Molecular similarity: the introduction of flexible fitting

Rapid evaluation of molecular shape similarity index using pairwise calculation of the nearest atomic distances

Rapid evaluation method for obtaining molecular shape similarity index using pairwise calculation of the nearest atomic distance respected to the template atoms was investigated. This method for calculations of similarity indices remarkably reduced required time compared with hitherto methods (especially 2 or 3 orders of magnitude faster than the previous grid-based evaluation technique) and gave without clear loss of preciseness. The potential of these improvements and possible further enhancements are discussed.

Molecular surface-volume and property matching to superpose flexible dissimilar molecules

Steric complementarity is a prerequisite for ligand-receptor recognition; this implies that drugs with a common receptor binding site should possess sterically similar binding surfaces. This principle is used as the basis for an automatic and unbiased method that superposes molecules. One molecule is rotated and translated to maximize the overlap between the two molecular surface volumes. A fast grid-based method is used to determine the extent of this overlap, and this is optimized using simulated annealing. Matches with high steric similarity scores are then sorted on the basis of both hydrogen-bond and electrostatic similarity between the matched molecules. Flexible molecules are treated as a set of rigid representative conformers. The algorithm has correctly predicted superpositions between a number of paris of molecules, according to crystallographic data from ligands that have been co-crystallized at common enzyme binding sites.

Relative binding orientations of adenosine A1 receptor ligands--a test case for Distributed Multipole Analysis in medicinal chemistry

The electrostatic properties of adenosine-based agonists and xanthine-based antagonists for the adenosine A1 receptor were used to assess various proposals for their relative orientation in the unknown binding site. The electrostatic properties were calculated from distributed multipole representations of SCF wavefunctions. A range of methods of assessing the electrostatic similarity of the ligands were used in the comparison. One of the methods, comparing the sign of the potential around the two molecules, gave inconclusive results. The other approaches, however, provided a mutually complementary and consistent picture of the electrostatic similarity and dissimilarity of the molecules in the three proposed relative orientations. This was significantly different from the results obtained previously with MOPAC AM1 point charges. In the standard model overlay, where the aromatic nitrogen atoms of both agonists and antagonists are in the same position relative to the binding site, the electrostatic potentials are so dissimilar that binding to the same receptor site is highly unlikely. Overlaying the N6-region of adenosine with that near C8 of theophylline (the N6-C8 model) produces the greatest similarity in electrostatic properties for these ligands. However, N6-cyclopentyladenosine (CPA) and 1,3-dipropyl-8-cyclopentyl-xanthine (DPCPX) show greater electrostatic similarity when the aromatic rings are superimposed according to the flipped model, in which the xanthine ring is rotated around its horizontal axis. This difference is mainly attributed to the change in conformation of N6-substituted adenosines and could result in a different orientation for theophylline and DPCPX within the receptor binding site. However, it is more likely that DPCPX also binds according to the N6-C8 model, as this model gives the best steric overlay and would be favoured by the lipophilic forces, provided that the binding site residues could accommodate the different electrostatic properties in the N6/N7-region. Finally, we have shown that Distributed Multipole Analysis (DMA) offers a new, feasible tool for the medicinal chemist, because it provides the use of reliable electrostatic models to determine plausible relative binding orientations.

Fundamentals of drug design from a biophysical viewpoint

Drug design means many things to many people. Commercially the aim is the development of compounds that can be patented and meet a variety of regulatory standards. In drug design, for medical purposes, toxicity and bio-availability are major considerations.

An exploration of a novel strategy for superposing several flexible molecules

This paper describes a computational strategy for the superposition of a set of flexible molecules. The combinatorial problems of searching conformational space and molecular matching are reduced drastically by the combined use of simulated annealing methods and cluster analysis. For each molecule, the global minimum of the conformational energy is determined by annealing and the search trajectory is retained in a history file. All the significantly different low-energy conformations are extracted by cluster analysis of data in the history file. Each pair of molecules, in each of their significantly different conformations, is then matched by simulated annealing, using the difference-distance matrix as the objective function. A set of match statistics is then obtained, from which the best match taken from all different conformations can be found. The molecules are then superposed either by reference to a base molecule or by a consensus method. This strategy ensures that as wide a range of conformations as possible is considered, but at the same time that the smallest number of significantly different conformations is used. The method has been tested on a set of six angiotensin II antagonists with between 7-11 rotatable bonds.

Similarity screening of molecular data sets

Three-dimensional (3D)-database searches are now being widely applied to determine potential new active molecules. Many structural data sets obtained as a result of these searches are still large in size. In this paper we apply molecular similarity calculations as a rapid method to screen two such data sets. In the first investigation, synthetic candidates, produced as a result of a tendamistat beta-turn mimic search, were tested for their ability to imitate the beta-turn backbone. In the second study, structures extracted through a histamine pharmacophore query search were examined on the basis of their electronic similarity to histamine. Molecular similarity is shown to provide a rapid means of gaining insight into the composition of molecular data sets, with possible implications for future full 3D-database searches.

The calculation of molecular similarity: alternative formulas, data manipulation and graphical display

The use of electrostatic potential comparisons between molecules for the elucidation of structure activity relationships is now a well-established modeling technique. The Carbo and Hodgkin similarity indices are used extensively to make quantitative comparisons of this nature; yet their roots are found in the overlap of electron density distribution, with both formulas utilizing a product-based numerator. Two new similarity indices are suggested that calculate the electrostatic potential similarity using a difference-based numerator. The form of the new indices allows the creation of additional software functions that enhance the flexibility of similarity calculations and permit the creation of similarity maps. The general properties of these software functions and all indices are discussed and applied to a series of dopamine D2 receptor agonists.

OVID and SUPER: two overlap programs for drug design

Two programs, OVID and SUPER, for exploring the similarity of molecules with respect to their action at a receptor are described. OVID accepts two molecules as input and optimizes the three-dimensional overlap of specified atoms in one molecule with specified atoms in the second molecule. The result is expressed as a percent of the theoretical maximum. OVID gives a quantitative measure of the extent of a guessed correspondence between two molecules based on volume overlap of selected atoms. The Achilles' heel of OVID is that the correspondence between the two molecules has to be guessed. We realized that it would be better to systematically examine all possible correspondences of two structures to minimize the chance of overlooking a superior correspondence. We created SUPER to satisfy this need. SUPER accepts two molecules as input and finds the top twenty correspondences of their surfaces and charge distributions, giving a quantitative measure of the extent of each correspondence. An instructive example of the application of OVID and SUPER to the design of leukotriene D4 receptor antagonists is described. SUPER appears to be a practical brain-storming tool for the medicinal chemist trying to understand how molecules whose structures may not resemble one another in an obvious way can bind to the same site.