Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly homologous and convergent binding sites. Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB

Contact area difference (cad): A robust measure to evaluate accuracy of protein models

A simple uni®ed measure to evaluate the accuracy of three-dimensional atomic protein models is proposed. This measure is a normalized sum of absolute differences of residue-residue contact surface areas calculated for a reference structure and a model. It employs more rigorous quantitative evaluation of a contact than previously used contact measures. We argue that the contact area difference (CAD) number is a robust single measure to evaluate protein structure predictions in a wide range of model accuracies, from ab initio and threading models to models by homology, since it re¯ects both backbone topology and side-chain packing, is smooth, continuous and threshold-free, is not sensitive to typical crystallographic errors and ambiguities, adequately penalizes domain and/or secondary structure rearrangements and protein plasticity, and has consistent linear and matrix representations for more detailed analysis. The CAD quality of crystallographic structures, NMR structures, models by homology, and unfolded and misfolded structures is evaluated. It is shown that the CAD number discriminates between models better than Cartesian rootmean-square deviation (cRMSD). Structural variability of the NMR structures was found to be three times larger than deformations of crystallographic structures in different packing environments. # 1997 Academic Press Limite

Bivalent Carbamates as Novel Control Agents of the Malaria Mosquito, Anopheles gambiae

Widespread pyrethroid resistance has caused an urgent need to develop new insecticides for control of the malaria mosquito, Anopheles gambiae. Insecticide discovery efforts were directed towards the construction of bivalent inhibitors that occupy both the peripheral and catalytic sites of the mosquito acetylcholinesterase (AChE). It was hypothesized that this approach would yield a selective, high potency inhibitor that would also circumvent known catalytic site mutations (e.g. G119S) causing target site resistance. Accordingly, a series of bivalent phthalimide-pyrazole carbamates were prepared having an alkyl chain linker of varying length, along with other modifications. The most active compound was (1-(3-(1,3-dioxoisoindolin-2-yl)propyl)-1H-pyrazol-4-yl methylcarbamate, 8a), which has a chain length of three carbons, good mosquito anticholinesterase activity, and ca. 5-fold selectivity compared to human AChE. Moreover, this compound was toxic to mosquitoes by topical application (LD50 = 63 ng/female) with only 6-fold cross resistance in the Akron strain of Anopheles gambiae that showed 50- to 60-fold resistance to conventional carbamate insecticides. However, contact lethality in the WHO paper assay was disappointing. The implications of these results for design of new mosquitocides are discussed

Select Small Core Structure Carbamates Exhibit High Contact Toxicity to “Carbamate-Resistant” Strain Malaria Mosquitoes, <em>Anopheles gambiae</em> (Akron)

<div><p>Acetylcholinesterase (AChE) is a proven target for control of the malaria mosquito (<em>Anopheles gambiae</em>). Unfortunately, a single amino acid mutation (G119S) in <em>An. gambiae</em> AChE-1 (<em>Ag</em>AChE) confers resistance to the AChE inhibitors currently approved by the World Health Organization for indoor residual spraying. In this report, we describe several carbamate inhibitors that potently inhibit G119S <em>Ag</em>AChE and that are contact-toxic to carbamate-resistant <em>An. gambiae</em>. PCR-RFLP analysis was used to confirm that carbamate-susceptible G3 and carbamate-resistant Akron strains of <em>An. gambiae</em> carry wild-type (WT) and G119S AChE, respectively. G119S <em>Ag</em>AChE was expressed and purified for the first time, and was shown to have only 3% of the turnover number (<em>k</em>_cat) of the WT enzyme. Twelve carbamates were then assayed for inhibition of these enzymes. High resistance ratios (>2,500-fold) were observed for carbamates bearing a benzene ring core, consistent with the carbamate-resistant phenotype of the G119S enzyme. Interestingly, resistance ratios for two oxime methylcarbamates, and for five pyrazol-4-yl methylcarbamates were found to be much lower (4- to 65-fold). The toxicities of these carbamates to live G3 and Akron strain <em>An. gambiae</em> were determined. As expected from the enzyme resistance ratios, carbamates bearing a benzene ring core showed low toxicity to Akron strain <em>An. gambiae</em> (LC₅₀>5,000 μg/mL). However, one oxime methylcarbamate (aldicarb) and five pyrazol-4-yl methylcarbamates (<b>4a</b>–<b>e</b>) showed good to excellent toxicity to the Akron strain (LC₅₀ = 32–650 μg/mL). These results suggest that appropriately functionalized “small-core” carbamates could function as a resistance-breaking anticholinesterase insecticides against the malaria mosquito.</p> </div