A comparative QSAR on 1,2,5-thiadiazolidin-3-one 1,1-dioxide compounds as selective inhibitors of human serine proteinases

Journal of Molecular Graphics and Modelling

Volumn 31, Issue , 2011, Pages 10-19

  García, Javier ^a   Duchowicz, Pablo R ^a   Rozas, María F ^a   Caram, José A ^a,b   Mirífico, María V ^a,c   Fernández, Francisco M ^a   Castro, Eduardo A ^a  

^a INSTITUTO DE INVESTIGACIONES FISICOQUÍMICAS TEÓRICAS Y APLICADAS INIFTA   (Argentina)

^b FACULTAD DE CIENCIAS EXACTAS   (Argentina)

^c UNIVERSIDAD NACIONAL DE LA PLATA   (Argentina)

Author keywords

1,2,5 Thiadiazolidin 3 one 1,1 dioxide; Flexible descriptors; Molecular Dynamics; QSAR theory; Serine proteases

Indexed keywords

1,2,5-THIADIAZOLIDIN-3-ONE 1,1-DIOXIDE; BIOCHEMICAL STUDIES; CLASSICAL MOLECULAR DYNAMICS; DESCRIPTORS; IN-VITRO; MODELING APPROACH; MULTI-VARIABLE LINEAR REGRESSION; QSAR MODEL; QSAR THEORY; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; REPLACEMENT METHODS; SELECTIVE INHIBITORS; SERINE PROTEASE; SERINE PROTEINASE; STANDARD PROCEDURES; STEPWISE REGRESSION; STRUCTURAL DESCRIPTORS;

AMINO ACIDS; BIOSYNTHESIS; DYNAMICS; MOLECULAR DYNAMICS; MOLECULAR GRAPHICS; SOFTWARE TESTING;

COMPUTATIONAL CHEMISTRY;

1,2,5 THIADIAZOLIDINE 1,1 DIOXIDE DERIVATIVE; CATHEPSIN G; LEUKOCYTE ELASTASE; MOLECULAR SCAFFOLD; MYELOBLASTIN; SERINE PROTEINASE INHIBITOR;

ARTICLE; CHEMICAL STRUCTURE; HUMAN; MOLECULAR DYNAMICS; MULTIPLE LINEAR REGRESSION ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

CYCLIC S-OXIDES; DRUG DESIGN; HUMANS; LINEAR MODELS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SERINE PROTEASES; SERINE PROTEINASE INHIBITORS; THIAZOLES;

EID: 80053909411     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.07.007     Document Type: Article

References (55)

1. W.C. Groutas, R. Kuang, R. Venkataraman, J.B. Epp, S. Ruan, and O. Prakash Structure-based design of a general class of mechanism-based inhibitors of the serine proteinases employing a novel amino acid-derived heterocyclic scaffold Biochemistry 36 1997 4739 4750 (Pubitemid 27180954)
2. R. Dhami, B. Gilks, C. Xie, K. Zay, J.L. Wright, and A. Churg Acute cigarette smoke-induced connective tissue breakdown is mediated by neutrophils and prevented by 1-antitrypsin Am. J. Respir. Cell Mol. Biol. 22 2000 244 252 (Pubitemid 30351488)
3. R.A. Stockley The role of proteinases in the pathogenesis of chronic bronchitis Am. J. Respir. Crit. Care Med. 150 1994 S109 S113 (Pubitemid 24364333)
4. P.J. Barnes Novel approaches and targets for treatment of chronic obstructive pulmonary disease Respir. Crit. Care Med. 160 1999 S72 S79
5. L.J. Copp, A. Krantz, and R.W. Spencer Kinetics and mechanism of human leukocyte elastase inactivation by ynenol lactones Biochemistry 2 1987 169 178 (Pubitemid 17014425)
6. J.A. Katzenellenbogen, R. Rai, and W. Dai Enol lactone derivatives as inhibitors of human neutrophil elastase and trypsin-like proteases Bioorg. Med. Chem. Lett. 2 1992 1399 1404
7. M.A. Hernandez, J.C. Powers, J. Glinski, J. Oleksyszyn, J. Vijayalakshmi, and E.F. Meyer Effect of the 7-amino substituent on the inhibitory potency of mechanism-based isocoumarin inhibitors for porcine pancreatic and human neutrophil elastases: a 1.85- X-ray structure of the complex between porcine pancreatic elastase and 7-[(N-tosylphenylalanyl)amino]-4-chloro-3- methoxyisocoumarin J. Med. Chem. 35 1992 1121 1129
8. W.C. Groutas, M.J. Brubaker, M.A. Stanga, J.C. Castrisos, J.P. Crowley, and E.J. Shatz Inhibition of human leukocyte elastase by derivatives of N-hydroxysuccinimide. A structure-activity-relationship study J. Med. Chem. 32 1989 1607 1611 (Pubitemid 19205373)
9. W.C. Groutas, R. Venkataraman, M.J. Brubaker, and M.A. Stanga Inhibition of human leukocyte elastase by phosphate esters of N-hydroxysuccinimide and its derivatives: direct observation of a phosphorylated enzyme by sup 31 P nuclear magnetic resonance spectroscopy Biochemistry 30 1991 4132 4136
10. W.C. Groutas, R. Venkataraman, M.J. Brubaker, J.B. Epp, L.S. Chong, M.A. Stanga, J.J. McClenahan, and F. Tagusagawa 3-(Alkylthio)-N-hydroxysuccinimide derivatives: potent inhibitors of human leukocyte elastase Biochim. Biophys. Acta 1164 1993 283 288 (Pubitemid 23234579)
11. W.C. Groutas, H. Huang, J.B. Epp, R. Venkataraman, J.J. McClenahan, and F. Tagusagawa Mechanism-based inhibition of human leukocyte elastase and cathepsin G by susbtituted dihydrouracils Biochim. Biophys. Acta 1227 1994 130 136 (Pubitemid 24371739)
12. D.J. Underwood, B.G. Green, R. Chabin, S. Mills, J.B. Doherty, P.E. Finke, M. MacGoss, S.K. Shah, C.S. Burgey, T.A. Dickinson, P.R. Griffin, T.E. Lee, K.M. Swiderek, T. Covey, W.M. Westler, and W.B. Knight Mechanism of inhibition of human leukocyte elastase by β-lactams. 3. Use of electrospray ionization mass spectrometry and two-dimensional NMR techniques to identify β-lactam-derived E-I complexes Biochemistry 34 1995 14344 14355
13. W.C. Groutas, N. Houser-Archield, L.S. Chong, R. Venkataraman, J.B. Epp, H. Huang, and J.J. McClenahan Efficient inhibition of human leukocyte elastase and cathepsin G by saccharin derivatives J. Med. Chem. 36 1993 3178 3181 (Pubitemid 23326273)
14. W.C. Groutas, L.S. Chong, R. Venkataraman, R. Kuang, J.B. Epp, N. Houser-Archield, H. Huang, and J.R. Hoidal Amino acid-derived phthalimide and saccharin derivatives as inhibitors of human leukocyte elastase, cathepsin G, and proteinase 3 Arch. Biochem. Biophys. 332 1996 335 340 (Pubitemid 26260397)
15. D.J. Hlasta, C. Subramanyam, M.R. Bell, P.M. Carabateas, J.J. Court, R.C. Desai, M.L. Drozd, W.M. Eickhoff, E.W. Ferguson, R.J. Gordon, J.A. Johnson, V. Kumar, A.L. Maycock, K.R. Mueller, E.D. Pagani, D.T. Robinson, M.T. Saindane, P.J. Silver, and S. Subramanian A novel class of cyclic β-dicarbonyl leaving groups and their use in the design of benzisothiazolone human leukocyte elastase inhibitors J. Med. Chem. 38 1995 739 744
16. W.C. Groutas, J.B. Epp, R. Kuang, S. Ruan, L.S. Chong, R. Venkataraman, J.Tu.S. He, H. Yu, Q. Fu, Y.H. Li, T.M. Truong, and N.T. Vu 1,2,5- Thiadiazolidin-3-one 1,1 dioxide: a powerful scaffold for probing the S9 subsites of (chymo)trypsin-like serine proteases Arch. Biochem. Biophys. 385 2001 162 169 (Pubitemid 32988994)
17. C. Hansch, and A. Leo Exploring QSAR. Fundamentals and Applications in Chemistry and Biology 1995 American Chemical Society Washington, DC
18. H. Kubinyi QSAR: Hansch Analysis and Related Approaches 2008 Wiley-Interscience New York
19. T. Puzyn, J. Leszczynski, and M.T. Cronin Recent Advances in QSAR Studies: Methods and Applications 1st ed. 2009 Springer New York
20. W.C. Groutas, R. Kuang, S. Ruan, J.B. Epp, R. Venkataraman, and T.M. Truong Potent and specific inhibition of human leukocyte elastase, cathepsin G and proteinase 3 by sulfone derivatives employing the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold Bioorg. Med. Chem. 6 1998 661 671 (Pubitemid 28287268)
21. R. Kuang, J.B. Epp, S. Ruan, L.S. Chong, R. Venkataraman, J. Tu, S. He, T.M. Truong, and W.C. Groutas Utilization of the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold in the design of potent inhibitors of serine proteases: SAR studies using carboxylates Bioorg. Med. Chem. 8 2000 1005 1016 (Pubitemid 30336396)
22. S. He, R. Kuang, R. Venkataraman, J. Tu, T.M. Truong, H.-K. Chan, and W.C. Groutas Potent inhibition of serine proteases by heterocyclic sulfide derivatives of 1,2,5-thiadiazolidin-3-one 1,1 dioxide Bioorg. Med. Chem. 8 2000 1713 1717 (Pubitemid 30427236)
23. W.C. Groutas, S. He, R. Kuang, S. Ruan, J. Tu, and H.-K. Chan Inhibition of serine proteases by functionalized sulfonamides coupled to the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold Bioorg. Med. Chem. 9 2001 1543 1548 (Pubitemid 32640170)
24. W.C. Groutas, N.M. Schechter, S. He, H. Yu, P. Huang, and J. Tu Human chymase inhibitors based on the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold Bioorg. Med. Chem. Lett. 9 1999 2199 2204 (Pubitemid 29371935)
25. R. Kuang, J.B. Epp, S. Ruan, H. Yu, P. Huang, S. He, J. Tu, N.M. Schechter, J. Turbov, C.J. Froelich, and W.C. Groutas A general inhibitor scaffold for serine proteases with a (Chymo) trypsin-like fold: solution-phase construction and evaluation of the first series of libraries of mechanism-based inhibitors J. Am. Chem. Soc. 121 1999 8128 8129 (Pubitemid 29430568)
26. J.F. Morrison, and C.T. Walsh The behavior and significance of slow-binding enzyme inhibitors Adv. Enzymol. 61 1988 201 301
27. Hyperchem 7 2007 Hypercube, Inc. Gainesville http://www.hyper.com
28. Dragon Milano Chemometrics and QSAR Research Group 2010 http://michem.disat.unimib.it/chm
29. R. Todeschini, and V. Consonni Molecular Descriptors for Chemoinformatics 2009 Wiley-VCH Weinheim
30. Recon Version 5.5 2002 Rensselaer Polytechnic Institute Troy, NY, USA http://www.drugmining.com
31. B.K. Lavine, C.E. Davidson, C. Breneman, and W.J. Katt Electronic Van der Waals surface property descriptors and genetic algorithms for developing structure-activity correlations in olfactory databases J. Chem. Inf. Comput. Sci. 43 2003 1890 1905
32. A. Worachartcheewan, C. Nantasenamat, T. Naenna, C. Isarankura-Na- Ayudhya, and V. Prachayasittikul Modeling the activity of furin inhibitors using artificial neural network Eur. J. Med. Chem. 44 2009 1664 1673
33. R.F.W. Bader Atoms in Molecules - A Quantum Theory 1990 Clarendon Press Oxford
34. C.M. Breneman, and L.W. Weber Transferable atom equivalents. Assembling accurate electrostatic potential fields for large molecules from ab initio and PROAIMS results on model systems G.A. Jeffrey, J.F. Piniella, The Application of Charge Density Research to Chemistry and Drug Design 1991 Plenum New York
35. Matlab 5.0 1996 The MathWorks, Inc Natick, MA, USA http://www.mathworks. com
36. P.R. Duchowicz, E.A. Castro, F.M. Fernández, and M.P. González A new search algorithm of QSPR/QSAR theories: normal boiling points of some organic molecules Chem. Phys. Lett. 412 2005 376 380 (Pubitemid 41203394)
37. A.G. Mercader, P.R. Duchowicz, F.M. Fernández, and E.A. Castro Modified and enhanced replacement method for the selection of molecular descriptors in QSAR and QSPR theories Chemom. Intell. Lab. Syst. 92 2008 138 144
38. P.R. Duchowicz, M. Fernández, J. Caballero, E.A. Castro, and F.M. Fernández QSAR of non-nucleoside inhibitors of HIV-1 reverse transcriptase Bioorg. Med. Chem. 14 2006 5876 5889 (Pubitemid 44096998)
39. P.R. Duchowicz, M.G. Vitale, E.A. Castro, M. Fernandez, and J. Caballero QSAR analysis for heterocyclic antifungals Bioorg. Med. Chem. 15 2007 2680 2689 (Pubitemid 46389586)
40. P.R. Duchowicz, A. Talevi, L.E. Bruno-Blanch, and E.A. Castro New QSPR study for the prediction of aqueous solubility of drug-like compounds Bioorg. Med. Chem. 16 2008 7944 7955
41. P.R. Duchowicz, M. Goodarzi, M.A. Ocsachoque, G.P. Romanelli, E.V. Ortiz, J.C. Autino, D.O. Bennardi, D. Ruiz, and E.A. Castro QSAR analysis on Spodoptera litura antifeedant activities for flavone derivatives Sci. Total Environ. 408 2009 277 285
42. M. Goodarzi, P.R. Duchowicz, C.H. Wu, F.M. Fernández, and E.A. Castro New hybrid genetic based support vector regression as QSAR approach for analyzing flavonoids-GABA(A) complexes J. Chem. Inf. Model. 49 2009 1475 1485
43. © 2002 Jeeshim and KUCC625 (2003-05-09).
44. J.D. Curto, and J.C. Pinto New multicollinearity indicators in linear regression models Int. Stat. Rev. 75 2007 114 121
45. N.R. Draper, and H. Smith Applied Regression Analysis 1981 John Wiley & Sons New York
46. Coral 1.5 2010 http://www.insilico.eu/coral
47. ACD/ChemSketch Freeware, version 12.01 2009 Advanced Chemistry Development, Inc Toronto, ON, Canada http://www.acdlabs.com
48. A.A. Toropov, and E. Benfenati SMILES in QSPR/QSAR modeling: results and perspectives Curr. Drug Discov. Technol. 4 2007 77 116 (Pubitemid 47359070)
49. A.A. Toropov, and E. Benfenati Additive SMILES-based optimal descriptors in QSAR modelling bee toxicity: using rare SMILES attributes to define the applicability domain Bioorg. Med. Chem. 26 2008 4801 4809 (Pubitemid 351625898)
50. A.A. Toropov, A.P. Toropova, and E. Benfenati Simplified molecular input line entry system-based optimal descriptors: quantitative structure-activity relationship modeling mutagenicity of nitrated polycyclic aromatic hydrocarbons Chem. Biol. Drug Des. 73 2009 515 525
51. A.A. Toropov, A.P. Toropova, E. Benfenati, D. Leszczynska, and J. Leszczynski InChI-based optimal descriptors: QSAR analysis of fullerene [C60]-based HIV-1 PR inhibitors by correlation balance Eur. J. Med. Chem. 45 2010 1387 1394
52. S. Wold, and L. Eriksson Statistical validation of QSAR results H. van de Waterbeemd, Chemometrics Methods in Molecular Design 1995 VCH Weinheim 309 318
53. D.M. Hawkins, S.C. Basak, and D.J. Mills Assessing model fit by cross validation J. Chem. Inf. Model. 43 2003 579 586
54. A. Golbraikh, and A. Tropsha Beware of q2! J. Mol. Graphics Modell. 20 2002 269 276
55. P.R. Duchowicz, E.A. Castro, and F.M. Fernández Alternative algorithm for the search of an optimal set of descriptors in QSAR-QSPR studies MATCH Commun. Math. Comput. Chem. 55 2006 179 192