Luminita Crisan

MTD-PLS: a PLS variant of the minimal topologic difference method. III. Mapping interactions between estradiol derivatives and the alpha estrogenic receptor.

A homogeneous collection of 45 estrogen agonist derivatives with relative binding affinities measured to the estrogen receptor from Ratus norvegicus was used. The quantitative structure-activity relationships were derived using an improved minimal topologic difference (MTD) method in a partial least-squares (PLS) variant. The spatially assigned analysis of fragment properties can provide receptor site maps, within the limits of the existing series. A steric misfit was found for the steroidal position 2; benefic hydrophobic and van der Waals (enhanced by high polarizability) interactions were found for the 17alpha-CH=CH-X group. MTD-PLS mapping results are confirmed by the experimentally derived estradiol-estrogen receptor binding site contacts (based on X-ray crystallography). Our results suggest that this MTD-PLS method can yield useful results for interactions with receptors of unknown 3D structure and, generally, for the steric rigidity of receptor sites.

ColBioS-FlavRC: A Collection of Bioselective Flavonoids and Related Compounds Filtered from High-Throughput Screening Outcomes

Flavonoids, the vastest class of natural polyphenols, are extensively investigated for their multiple benefits on human health. Due to their physicochemical or biological properties, many representatives are considered to exhibit low selectivity among various protein targets or to plague high-throughput screening (HTS) outcomes. The aim of this study is to highlight reliable, bioselective compounds sharing flavonoidic scaffolds in HTS experiments. A filtering scheme was applied to remove undesired flavonoids (and related compounds) from confirmatory PubChem bioassays. A number of 433 compounds addressing various protein targets form the core of the collection of bioselective flavonoids and related compounds (ColBioS-FlavRC). With an additional set of 2908 inactive related compounds, ColBioS-FlavRC offers the grounds for method optimization and validation. We exemplified the use of ColBioS-FlavRC by pharmacophore modeling, subsequently (externally) validated for virtual screening purposes. The early enrichment capabilities of the pharmacophore hypotheses were measured by means of the median exponential retriever operating curve enrichment (MeROCE), a suited metric in comparative evaluations of virtual screening methods. ColBioS-FlavRC is available in the Supporting Information and is freely accessible for further studies.

Retrospective group fusion similarity search based on eROCE evaluation metric.

In this study, a simple evaluation metric, denoted as eROCE was proposed to measure the early enrichment of predictive methods. We demonstrated the superior robustness of eROCE compared to other known metrics throughout several active to inactive ratios ranging from 1:10 to 1:1000. Group fusion similarity search was investigated by varying 16 similarity coefficients, five molecular representations (binary and non-binary) and two group fusion rules using two reference structure set sizes. We used a dataset of 3478 actives and 43,938 inactive molecules and the enrichment was analyzed by means of eROCE. This retrospective study provides optimal similarity search parameters in the case of ALDH1A1 inhibitors.

Combined molecular docking and QSAR study of fused heterocyclic herbicide inhibitors of D1 protein in photosystem II of plants

Cinnoline, pyridine, pyrimidine, and triazine herbicides were found be inhibitors of the D1 protein in photosystem II (D1 PSII) electron transport of plants. The photosystem II inhibitory activity of these herbicides, expressed by experimental

QSAR study and molecular docking on indirubin inhibitors of Glycogen Synthase Kinase-3

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Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors

pIC50 values, was modeled by a docking and quantitative structure-activity relationships study. A conformer ensemble for each of the herbicide structure was generated using the MMFF94s force field. These conformers were further employed in a docking approach, which provided new information about the rational “active conformations” and various interaction patterns of the herbicide derivatives with D1 PSII. The most “active conformers” from the docking study were used to calculate structural descriptors, which were further related to the inhibitory experimental

Structure-flammability relationship study of phosphoester dimers by MLR and PLS

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