Modeling topoisomerase-DNA interactions and design of trapping inhibitors used for cancer

Persistent Link:
http://hdl.handle.net/10150/282629
Title:
Modeling topoisomerase-DNA interactions and design of trapping inhibitors used for cancer
Author:
Soaring Bear, 1947-
Issue Date:
1998
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Topoisomerase inhibiting chemotherapy is most appropriate in cancers containing high levels of topoisomerase. Study of these drugs is particularly difficult because two receptors, enzyme plus DNA, are involved. Genes of all three known human topoisomerases have neighboring oncogenes and those amplified receptors may be used to target topoisomerase inhibitors to transformed cells. To facilitate design of inhibitors, modeling tools of graphic imaging, sequence analysis, homology, molecular dynamics, energy evaluation, and QSAR were used. The principle findings are: (a) The widely accepted model of 5' attachment to DNA and 5' overhang is inconsistent with topoisomerase structure; 3' overhang is more likely. (b) The active site region near the catalytic tyrosine hydroxyl is well conserved between yeast and humans with some exceptions: 4 Å away Glu554->His566 is likely to modify the proton transport of the trans-esterification reaction conducted by this enzyme; two base pairs away, the yeast Asp 552 appears to probe the DNA major groove and becomes an oppositely charged Arg 565 in humans; 8-15 A away along the probable location of DNA backbone, the acid pair Glu-Asp 512-13 is conserved and repeated in humans as Glu-Asp-Glu-Asp (522-5); these residues might coordinate the required Mg2+ along with the conserved Asp 635 (644 in humans); the acidic triad 590-2 evolves to a hydroxy triad and might provide a proton transport pathway for the trans-esterification reaction. (c) Drug resistant mutant structure analysis suggests multiple sites of action on topoisomerase and suggests the region of DNA binding. (d) Prediction of intercalator binding to DNA is correctly ranked by molecular mechanics for amonafide and azonafide; however, there remains significant error from experimental cytotoxicity; force field error derives from the approximation of electron orbitals as van der Waals spheres, lack of polarization functions, poor handling of hydrogen bond variability, and force field parameterization from packed protein crystals. (e) Wide variability of the azonafide analogs on whole cell assays makes QSAR difficult and suggests other biochemical pathways are affected; the measurements need to be redone on a simple enzyme-DNA assay.
Type:
text; Dissertation-Reproduction (electronic)
Keywords:
Health Sciences, Oncology.; Health Sciences, Pharmacology.; Biophysics, Medical.; Health Sciences, Oncology.
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Pharmacy Practice and Science
Degree Grantor:
University of Arizona
Advisor:
Remers, William A.

Full metadata record

DC FieldValue Language
dc.language.isoen_USen_US
dc.titleModeling topoisomerase-DNA interactions and design of trapping inhibitors used for canceren_US
dc.creatorSoaring Bear, 1947-en_US
dc.contributor.authorSoaring Bear, 1947-en_US
dc.date.issued1998en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractTopoisomerase inhibiting chemotherapy is most appropriate in cancers containing high levels of topoisomerase. Study of these drugs is particularly difficult because two receptors, enzyme plus DNA, are involved. Genes of all three known human topoisomerases have neighboring oncogenes and those amplified receptors may be used to target topoisomerase inhibitors to transformed cells. To facilitate design of inhibitors, modeling tools of graphic imaging, sequence analysis, homology, molecular dynamics, energy evaluation, and QSAR were used. The principle findings are: (a) The widely accepted model of 5' attachment to DNA and 5' overhang is inconsistent with topoisomerase structure; 3' overhang is more likely. (b) The active site region near the catalytic tyrosine hydroxyl is well conserved between yeast and humans with some exceptions: 4 Å away Glu554->His566 is likely to modify the proton transport of the trans-esterification reaction conducted by this enzyme; two base pairs away, the yeast Asp 552 appears to probe the DNA major groove and becomes an oppositely charged Arg 565 in humans; 8-15 A away along the probable location of DNA backbone, the acid pair Glu-Asp 512-13 is conserved and repeated in humans as Glu-Asp-Glu-Asp (522-5); these residues might coordinate the required Mg2+ along with the conserved Asp 635 (644 in humans); the acidic triad 590-2 evolves to a hydroxy triad and might provide a proton transport pathway for the trans-esterification reaction. (c) Drug resistant mutant structure analysis suggests multiple sites of action on topoisomerase and suggests the region of DNA binding. (d) Prediction of intercalator binding to DNA is correctly ranked by molecular mechanics for amonafide and azonafide; however, there remains significant error from experimental cytotoxicity; force field error derives from the approximation of electron orbitals as van der Waals spheres, lack of polarization functions, poor handling of hydrogen bond variability, and force field parameterization from packed protein crystals. (e) Wide variability of the azonafide analogs on whole cell assays makes QSAR difficult and suggests other biochemical pathways are affected; the measurements need to be redone on a simple enzyme-DNA assay.en_US
dc.typetexten_US
dc.typeDissertation-Reproduction (electronic)en_US
dc.subjectHealth Sciences, Oncology.en_US
dc.subjectHealth Sciences, Pharmacology.en_US
dc.subjectBiophysics, Medical.en_US
dc.subjectHealth Sciences, Oncology.en_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplinePharmacy Practice and Scienceen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorRemers, William A.en_US
dc.identifier.proquest9829368en_US
dc.identifier.bibrecord.b38554306en_US
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