273
Views
3
CrossRef citations to date
0
Altmetric
Original Articles

Homology modelling, virtual screening and molecular dynamics of the MARK3 KA1 domain for cancer drug design

, &
Pages 1186-1206 | Received 11 Apr 2011, Accepted 12 May 2011, Published online: 07 Jul 2011

References

  • Silva , C.H.T.P. and Taft , C.A. 2011 . New Developments in Medicinal Chemistry , 1st ed. , Vol. 1 , 1 – 153 . Dubai : Bentham Science Publishers .
  • Semighini , E.P. , Resende , J. , Andrade , P. , Morais , P.A.B. , Carvalho , I. , Taft , C.A. and Silva , C.H.T.P. 2011 . Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes . J. Biomol. Struct. Dynam. , 28 : 787 – 796 .
  • Silva , C.H.T.P. , Silva , V.B. , Resende , J. , Rodrigues , P.F. , Bononi , F.C. , Benevenuto , C.G. and Taft , C.A. 2010 . Computer-aided drug design and ADMET predictions for identification and evaluation of novel potential farnesyltransferase inhibitors in cancer therapy . J. Mol. Graph. Model. , 28 : 513 – 523 .
  • Silva , V.B. , Taft , C.A. and Silva , C.H.T.P. 2008 . Use of virtual screening, flexible docking, and molecular interaction fields to design novel HMG-CoA reductase inhibitors for the treatment of hypercholesterolemia . J. Phys. Chem. A Mol. Spectrosc. Kinet. Environ. Gen. Theory , 112 : 2007 – 2011 .
  • Silva , V.B. , Kawano , D.F. , Gomes , A.S. , Carvalho , I. , Taft , C.A. and Silva , C.H.T.P. 2008 . Molecular dynamics, density functional, ADMET predictions, virtual screening and molecular interaction field studies for identification and evaluation of novel potential CDK2 inhibitors in cancer therapy . J. Phys. Chem. A Mol. Spectrosc. Kinet. Environ. Gen. Theory , 112 : 8902 – 8910 .
  • Cotram , R.S. , Kumar , V. and Collins , T.R. 2000 . Robbins, Patologia Estrutural e Funcional , 6a ed. , Guanabara Koogan . cap. 8
  • Herchenhorn , D. and Dias , F.L. 2004 . Avanço epidemiologica de pacientes com câncer de cabeça e pescoço em um hospital universitario do noroeste do estado de São Paulo . Ver. Hosp. Clin. Fac. Med. S. Paulo , 59 : 39 – 46 .
  • Alvarenga , L.M. , Ruiz , M.T. , Pavarino-Bertelli , E.C. , Ruback , M.J.C. , Maniglia , J.V. and Goloni-Bertollo , E.M. 2008 . Rev. Bras. Otorrinolaringol. , 74 : 68 – 73 .
  • Ebneth , A. , Drewes , G. , Mandelkow , E.M. and Mandelkow , E.C. 1999 . Phosphorylation of MAP2c and MAP4 by MARK kinases leads to the destabilization of microtubules in cells . Cell Motil. Cytoskeleton , 44 : 209 – 224 .
  • Brajenovic , M. , Joberty , G. , Kuester , B. , Bernhard , B. , Tewis , D. , Drewes , G. and Celizome , A.G. 2004 . Comprehensive proteomic analysis of human Par protein complexes reveals an interconnected protein network . J. Biol. Chem. , 279 : 12804 – 12811 .
  • Trinczek , B. , Brajenovic , M. , Ebneth , A. and Drewes , G. 2004 . MARK4 is a novel microtubule-associated proteins/Microtubule affinity-regulating kinase that binds to the cellular microtubule network and to centrosomes . J. Biol. Chem. , 279 : 5915 – 5923 .
  • Drewes , G. , Ebneth , A. , Preuss , U. , Ute , M. , Eva-Marie , M. and Mandelkow , E. 1997 . MARK, a novel family of protein kinases that phosphorylate microtubule-associated proteins and trigger microtubule disruption . Cell , 89 : 297 – 308 .
  • Matenia , D. , Griesshaber , B. , Li , X.-Y. , Thiessen , A. , Johne , C. , Jiao , J. , Mandelkow , M.E. and Mandelkow , E.-M. 2005 . PAK5 kinase is an inhibitor of MARK/Par-1, which leads to stable microtubules and dynamic actin . Mol. Biol. Cell , 16 : 4410 – 4422 .
  • Parsons , D.W. , Wang , T.-L. , Samuels , Y. , Bardelli , A. , Cummins , J.M. , DeLong , L. , Stillman , N. , Ptak , J. , Szabo , S. , Wilson , J.K.V. , Markowitz , S. , Sanford , K. , Kenneth , W. , Vogelstein , B. , Lengauer , C. , Christoph , V. and Victor , E. 2005 . Colorectal cancer: Mutations in a signaling pathway . Nature , 436 : 792
  • Tassan , J.-P. and Le Goff , X. 2004 . An overview of the KIN1/PAR-1/MARK kinase family . Biol. Cell , 96 : 193 – 199 .
  • Kato , T. , Satoh , S. , Okabe , H. , Kitahara , O. , Ono , K. , Kihara , C. , Tanaka , T. , Ssumoda , T. , Yamaoka , Y. , Yakamura , Y. and Funukawa , Y. 2001 . Isolation of a novel human gene, MARKL1, homologous to MARK3 and its involvement in hepatocellular carcinogenesis . Neoplasia , 3 : 4 – 9 .
  • Scott , J.M. and Johnson , G.V.W. 2004 . Microtubule/MAP-affinity regulating kinase (MARK) is activated by phenylarsine oxide in situ and phosphorylates Tau within its microtubule-binding domain . J. Neurochem. , 74 : 1463 – 1468 .
  • Churcher , I. 2006 . Tau therapeutic strategies for the treatment of Alzheimer's disease . Curr. Topics Med. Chem. , 6 : 579 – 595 .
  • Dancey , J. and Sausville , E.A. 2003 . Issues and progress with protein kinase inhibitors for cancer treatment . Nat. Rev. Drug Discov. , 2 : 296 – 313 . doi:10.1038/nrd1066
  • Fabian , M.A. , Biggs , W.H. , Treiber , D. , Daniel , A.K. , Atteridge , C. , Cory , E. , Azimiora , M.D. , Benedetti , M.G. , Carter , T.A. , Ciceri , P. , Edeen , P.T. , Floyd , M. , Ford , J.M. , Galvin , M. , Margaret , G. , Jay , L. , Grotzfeld , R.M. , Herrgard , S. , Insko , D.e. , Insko , M.A. , Lai , A.G. , Lelias , J.M. , Mehta , S.A. , Milanov , Z.V. , Velasco , A.M. , Wodicka , L.M. , Patel , H.K. , Zarrinkar , P.P. and Lockhart , D.J. 2005 . A small molecule-kinase interaction map for clinical kinase inhibitors . Nat. Biotechnol. , 23 : 329 – 336 .
  • Murphy , J.M. , Korzhnev , D.M. , Ceccarelli , D.F. , Briant , D.J. , Zarrine-Afsar , A. , Sicheri , F. , Lewis , E. and Pawson , T. 2007 . Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain . Proc. Natl Acad. Sci. , 104 : 14336 – 14341 .
  • Kojima , Y. , Miyoshi , H. , Clevers , H.C. , Oshima , M. , Aoki , M. and Taketo , M.M. 2007 . Suppression of tubulin polymerization by the LKB1-microtubule-associated protein/microtubule affinity-regulating kinase signaling . J. Biol. Chem. , 282 : 23532 – 23540 .
  • Göransson , O. , Deak , M. , Wullschleger , S. , Morrice , N.A. , Prescott , A.R. and Alessi , D.R. 2006 . Regulation of the polarity kinases PAR-1/MARK by 14-3-3 interaction and phosphorylation . J. Cell Sci. , 119 : 4059 – 4070 .
  • Terabayashi , T. , Itoh , T.J. , Yamaguchi , H. , Yoshimura , Y. , Funato , Y. , Ohno , S. and Miki , H. 2007 . Polarity-regulating kinase partitioning-defective 1/microtubule affinity-regulating kinase 2 negatively regulates development of dendrites on hippocampal neurons . J Neurosci , 27 : 13098 – 13107 .
  • Li , L. , Chen , R. and Weng , Z. 2003 . RDOCK: Refinement of rigid-body protein docking predictions . PROTEINS: Struct. Funct. Genet. , 53 : 693 – 707 .
  • Beullens , M. , Vancauwenbergh , S. , Morrice , N. , Derua , R. , Ceulemans , H. , Waelkens , E. and Bollen , M. 2005 . Substrate specificity and activity regulation of protein kinase MELK . J. Biol. Chem. , 280 : 40003 – 40011 .
  • Elbert , M. , Rossi , G. and Brennwald , P. 2005 . The yeast Par-1 homologs Kin1 and Kin2 show genetic and physical interactions with components of the exocytic machinery . Mol. Biol. Cell , 16 : 532 – 549 .
  • Tochio , N. , Koshiba , S. , Kobayashi , N. , Inoue , M. , Yabuki , T. , Aoki , M. , Seki , E. , Matsuda , T. , Tomo , Y. , Motoda , Y. , Kobayashi , A. , Tanaka , A. , Hayashizaki , Y. , Terada , T. , Shirouzu , M. , Kigawa , T. and Yokoyama , S. 2006 . Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3 . Protein Sci. , 15 : 2534 – 2543 .
  • Lizcano , J.M. , Goransson , O. , Toth , R. , Deak , M. , Morice , N.A. , Boudeau , J. , Hawley , S.A. , Udd , L. , Makela , T.P. , Hardie , D.G. and Alessi , D.R. 2004 . LKB1 is a master kinase that activates 13 kinases of the AMPK subfamily, including MARK/PAR-1 . EMBO J. , 23 : 833 – 843 .
  • Songhee Jeon , J. , Yong-Sik , K. , Park , J. and Dae Bae , C. 2005 . Microtubule affinity-regulating kinase 1 (MARK1) is activated by electroconvulsive schock in the rat hippocampus . J. Neurochem. , 95 : 1608 – 1618 .
  • Thies , E. and Mandelkow , E.M. 2007 . Missorting of tau in neurons causes degeneration of synapses that can be rescued by the kinase MARK2/Par-1 . J. Neurosci. , 27 : 2896 – 2907 .
  • Mandelkow , E. , von Bergen , M. , Biernat , J. and Mandelkow , E.M. 2007 . Structural principles of Tau and the paired helical filaments of Alzheimer's disease; Journal Compilation; 83–90; International Society of Neuropathology . Brain Pathol. , : 83 – 90 .
  • Barton , G.J. 1990 . Protein multiple sequence alignment and flexible pattern matching . Meth. Enzymol. , 183 : 403 – 428 .
  • Marti-Renom , M.A. , Stuart , A. , Fiser , A. , Sánchez , R. , Melo , F. and Sali , A. 2000 . Comparative protein structure modeling of genes and genomes . Annu. Rev. Biophys. Biomol. Struct. , 29 : 291 – 325 .
  • Laskowski , R.A. , MacArthur , M.W. , Moss , D.S. and Thornton , J.M. 1993 . PROCHECK: A program to check the stereochemical quality of protein structures . J. Appl. Cryst. , 26 : 283 – 291 .
  • Vriend , G. 1990 . WHAT IF: A molecular modeling and drug design program . J. Mol. Graph. , 8 : 52 – 56 .
  • Bowie , J. , Lüthy , R. and Eisenberg , D. 1991 . A method to identify protein sequences that fold into a known three-dimensional structure . Science , 253 : 164 – 170 .
  • Insight II User Guide . 2005 . Version 2005 , San Diego, CA, USA : Accelrys .
  • Sybyl User Guide . 2005 . Version 7.1 , San Diego, CA, USA : Tripos Inc. .
  • Jones , G. , Willett , P. and Glen , R.C. 1995 . Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation . J. Mol. Biol. , 245 : 43 – 53 .
  • Schneidman-Duhovny , D. , Dror , O. , Inbar , Y. , Nussinov , R. and Wolfson , H.J. 2008 . PharmaGist: A webserver for ligand-based pharmacophore detection . Nucl. Acids Res. , 36 : W223 – W228 .
  • Discovery Studio 2.0 . 2007 . “ User Guide ” . 92121 San Diego, CA : Accelrys, Inc. .
  • DEREK and METEOR 8.0 . 2004 . Leeds, LS2 9HD, UK : LHASA Limited .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.