Jeffrey J. Sutherland

Relating molecular properties and in vitro assay results to in vivo drug disposition and toxicity outcomes.

A primary goal of lead optimization is to identify compounds with improved absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. A number of reports have linked computed molecular properties to desirable in vivo ADMET outcomes, but a significant limitation of these analyses is the failure to control statistically for possible covariates. We examine the relationship between molecular properties and in vitro surrogate assays vs in vivo properties within 173 chemical series from a database of 3773 compounds with rodent pharmacokinetic and toxicology data. This approach identifies the following pairs of surrogates as most predictive among those examined: rat primary hepatocyte (RPH) cytolethality/volume of distribution (V(d)) for in vivo toxicology outcomes, scaled microsome metabolism/calculated logP for in vivo unbound clearance, and calculated logD/kinetic aqueous solubility for thermodynamic solubility. The impact of common functional group substitutions is examined and provides insights for compound design.

A novel type 2A (Group II) von Willebrand disease mutation (L1503Q) associated with loss of the highest molecular weight von Willebrand factor multimers

Summary.  Type 2A von Willebrand disease (VWD) is characterized by decreased platelet‐dependent function of von Willebrand factor (VWF) associated with an absence of high‐molecular‐weight multimers. In this study, sequence analysis of the VWF gene from a Type 2A VWD patient showed a novel, heterozygous T→A transversion at nucleotide 4510, resulting in the non‐conservative substitution of L1503Q in the mature VWF subunit. This substitution, which was not found in 55 unrelated normal individuals, was reproduced by in vitro site directed mutagenesis of a full‐length VWF cDNA and was subsequently expressed in COS‐7 cells. The corresponding recombinant mutant VWF protein was partially retained in COS‐7 cells yet the full spectrum of multimers was observed, suggesting that the absence of the highest molecular weight multimers results from increased proteolysis. The recombinant mutant VWF protein was digested with the ADAMTS13 protease from VWF‐depleted plasma and the aberrant VWF multimer pattern was observed. These results suggest that the L1503Q substitution induces a conformational change in the VWF protein, which increases the proteins susceptibility to proteolysis. A three‐dimensional model of the A2 domain demonstrates that the L1503Q mutation and the physiological proteolytic cleavage site for ADAMTS13 (Y1605‐M1606) are localized close together in two adjacent parallel β‐sheets. The mutation L1503Q does not significantly disrupt the conformation of the protein; thus the subtle loss of multimers in this patient may be due to altered interactions with the ADAMTS13 protease.

Theoretical structural explanation for Group I and Group II, type 2A von Willebrand disease mutations

L . A . O ’BR I E N , J . J . SUTHER LAND,* D . F . WEAVER and D . L I LL ICRAP Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, K7L 3 N6, Canada; *Department of Chemistry, Queen’s University, Kingston, Ontario, K7L 3 N6, Canada; and Departments of Medicine and Chemistry, and School of Biomedical Engineering, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada

Predicting the Accuracy of Ligand Overlay Methods with Random Forest Models

The accuracy of binding mode prediction using standard molecular overlay methods (ROCS, FlexS, Phase, and FieldCompare) is studied. Previous work has shown that simple decision tree modeling can be used to improve accuracy by selection of the best overlay template. This concept is extended to the use of Random Forest (RF) modeling for template and algorithm selection. An extensive data set of 815 ligand-bound X-ray structures representing 5 gene families was used for generating ca. 70,000 overlays using four programs. RF models, trained using standard measures of ligand and protein similarity and Lipinski-related descriptors, are used for automatically selecting the reference ligand and overlay method maximizing the probability of reproducing the overlay deduced from X-ray structures (i.e., using rmsd < or = 2 A as the criteria for success). RF model scores are highly predictive of overlay accuracy, and their use in template and method selection produces correct overlays in 57% of cases for 349 overlay ligands not used for training RF models. The inclusion in the models of protein sequence similarity enables the use of templates bound to related protein structures, yielding useful results even for proteins having no available X-ray structures.

A new dopant for ferroelectric liquid crystals with a chiral 2,2′-spirobiindan-1,1′-dione core

The synthesis and resolution of the chiral dopant (R)-2,2′-spirobiindan-5,5′-diheptyloxy-1,1′-dione is described. This new compound is doped in achiral SmC liquid crystal hosts to give a ferroelectric SmC* phase. The polarization power of the dopant varies with the core structure of the SmC host, from <+10 to +803 nC cm−2, and the sign of spontaneous polarization induced by the (R)-enantiomer of the chiral dopant is consistent with that predicted by the Boulder model.

Synthesis of 4-Ethoxycarbonyl-5-arylisoxazolidines via Regioselective Cycloaddition

Abstract Convenient synthesis of a series of 4-ethoxycarbonyl-5-arylisoxazolidines (6a–c) is described, via N-tetrahydropyran-2-yl protected intermediates (5a–c). Regioselectivity of this reaction is confirmed by high-field NMR experiments, and is shown to agree with theoretical predictions