135
Views
9
CrossRef citations to date
0
Altmetric
Original Articles

Quantitative structure-activity relationships for cycloguanil analogs as PfDHFR inhibitors using mathematical molecular descriptors

&
Pages 215-229 | Received 13 Nov 2009, Accepted 21 Feb 2010, Published online: 08 Jun 2010

References

  • Hyde , JE . 2005 . Drug-resistant malaria . Trends Parasitol. , 21 : 494 – 498 .
  • Biagini , GA , Viriyavejakul , P , O'Neill , PM , Bray , PG and Ward , SA . 2006 . Functional characterization and target validation of alternative complex I of Plasmodium falciparum mitochondria . Antimicrob. Agents Chemother. , 50 : 1841 – 1851 .
  • Gardner , MJ , Hall , N , Fung , E , White , O , Berriman , M , Hyman , RW , Carlton , JM , Pain , A , Nelson , KE , Bowman , S , Paulsen , IT , James , K , Eisen , JA , Rutherford , K , Salzberg , SL , Craig , A , Kyes , S , Chan , MS , Nene , V , Shallom , SJ , Suh , B , Peterson , J , Angiuoli , S , Pertea , M , Allen , J , Selengut , J , Haft , D , Mather , MW , Vaidya , AB , Martin , DM , Fairlamb , AH , Fraunholz , MJ , Roos , DS , Ralph , SA , McFadden , GI , Cummings , LM , Subramanian , GM , Mungall , C , Venter , JC , Carucci , DJ , Hoffman , SL , Newbold , RW , Davis , RW , Fraser , CM and Barrell , B . 2002 . Genome sequence of the human malaria parasite Plasmodium falciparum . Nature , 419 : 498 – 511 .
  • Florens , L , Washburn , MP , Raine , JD , Anthony , RM , Grainger , M , Haynes , JD , Moch , JK , Muster , N , Sacci , JB , Tabb , DL , Witney , AA , Wolters , D , Wu , YM , Gardner , MJ , Holder , AA , Sinden , RE , Yates , JR and Carucci , DJ . 2002 . A proteomic view of the Plasmodium falciparum life cycle . Nature , 419 : 520 – 526 .
  • Takala , SL , Coulibaly , D , Thera , MA , Dicko , A , Smith , DL , Guindo , AB , Kone , AK , Traore , K , Ouattara , A , Djimde , AA , Sehdev , PS , Lyke , KE , Diallo , DA , Doumbo , OK and Plowe , CV . 2007 . Dynamics of polymorphism in a malaria vaccine antigen at a vaccine-testing site in Mali . PLoS Med. , 4 : 523 – 534 .
  • Gregson , A and Plowe , CV . 2005 . Mechanisms of resistance of malaria parasites to antifolates . Pharmacol. Rev. , 57 : 117 – 145 .
  • Kompis , IM , Islam , K and Then , RL . 2005 . DNA and RNA synthesis: Antifolates . Chem. Rev. , 105 : 593 – 620 .
  • Yuthavong , Y , Yuvaniyama , J , Chitnumsub , P , Vanichtanankul , J , Chusacultanachai , S , Tarnchompoo , B , Vilaivan , T and Kamchonwongpaisan , S . 2005 . Malarial (Plasmodium falciparum) dihydrofolate reductasethymidylate synthase: structural basis for antifolate resistance and development of effective inhibitors . Parasitology , 130 : 249 – 259 .
  • Anderson , AC . 2005 . Targeting DHFR in parasitic protozoa . Drug Discovery Today , 10 : 121 – 128 .
  • Hyde , JE . 1990 . The dihydrofolate reductase-thymidylate synthetase gene in the drug resistance of malaria parasites . Pharmacol. Ther. , 48 : 45 – 59 .
  • Adane , L and Bharatam , PV . 2008 . Modelling and informatics in the analysis of P-falciparum DHFR enzyme inhibitors . Curr. Med. Chem. , 15 : 1552 – 1569 .
  • Fogel , GB , Cheung , M , Pittman , E and Hecht , D . 2008 . Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives . Comput. Aided Mol. Design , 22 : 29 – 38 .
  • Fogel , GB , Cheung , M , Pittman , E and Hecht , D . 2008 . In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase . J. Mol. Graph. Model. , 26 : 1145 – 1152 .
  • Hecht , D , Cheung , M and Fogel , GB . 2008 . QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives . Biosystems , 92 : 10 – 15 .
  • Santos , OA and Hopfinger , AJ . 2001 . A search for sources of drug resistance by the 4D-QSAR analysis of a set of antimalarial dihydrofolate reductase inhibitors . J. Comput. Aided Mol. Design , 15 : 1 – 12 .
  • Parenti , MD , Pacchioni , S , Ferrari , AM and Rastelli , G . 2004 . Three dimensional quantitative structure-activity relationship analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors using a pharmacophore generation approach . J. Med. Chem. , 47 : 4258 – 4267 .
  • Sivaprakasam , P , Tosso , PN and Doerksen , RJ . 2009 . Structure-activity relationship and comparative docking studies for cycloguanil analogs as PfDHFR-TS inhibitors . J. Chem. Inf. Model. , 49 : 1787 – 1796 .
  • Basak , SC , Mills , D and Hawkins , DM . 2008 . Predicting allergic contact dermatitis: A hierarchical structure-activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors . J. Comput. Aided Mol. Design , 22 : 339 – 343 .
  • Basak , SC , Mills , D and Gute , BD . 2006 . “ Quantitative structure-toxicity relationships using chemodescriptors and biodescriptors ” . In Biological Concepts and Techniques in Toxicology: An Integrated Approach , Edited by: Riviere , JE . 61 – 82 . New York : Taylor & Francis .
  • Basak , SC , Mills , D , Natarajan , R and Gute , BD . 2009 . “ Predicting chemical reactivity and bioactivity from structure: A mathematical-cum-computational approach ” . In Chemical Reactivity Theory: A Density Functional View , Edited by: Chattaraj , PK . 479 – 502 . CRC Press .
  • Basak , SC , Mills , D , Gute , BD and Natarajan , R . 2006 . “ Predicting pharmacological and toxicological activity of heterocyclic compounds using QSAR and molecular modeling ” . In Topics in Heterocyclic Chemistry Vol. 5: QSAR and Molecular Modeling Studies of Heterocyclic Drugs , Edited by: Gupta , SP . 39 – 80 . Berlin : Springer-Verlag .
  • Basak , SC , Mills , D , Gute , BD , Grunwald , GD and Balaban , AT . 2002 . “ Applications of topological indices in property/bioactivity/toxicity prediction of chemicals ” . In Topology in Chemistry: Discrete Mathematics of Molecules , Edited by: Rouvray , DH and King , RB . 113 – 184 . Chichester, England : Horwood Publishing Limited .
  • Basak , SC and Mills , D . 2009 . Predicting vapor pressure of chemicals from structure: A comparison of graph theoretic versus quantum chemical descriptors . SAR QSAR Environ. Res. , 20 : 119 – 132 .
  • Bagchi , MC , Maiti , BC , Mills , D and Basak , SC . 2004 . Usefulness of graphical invariants in quantitative structure-activity correlations of tuberculostatic drugs of isonicotinic acid hydrazide type . J. Mol. Modeling , 10 : 102 – 111 .
  • Basak , SC and Mills , D . Prediction of partitioning properties for environmental pollutants using mathematical structural descriptors, ARKIVOC 2005 (ii) (2005), pp. 60–76
  • Kamchonwongpaisan , S , Quarrell , R , Charoensetakul , N , Ponsinet , R , Vilaivan , T , Vanichtanankul , J , Tarnchompoo , B , Sirawaraporn , W , Lowe , G and Yuthavong , Y . 2004 . Inhibitors of multiple mutants of Plasmodium falciparum dihydrofolate reductase and their antimalarial activities . J. Med. Chem. , 47 : 673 – 680 .
  • Vilaivan , T , Saesaengseerung , N , Jarprung , D , Kamchonwongpaisan , S , Sirawaraporn , W and Yuthavong , Y . 2003 . Synthesis of solution-phase combinatorial library of 4,6-diamino-1,2-dihydro-1,3,5-triazine and identification of new leads against A16V + S108T mutant dihydrofolate reductase of Plasmodium falciparum . Bioorg. Med. Chem. , 11 : 217 – 224 .
  • Yuthavong , Y , Vilaivan , T , Chareonsethakul , N , Kamchonwongpaisan , S , Sirawaraporn , W , Quarrell , R and Lowe , G . 2000 . Development of a lead inhibitor for the A16V + S108T mutant of dihydrofolate reductase from the cycloguanil-resistant strain (T9/94) of Plasmodium falciparum . J. Med. Chem. , 43 : 2738 – 2744 .
  • Basak , SC , Harriss , DK and Magnuson , VR . 1988 . POLLY v. 2.3 , Copyright of the University of Minnesota .
  • Filip , PA , Balaban , TS and Balaban , AT . 1987 . A new approach for devising local graph invariants: Derived topological indices with low degeneracy and good correlational ability . J. Math. Chem. , 1 : 61 – 83 .
  • Molconn-Z Version 3.5. Hall Associates Consulting, Quincy, MA, 2000
  • Kier , LB and Hall , LH . 1986 . Molecular Connectivity in Structure-Activity Analysis , Letchworth, Hertfordshire, U.K. : Research Studies Press .
  • Randic , M . 1975 . On characterization of molecular branching . J. Am. Chem. Soc. , 97 : 6609 – 6615 .
  • Roy , AB , Basak , SC , Harriss , DK and Magnuson , VR . 1983 . “ Neighborhood complexities and symmetry of chemical graphs and their biological applications ” . In Mathematical Modelling Science Technology , Edited by: Avula , XJR , Kalman , RE , Liapis , AI and Rodin , EY . 745 – 750 . New York : Pergamon Press .
  • Kier , LB and Hall , LH . 1999 . Molecular Structure Description: The Electrotopological State , San Diego, CA : Academic Press .
  • Carhart , RE , Smith , DH and Venkataraghavan , R . 1985 . Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications . J. Chem. Inf. Comput. Sci. , 25 : 64 – 73 .
  • Basak , SC , Gute , BD and Mills , D . 2006 . Similarity methods in analog selection, property estimation and clustering of diverse chemicals . ARKIVOC , 2006 : 157 – 210 .
  • Basak , SC and Grunwald , GD . APProbe, Copyright of the University of Minnesota, 1993
  • In SAS/STAT User Guide, Release 6.03 Edition. SAS Institute Inc., Cary, NC, 1988
  • Hoerl , AE and Kennard , RW . 1970 . Ridge regression: Biased estimation for nonorthogonal problems . Technometrics , 12 : 55 – 67 .
  • Hoerl , AE and Kennard , RW . 2005 . Ridge regression: Applications to nonorthogonal problems . Technometrics , 12 : 69 – 82 .
  • Frank , IE and Friedman , JH . 1993 . A statistical view of some chemometrics regression tools . Technometrics , 35 : 109 – 135 .
  • Wold , S . 1993 . Discussion: PLS in chemical practice . Technometrics , 35 : 136 – 139 .
  • Hoskuldsson , A . 1995 . A combined theory for PCA and PLS . J. Chemom. , 9 : 91 – 123 .
  • Hoskuldsson , A . 1988 . PLS regression methods . J. Chemom. , 2 : 211 – 228 .
  • Basak , SC , Mills , D , Mumtaz , MM and Balasubramanian , K . 2003 . Use of topological indices in predicting aryl hydrocarbon receptor binding potency of dibenzofurans: A hierarchical QSAR approach . Indian J. Chem. , 42A : 1385 – 1391 .
  • Basak , SC , Mills , D , El-Masri , HA , Mumtaz , MM and Hawkins , DM . 2004 . Predicting blood:air partition coefficients using theoretical molecular descriptors . Environ. Toxicol. Pharmacol. , 16 : 45 – 55 .
  • Basak , SC , Mills , D , Hawkins , DM and El-Masri , H . 2003 . Prediction of human blood:air partition coefficient: A comparison of structure-based and property-based methods . Risk Analysis , 23 : 1173 – 1184 .
  • Basak , SC , Mills , D , Hawkins , DM and El-Masri , HA . 2002 . Prediction of tissue:air partition coefficients: A comparison of structure-based and property-based methods . SAR QSAR Environ. Res. , 13 : 649 – 665 .
  • Basak , SC , Mills , D and Gute , BD . 2006 . Prediction of tissue:air partition coefficients – theoretical vs experimental methods . SAR QSAR Environ. Res. , 17 : 515 – 532 .
  • Hawkins , DM . 2005 . “ LinMods v. 5.0 ” . In developed at the School of Statistics , Minneapolis, MN : University of Minnesota .
  • Hawkins , DM , Basak , SC and Mills , D . 2003 . Assessing model fit by cross-validation . J. Chem. Inf. Comput. Sci. , 43 : 579 – 586 .
  • Kraker , JJ , Hawkins , DM , Basak , SC , Natarajan , R and Mills , D . 2007 . Quantitative structure-activity relationship (QSAR) modeling of juvenile hormone activity: Comparison of validation procedures . Chemom. Intell. Lab. Syst. , 87 : 33 – 42 .
  • Basak , SC , Natarajan , R , Mills , D , Hawkins , DM and Kraker , JJ . 2006 . Quantitative structure-activity relationship modeling of juvenile hormone mimetic compounds for Culex pipiens larvae – with discussion of descriptor thinning methods . J. Chem. Inf. Model. , 46 : 65 – 77 .
  • Basak , SC and Mills , D . 2005 . Development of quantitative structure-activity relationship models for vapor pressure estimation using computed molecular descriptors . ARKIVOC , 2005 : 308 – 320 .
  • Basak , SC , Mills , D , Gute , BD and Hawkins , DM . 2003 . “ Predicting mutagenicity of congeneric and diverse sets of chemicals using computed molecular descriptors: A hierarchical approach ” . In Quantitative Structure-Activity Relationship (QSAR) Models of Mutagens and Carcinogens , Edited by: Benigni , R . 207 – 234 . Boca Raton, FL : CRC Press .
  • Ehrlich , P . 1909 . Present status of chemotherapy . Ber. dtsch. Chem. Ges. , 42 : 17 – 47 .
  • Gund , P . 1977 . Three-dimensional pharmacophore pattern searching . Prog. Mol. Subcell. Biol. , 5 : 117 – 143 .
  • Guner , OF . 2000 . Pharmacophore Perception, Development, and Use in Drug Design , La Jolla, CA : International University Line .
  • Langer , T and Hoffmann , RD . 2006 . Pharmacophores and Pharmacophore Searches , Weinheim, Germany : Wiley-VCH .

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.