Small molecules interaction predictions

Another way to predict protein-SM interactions is to assume that similar protein sequences bind similar SMs. This is a simple, yet powerful assumption, providing accurate interaction predictions, demonstrated in a number of studies. The actual implementation of this idea into a computational algorithm is limited only by human imagination and available time, so its discussion is beyond the scope of this chapter. One interesting sequence-based interaction prediction approach reported by Synder and co-workers [61] was used to create the small-molecule interaction database (SMID) (Fig. 2-12). Biologically relevant SMs were determined from three-dimensional x-ray crystal structures containing... 

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

GAs or other methods from evolutionary computation are applied in various fields of chemistry Its tasks include the geometry optimization of conformations of small molecules, the elaboration of models for the prediction of properties or biological activities, the design of molecules de novo, the analysis of the interaction of proteins and their ligands, or the selection of descriptors [18]. The last application is explained briefly in Section 9.7.6. 

The surface force apparatus (SFA) is a device that detects the variations of normal and tangential forces resulting from the molecule interactions, as a function of normal distance between two curved surfaces in relative motion. SFA has been successfully used over the past years for investigating various surface phenomena, such as adhesion, rheology of confined liquid and polymers, colloid stability, and boundary friction. The first SFA was invented in 1969 by Tabor and Winterton [23] and was further developed in 1972 by Israela-chivili and Tabor [24]. The device was employed for direct measurement of the van der Waals forces in the air or vacuum between molecularly smooth mica surfaces in the distance range of 1.5-130 nm. The results confirmed the prediction of the Lifshitz theory on van der Waals interactions down to the separations as small as 1.5 nm. 

The theory predicts a 1/R6 dependence of energy transfer rate on their separation distance, R, which is very steep. Deviation from this dependence is frequently observed for extended conjugated dye molecules, metal [38], and semiconductor [39] nanoparticles, the sizes of which are comparable with R, but the validity of this theory and 1/R6 dependence are confirmed in the studies of small dye molecules interacting at significant distances. 

For the optimal application of GPC to the separation of discrete small molecules, three factors should be considered. Solvent effects are minimal, but may contribute selectivity when solvent-solute interactions occur. The resolving power in SMGPC increases as the square root of the column efficiency (plate count). New, efficient GPC columns exist which make the separation of small molecules affordable and practical, as indicated by applications to polymer, pesticide, pharmaceutical, and food samples. Finally, the slope and range of the calibration curve are indicative of the distribution of pores available within a column. Transformation of the calibration curve data for individual columns yields pore size distributions from which useful predictions can be made regarding the characteristics of column sets. 

An application of the ROCS program has been reported recently (82). New scaffolds for small molecule inhibitors of the ZipA-FtsZ protein-protein interaction have been found. The shape comparisons are made relative to the bioactive conformation of a HTS hit, determined by X-ray crystallography. A followup X-ray crystallographic analysis also showed that ROCS accurately predicted the binding mode of the inhibitor. This result offers the first experimental evidence that validates the use of ROCS for scaffold hopping purposes. 

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