Biomedical subjects

Miklos Feher

Publications and source records attributed to Miklos Feher.

10 recordsLinked to original sources

PubMed2006

Consensus scoring for protein-ligand interactions.

This article reviews the application of consensus scoring for cases when the target 3D structure is known. Comparing the performance of different methods is not a trivial task, and it appears that consensus scoring usually substantially improves virtual screening performance, contributing to better enrichments. It also seems to improve--albeit less dramatically--the prediction of bound conformations and poses. The prediction of binding energies is still rather inaccurate and although consensus scoring generally improves these predictions, more development is required before it can be used for this purpose in routine lead optimization.

Binding Sites↗

PubMed2005

In vitro evaluation of the anti-estrogenic activity of hydroxyl substituted diphenylnaphthyl alkene ligands for the estrogen receptor.

There is still a need for additional scaffolds to further explore tissue selectivity and improving efficacy of selective estrogen receptor modulators (SERMs). A series of hydroxyl substituted diphenylnaphthyl alkene ligands for the two estrogen receptors are described that arose from an initial de novo designed diphenylnaphthyl propylene ligand 1. All compounds gave K(i)s under 10 nM when assayed in the presence of ERalpha. Generally these compounds had very high affinity for both ER isotypes. Moving the hydroxyl group on naphthalene from the 6- to the 5-position of the alpha-naphthalene attached compounds (6b and 6e vs 6c and 6f) had little affect on ER binding nor did altering the position of the naphthalene attachment (alpha or beta) to the alkene moiety. In transfection assays none of the compounds displayed agonistic activity in the absence of E(2). In MCF-7 proliferation assays 6a-d, 6f and 12a-c successfully abrogated E(2) stimulation and resulted in greater than 50% inhibition at 1 microM, a level of efficacy similar to that obtained when the cells were treated with raloxifene. Our results show that this new class of SERMs are good candidates for further study as therapeutic agents for the treatment of breast cancer and osteoporosis.

Alkenes↗

PubMed2003

De novo design, synthesis, and evaluation of novel nonsteroidal phenanthrene ligands for the estrogen receptor.

Although there are many estrogen receptor antagonists with improved tissue selectivity profiles compared with tamoxifen, optimal tissue selectivity has not yet been demonstrated. As such there is still a need for additional diversity and new chemical scaffolds to allow for exploration of improved tissue selectivity. Here, we describe the discovery of a novel phenanthrene scaffold for estrogen receptor ligands utilizing a ligand based de novo design approach. The nanomolar binding of phenanthrenes, 12b,c, 14b,c, and 15 against human recombinant ER(alpha) indicates that our ligand based de novo design approach was successful. From a gene transfection assay, 12b,c, 14b,c, and 15 displayed only antagonistic activity with no observable agonistic activity. The alkyl 9,10-dihydrophenanthrene 16 (presumably a racemic mixture) was a substantially more potent ER binder than the phenanthrenes. It also displayed only antagonistic activity and was effective at inhibiting estradiol stimulated MCF-7 cell proliferation. These results demonstrate that this phenanthrene (and 9,10-dihydrophenanthrene) scaffold warrants further study as potential selective estrogen receptor modulators and/or pure antiestrogens.

Animals↗

PubMed2003

Synthesis and evaluation of a novel nonsteroidal-specific endothelial cell proliferation inhibitor.

The identification of agents with specific antiproliferative or cytostatic activity against endothelial cells has significant value for the treatment of pathologies associated with angiogenesis, including solid tumors. Here, we describe a novel substituted dibenzo[b,d]pyran-6-one scaffold, exemplified by structures 9a and 10, and report preliminary in vitro activity data indicating that this scaffold is a promising lead for the development of specific inhibitors of endothelial cell proliferation.

2-Methoxyestradiol↗

PubMed2003

De novo design, synthesis and evaluation of a non-steroidal diphenylnaphthyl propylene ligand for the estrogen receptor.

There is still a strong need for additional diversity and new chemical scaffolds to allow for the exploration of improved tissue selectivity and finding better selective estrogen receptor modulators (SERMs). Using a de novo design technology a diphenylnaphthyl propylene scaffold, exemplified by (E)-9b, with ER antagonist activity has been generated. It was prepared by alkylating 1-[4-methoxyphenyl)-2-(4-(2-chloroethoxy)phenyl]-1-propanone under metal halogen exchange conditions with 1-iodo-6-methoxy-naphthalene. Following dehydration and cleavage of the methoxy groups, (E)-9b was formed by displacement of the chloro group with pyrrolidine. (E)-9b binding to ER generated calculated K(i) values of 3.7 nM for hER(alpha) and 72 nM for hER(beta). The antagonism of (E)-9b was demonstrated in cell transfection assays using the ERE from the vitA2 promotor and the natural ER-responsive pS2 promotor. With increasing concentrations of (E)-9b, the E(2)-dependent response was efficiently inhibited demonstrating that (E)-9b could function as an anti-estrogen in these assays. Interestingly, ER(alpha) activity was inhibited even below basal levels suggesting that ligand-independent activity of ER(alpha) was also inhibited. Computational docking studies suggest that the placement of the hydroxyl group on the naphthalene group may not be optimal and we are currently exploring additional analogues.

Cells, Cultured↗

PubMedDate not supplied

Property distributions: differences between drugs, natural products, and molecules from combinatorial chemistry.

The differences between three different compound classes, natural products, molecules from combinatorial synthesis, and drug molecules, were investigated. The major structural differences between natural and combinatorial compounds originate mainly from properties introduced to make combinatorial synthesis more efficient. These include the number of chiral centers, the prevalence of aromatic rings, the introduction of complex ring systems, and the degree of the saturation of the molecule as well as the number and ratios of different heteroatoms. As drug molecules derive from both natural and synthetic sources, they cover a joint area in property space of natural and combinatorial compounds. A PCA-based scheme is presented that differentiates the three classes of compounds. It is suggested that by mimicking certain distribution properties of natural compounds, combinatorial products might be made that are substantially more diverse and have greater biological relevance.

Biological Products↗

PubMedDate not supplied

Fuzzy clustering as a means of selecting representative conformers and molecular alignments.

This paper describes the first application of fuzzy c-means clustering for the selection of representatives from assemblies of conformations or alignments. In case of alignments, their quality is taken into account using a weighted c-means scheme, developed in this work. The performance of fuzzy cluster validity measures, such as compactness, partition function, and entropy, are studied on several examples, but the visual 3D representation of data points is shown to be most beneficial in determining the optimum number of clusters. Fuzzy clustering is expected to perform better than crisp clustering methods in cases where there are a significant number of "outliers", such as in molecular dynamics simulations and molecular alignments.

Journal Article↗

PubMedDate not supplied

BHB: a simple knowledge-based scoring function to improve the efficiency of database screening.

A new knowledge-based scoring function was developed in this work to facilitate the rapid ranking of ligands in databases. The acronym of the method is BHB based on the descriptors it utilizes: buriedness, hydrogen bonding, and binding energy. Receptor buriedness is a measure of how well molecules occupy the binding pocket in comparison to known high-affinity ligands or, alternatively, whether they have contact with identified residues in the pocket. The possibility of hydrogen bond formation is checked for selected residues that are recognized as being important in the binding of known ligands. The approximate binding energy is calculated from the thermodynamic cycle using the optimized bound and free solvent conformations of the ligand-receptor system. The information necessary for the scoring function can ideally be gleaned from the 3D structure of the receptor-ligand complex. Alternatively, the descriptors can be derived from the 3D structure of the unbound receptor, provided this receptor has a known ligand that binds to the given site with nanomolar activity. We show that the new scoring functions provide up to 12 times improvement in enrichment compared to the popular commercial docking program GOLD.

Journal Article↗

PubMedDate not supplied

The use of consensus scoring in ligand-based virtual screening.

A new consensus approach has been developed for ligand-based virtual screening. It involves combining highly disparate properties in order to improve performance in virtual screening. The properties include structural, 2D pharmacophore and property-based fingerprints, scores derived using BCUT descriptors, and 3D pharmacophore approaches. Different approaches for the combination of all or some of these methods have been tested. Logistic regression and sum ranks were found to be the most advantageous in different pharmaceutical applications. The three major reasons consensus scoring appears to enrich data sets better than single scoring functions are (1) using multiple scoring functions is similar to repeated samplings, in which case the mean is closer to the true value than any single value, (2) due to the better clustering of actives, multiple sampling will recover more actives than inactives, and (3) different methods seem to agree more on the ranking of the actives than on the inactives. Furthermore, consensus results are not only better but are also more consistent across receptor systems.

Journal Article↗

PubMedDate not supplied

Novel 2D fingerprints for ligand-based virtual screening.

This paper describes the development of a set of new 2D fingerprints for the purposes of virtual screening in a pharmaceutical environment. The new fingerprints are based on established ones: the changes in their design included the introduction of overlapping pharmacophore feature types, feature counts for pharmacophore and structural fingerprints, as well as changes in the resolution in property description for property fingerprints. The effects of each of these changes on virtual screening performance were monitored using two types of training sets, emulating different stages in the drug discovery process. The results demonstrate that these changes all lead to an improvement in virtual screening performance.

Chemistry↗