A new definition of molecula similarity in terms of electron density is proposed and a method for calculating similarity based on molecular electrostatic potential and molecular electric field introduced. It is applied to some simple isosteres.

The presence of multiple a,a-dialkyl amino acids such as a-methylalanine (a-aminoisobutyric acid, Aib) leads to predominantly helical structures, either with a-helical or 310-helical hydrogen bonding patterns. The crystal structure of emerimicin-(1-9) benzyl ester (Ac-Phe-Aib-Aib-AibVal-Gly-Leu-Aib-Aib-OBzl) reported here shows essentially pure a-helical character, whereas other similar compounds show predominantly 310-helical structures. The factors that govern helical preference include the inherent relative stability of the a-helix compared with the 310-helix, the extra hydrogen bond seen with 310-helices, and the enhanced electrostatic dipolar interaction of the 310-helix when packed in a crystalline lattice. The balance of these forces, when combined with the steric requirements of the amino acid side chains, determines the relative stability of the two helical conformations under a given set of experimental conditions. The presence of a,a-dialkyl amino acids in microbial natural products, such as the peptaibol antibiotics, requires novel biosynthetic pathways to produce and incorporate these unusual amino acids in the face of the usual ribosomal mechanisms available for normal amino acids. This argues strongly for a special role related to function, one aspect of which may be their increased resistance to proteolytic degradation. Another aspect is the conformational restrictions imposed by these amino acids as first pointed out by Marshall and Bosshard (1, 2) and verified by others (3-7). While most work has focused on a-methylalanine (a-aminoisobutyric acid, Aib), a-ethylalanine (isovaline) has also been found to be a natural component of several peptaibol antibiotics (8,9). In addition, chiral a,a-dialkyl amino acids, such as amethylphenylalanine, have been incorporated into naturally occurring peptides in an effort to restrict their conformational freedom (10, 11).From the Ramachandran plots published by Marshall and Bosshard in 1972 (1), the presence of an additional alkyl substituent on the a-carbon severely restricted the values of the torsional variables 4 and qk as compared with those available to normal amino acids. While the two major allowed conformational areas were associated with either right-or left-handed helical conformations (both a and 310), the calculation also revealed other sets of energetically feasible values for 4 and q, adjacent to the a,a-dialkyl residue associated with extended structures as well as turns. The effect on conformation of alkyl groups larger than methyl as substituents in a,a-dialkyl amino acids has also been investigated (11,12). Despite the variety of conformations theoretically available to a,a-dialkyl amino acids, the impact of multiple substitutions ofthis type of amino acid on the overall conformation of a peptide is dramatic. The crystal structure of alamethicin (13), which contains 8 Aib residues out of 20, is predominantly a-helical, with NMR data (14) supporting a similar solution conformation in methanol. A review (15) of crystal structures of tr...

In order to identify novel chemical classes of factor Xa inhibitors, five scoring functions (FlexX, DOCK, GOLD, ChemScore and PMF) were engaged to evaluate the multiple docking poses generated by FlexX. The compound collection was composed of confirmed potent factor Xa inhibitors and a subset of the LeadQuest screening compound library. Except for PMF the other four scoring functions succeeded in reproducing the crystal complex (PDB code: 1FAX). During virtual screening the highest hit rate (80%) was demonstrated by FlexX at an energy cutoff of -40 kJ/mol, which is about 40-fold over random screening (2.06%). Limited results suggest that presenting more poses of a single molecule to the scoring functions could deteriorate their enrichment factors. A series of promising scaffolds with favorable binding scores was retrieved from LeadQuest. Consensus scoring by pair-wise intersection failed to enrich the hit rate yielded by single scorings (i.e. FlexX). We note that reported successes of consensus scoring in hit rate enrichment could be artificial because their comparisons were based on a selected subset of single scoring and a markedly reduced subset of double or triple scoring. The findings presented in this report are based upon a single biological system and support further studies.

An analytic method which permits the comparison of molecular electrostatic potential is introduced. The new technique fits the inverse distance dependence of the potential to an expansion of Gaussian functions and applies these functions to the Carbo similarity index. The major advantages of this approach are the very rapid computational speeds (2 orders of magnitude faster than previous methods) and superior convergence properties achieved during optimization of intermolecular electrostatic potential overlaps.

No abstract