Biomedical subjects

Georgia B McGaughey

Publications and source records attributed to Georgia B McGaughey.

9 recordsLinked to original sources

PubMed2006

Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1).

We describe the discovery and optimization of tertiary carbinamine derived inhibitors of the enzyme beta-secretase (BACE-1). These novel non-transition-state-derived ligands incorporate a single primary amine to interact with the catalytic aspartates of the target enzyme. Optimization of this series provided inhibitors with intrinsic and functional potency comparable to evolved transition state isostere derived inhibitors of BACE-1.

Amyloid Precursor Protein Secretases↗

PubMed2006

Beta-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites.

BACE-1 is a flexible enzyme with experimentally determined motion in the flap region, the catalytic aspartates, and the 10s loop. Four in-house crystallographically determined complexes of tertiary carbinamine inhibitors revealed 10s loop motion in the S(3) pocket. These X-ray structures were used to correlate K(i) values, which span over five orders of magnitude, with the calculated interaction energy, using the Merck Molecular Force Field for a series of 19 tertiary carbinamine inhibitors.

Amyloid Precursor Protein Secretases↗

PubMed2006

Evaluating scoring functions for docking and designing beta-secretase inhibitors.

Several simple scoring methods were examined for 2 series of beta-secretase (BACE-1) inhibitors to identify a docking/scoring protocol which could be used to design BACE-1 inhibitors in a drug discovery program. Both the PLP1 score and MMFFs interaction energy (E(inter)) performed as well or better than more computationally intensive methods for a set of substrate-based inhibitors, while the latter performed well for both sets of inhibitors.

Amyloid Precursor Protein Secretases↗

PubMed2006

Scoring of KDR kinase inhibitors: using interaction energy as a guide for ranking.

Within a congeneric series of ATP-competitive KDR kinase inhibitors, we determined that the IC(50) values, which span four orders of magnitude, correlated best with the calculated ligand-protein interaction energy using the Merck Molecular Force Field (MMFFs(94)). Using the ligand-protein interaction energy as a guide, we outline a workflow to rank order virtual KDR kinase inhibitors prior to synthesis. When structural information of the target is available, the ability to score molecules a priori can be used to rationally select reagents. Our implementation allows one to select thousands of readily available reagents, enumerate compounds in multiple poses and score molecules in the active site of a protein within a few hours. In our experience, virtual library enumeration is best used when a correlation between computed descriptors/properties and IC(50) or K (i) values has been established.

Binding Sites↗

PubMed2005

Web enabling technology for the design, enumeration, optimization and tracking of compound libraries.

Motivated by the need to augment Merck's in-house small molecule collection, web-based tools for designing, enumerating, optimizing and tracking compound libraries have been developed. The path leading to the current version of this Virtual Library Tool Kit (VLTK) is discussed in context of the (then) available commercial offerings and the constraints and requirements imposed by the end users. Though the effort was initiated to simplify the tasks of designing novel, drug-like and diverse compound libraries containing between 2K-10K unique entities, it has also evolved into a powerful tool for outsourcing syntheses as well as lead identification and optimization. The web tool includes components that select reagents, analyze synthons, identify backup reagents, enumerate libraries, calculate properties, optimize libraries and finally track the synthesized compounds through biological assays. In addition to accommodating project specific designs and virtual 3D library scanning, the application includes tools for parallel synthesis, laboratory automation and compound registration.

Combinatorial Chemistry Techniques↗

PubMed2004

The discovery of N-(1,3-thiazol-2-yl)pyridin-2-amines as potent inhibitors of KDR kinase.

An azo-dye lead was modified to a novel N-(1,3-thiazol-2-yl)pyridin-2-amine series of KDR kinase inhibitors through the use of rapid analog libraries. This new class has been found to be potent, selective, and of low molecular weight. Molecular modeling has postulated an interesting conformational preference and binding mode for these compounds in the active site of the enzyme.

Amines↗

PubMed2004

Three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses of choline acetyltransferase inhibitors.

As a basis for predicting structural features that may lead to the design of more potent and selective inhibitors of choline acetyltransferase (ChAT), the three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were carried out on a series of trans-1-methyl-4-(1-naphthylvinyl)pyridinium (MNVP+) analogs, which are known ChAT inhibitors. 3D-QSAR studies were carried out using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. Since these inhibitors have extremely shallow potential energy minimum energy wells and low barriers to rotation, two dihedral angles unique to these inhibitors were systematically modified to reflect the energetically preferred conformations as determined by force field calculations. An optimum alignment rule was devised based on the conformations obtained from the molecular mechanics studies, using a common substructure alignment method. The studies involve a set of 21 compounds and experimentally determined molar IC50 values were used as the dependent variable in the analysis. The 3D-QSAR models have conventional r2-values of 0.953 and 0.954 for CoMFA and CoMSIA, respectively; similarly, cross-validated coefficient q2-values of 0.755 and 0.834 for CoMFA and CoMSIA, respectively, were obtained. On the basis of these predictive r2-values the model was tested using previously determined IC50 values. CoMSIA 3D-QSAR yielded better results than CoMFA.

Choline O-Acetyltransferase↗

PubMed2004

Property-based design of KDR kinase inhibitors.

Small molecule inhibitors of KDR kinase activity have typically possessed poor intrinsic physical properties including low aqueous solubility and high lipophilicity. These features have often conferred limited cell permeability manifested in low levels of cell-based KDR inhibitory activity and oral bioavailability. Thus, the design of inhibitors with appropriate physical properties has played a critical role in the development of clinical candidates. We present a variety of structural modifications that have afforded improvements in physical properties and thereby have addressed suboptimal cellular potency and pharmacokinetics for three unique classes of KDR kinase inhibitors.

Animals↗

PubMed2004

Progress towards the development of a HIV-1 gp41-directed vaccine.

The HIV-1 gp41 envelope glycoprotein mediates fusion of the viral and cellular membranes. The core of the gp41 ectodomain undergoes a receptor-triggered conformational transition forming a trimeric, alpha-helical coiled-coil structure. This trimer-of-hairpins species facilitates insertion of the viral envelope protein into the host cell membrane promoting viral entry. The prefusogenic conformation of gp41 is capable of stimulating a neutralizing antibody immune response and is therefore an attractive therapeutic target. Several broadly neutralizing HIV-1 monoclonal antibodies which bind to gp41 have been characterized and include 4E10, Z13 and 2F5. A conserved segment of gp41 (residues 661-684) has been identified as the epitope for the HIV-1 neutralizing antibody 2F5 (MAb 2F5). MAb 2F5 has attracted considerable attention because of the highly conserved recognition epitope and the ability to neutralize both laboratory-adapted and primary viral isolates. Antibodies which recognize the immunodominant regions of gp41 may provide protection against HIV infection if elicited at appropriate concentrations. Here we review the rational design, structure-activity relationships and conformational features of both linear and constrained peptide immunogens incorporating variants of both the 2F5 epitope and the gp41 ectodomain. This review describes a rational design approach combining structural characterization with traditional SAR to optimize MAb 2F5 antibody affinities of gp41-based peptide immunogens. The immunogens are shown to stimulate a high titer, peptide-specific immune response; however, the resulting antisera were incapable of viral neutralization. The implication of these findings with regard to structural and immunological considerations is discussed.

AIDS Vaccines↗