/j.febslet.2006.04.046 CrossRef Google Scholar
Scherr N, Honnappa S, Kunz G et al (2007) Structural basis for the specific inhibition of protein kinase G, a virulence factor of
. Proc Natl Acad Sci USA 104:12151–12156.
https://doi.org/10.1073/pnas.0702842104 CrossRef Google Scholar
Maestro (2014) version 9.7, Schrödinger. LLC, New York
Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput 7:525–537.
https://doi.org/10.1021/ct100578z CrossRef Google Scholar
Madhavi Sastry G, Adzhigirey M, Day T et al (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 27:221–234.
https://doi.org/10.1007/s10822-013-9644-8 CrossRef Google Scholar
LigPrep (2014) version 2.9, Schrödinger. LLC, New York
Epik (2014) version 2.7, Schrödinger. LLC, New York
Friesner RA, Banks JL, Murphy RB et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739–1749.
https://doi.org/10.1021/jm0306430 CrossRef Google Scholar
Friesner RA, Murphy RB, Repasky MP et al (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein—ligand complexes. J Med Chem 49:6177–6196.
https://doi.org/10.1021/jm051256o CrossRef Google Scholar
Muñoz-Gutierrez C, Adasme-Carreño F, Fuentes E et al (2016) Computational study of the binding orientation and affinity of PPARγ agonists: inclusion of ligand-induced fit by cross-docking. RSC Adv 6:64756–64768.
https://doi.org/10.1039/C6RA12084A CrossRef Google Scholar
Ramírez D, Caballero J (2018) Is it reliable to take the molecular docking top scoring position as the best solution without considering available. structural data? Molecules 23:1038.
https://doi.org/10.3390/molecules23051038 CrossRef Google Scholar
Bateman A, Martin MJ, O’Donovan C et al (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169.
https://doi.org/10.1093/nar/gkw1099 CrossRef Google Scholar
Bordoli L, Kiefer F, Arnold K et al (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4:1–13.
https://doi.org/10.1038/nprot.2008.197 CrossRef Google Scholar
Van Der Spoel D, Lindahl E, Hess B et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718.
https://doi.org/10.1002/jcc.20291 CrossRef Google Scholar
Abraham MJ, Murtola T, Schulz R et al (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2:19–25.
https://doi.org/10.1016/j.softx.2015.06.001 CrossRef Google Scholar
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472
CrossRef Google Scholar
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291.
https://doi.org/10.1107/S0021889892009944 CrossRef Google Scholar
Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52–56, 29
CrossRef Google Scholar
Hooft RW, Vriend G, Sander C, Abola EE (1996) Errors in protein structures. Nature 381:272.
https://doi.org/10.1038/381272a0 CrossRef Google Scholar
MacArthur MW, Laskowski RA, Thornton JM (1994) Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr Opin Struct Biol 4:731–737.
https://doi.org/10.1016/S0959-440X(94)90172-4 CrossRef Google Scholar
Bowie JU, Lüthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164–170
CrossRef Google Scholar
Pontius J, Richelle J, Wodak SJ (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 264:121–136.
https://doi.org/10.1006/jmbi.1996.0628 CrossRef Google Scholar
Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410.
https://doi.org/10.1093/nar/gkm290 CrossRef Google Scholar Copyright information
© Springer Nature Switzerland AG 2018