Biomedical subjects

Roberta Bursi

Publications and source records attributed to Roberta Bursi.

4 recordsLinked to original sources

PubMed2005

Derivation and validation of toxicophores for mutagenicity prediction.

Mutagenicity is one of the numerous adverse properties of a compound that hampers its potential to become a marketable drug. Toxic properties can often be related to chemical structure, more specifically, to particular substructures, which are generally identified as toxicophores. A number of toxicophores have already been identified in the literature. This study aims at increasing the current degree of reliability and accuracy of mutagenicity predictions by identifying novel toxicophores from the application of new criteria for toxicophore rule derivation and validation to a considerably sized mutagenicity dataset. For this purpose, a dataset of 4337 molecular structures with corresponding Ames test data (2401 mutagens and 1936 nonmutagens) was constructed. An initial substructure-search of this dataset showed that most mutagens were detected by applying only eight general toxicophores. From these eight, more specific toxicophores were derived and approved by employing chemical and mechanistic knowledge in combination with statistical criteria. A final set of 29 toxicophores containing new substructures was assembled that could classify the mutagenicity of the investigated dataset with a total classification error of 18%. Furthermore, mutagenicity predictions of an independent validation set of 535 compounds were performed with an error percentage of 15%. Since these error percentages approach the average interlaboratory reproducibility error of Ames tests, which is 15%, it was concluded that these toxicophores can be applied to risk assessment processes and can guide the design of chemical libraries for hit and lead optimization.

Databases, Factual↗

PubMed2003

The binding mode of progesterone to its receptor deduced from molecular dynamics simulations.

An unambiguous understanding of the binding mode of human progesterone to its receptor still eludes experimental search. According to the X-ray structure of the ligand-binding domain, only one (O3) of the two keto groups at the ligand ends (O3 and O20) should play a role. This result is in conflict with chemical intuition and the results of site-directed mutagenesis experiments. Herein, we report classical molecular dynamics simulations that reveal the dynamic nature of the binding in solution, elucidate the reasons why X-ray studies failed to determine the role of O20, and clarify the effects of the mutations. The predictive power of the force field is ensured by the consistent introduction of a first-principles representation of the ligand.

Binding Sites↗

PubMed2003

Structure-activity relationship study of human liver microsomes-catalyzed hydrolysis rate of ester prodrugs of MENT by comparative molecular field analysis (CoMFA).

A series of MENT esters (3-71) was designed, prepared and tested to study the structure-activity relationship (SAR) of the hydrolysis rate with human liver microsomes of these prodrugs. Compounds were obtained covering a wide range of metabolic stability. The results are useful for the proper selection of prodrugs for different pharmaceutical formulations to deliver the potent and prostate-sparing androgen MENT. The MENT esters can especially be administered for male hormone replacement therapy and male contraception. Comparative molecular field analysis (CoMFA) was applied to a dataset of 28 esters, for which ED50 values could be obtained. The CoMFA model where the electrostatic and H-bond molecular fields were combined turned out to be most predictive. Despite the limited size of the dataset, CoMFA can help to rationalize the SAR of the ester hydrolysis rate of ester prodrugs of MENT.

Esters↗

PubMed2002

A three-dimensional quantitative structure-activity relationship study of heparin-binding epidermal growth factor shedding inhibitors using comparative molecular field analysis.

Despite the lack of structural information on the heparin-binding (HB) epidermal growth factor (EGF) shedding putative target enzyme, the design of potent HB-EGF shedding inhibitors has been attempted by means of comparative molecular field analysis (CoMFA), a well-established 3D-QSAR technique. Two different binding modes, obtained by docking a flexible representative into the MMP-3 and TACE target enzymes, were considered as alignment rules for an in-house data set of 50 HB-EGF shedding inhibitors. CoMFA models were derived with the standard steric, electrostatic, and Bohacek and McMartin's H-bond molecular fields. These fields were used individually or in combination. For both alignments, the H-bond field alone yielded the best statistical models. From the analysis of the CoMFA contours, ideas for testing the size of the S1' pocket and suggestions for the design of new inhibitors came forward, resulting in the synthesis and testing of four new inhibitors. Three of four compounds turned out to possess from good (IC(50) = 0.56 and 0.60 microM) to excellent (IC(50) = 0.13 microM) inhibitory activity. The hypothesis that, upon binding, the S1' pocket in the vicinity of the R(1) benzene ring must be narrow in size was confirmed by the weak activity (IC(50) = 1.1 microM) of the fourth compound. The experimental profile of these new inhibitors does suggest the MMP-3 alignment as the most plausible one for HB-EGF shedding inhibitors.

Epidermal Growth Factor↗