The performance of several commercially available docking programs is compared in the context of virtual screening. Five different protein targets are used, each with several known ligands. The simulated screening deck comprised 1000 molecules from a cleansed version of the MDL drug data report and 49 known ligands. For many of the known ligands, crystal structures of the relevant protein-ligand complexes were available. We attempted to run experiments with each docking method that were as similar as possible. For a given docking method, hit rates were improved versus what would be expected for random selection for most protein targets. However, the ability to prioritize known ligands on the basis of docking poses that resemble known crystal structures is both method- and target-dependent.

The electrostatic contributions to free energies of solvation of several small molecules have been calculated, treating the solvent as a statistical continuum. The computational method is based on solving the linearized Poisson-Boltzmann equation for the electrostatic potentials using the finite-difference scheme. A careful study of convergence indicates the importance of a fine grid spacing, as well as the short comings of rotational averaging. The computed free energies of solvation are in excellent agreement with the experimental results as well as the free energy perturbation calculations. The free energies of hydration of the natural nucleic acid bases are calculated and shown to be somewhat sensitive to charge model.

The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fundamental issues and challenges involved in comparing various docking methods are discussed. Limitations of current technologies as well as future prospects are presented.

Oligonucleotides containing 2'-O-aminopropyl-substituted RNA have been synthesized. The 2'-O-(aminopropyl)adenosine (APA), 2'-O-(aminopropyl)cytidine (APC), 2'-O-(aminopropyl)-guanosine (APG), and 2'-O-(aminopropyl)uridine (APU) have been prepared in high yield from the ribonucleoside, protected, and incorporated into an oligonucleotide using conventional phosphoramidite chemistry. Molecular dynamics studies of a dinucleotide in water demonstrates that a short alkylamine located off the 2'-oxygen of ribonucleotides alters the sugar pucker of the nucleoside but does not form a tight ion pair with the proximate phosphate. A 5-mer with the sequence ACTUC has been characterized using NMR. As predicted from the modeling results, the sugar pucker of the APU moiety is shifted toward a C3'-endo geometry. In addition, the primary amine rotates freely and is not bound electrostatically to any phosphate group, as evidenced by the different sign of the NOE between sugar proton resonances and the signals from the propylamine chain. Incorporation of aminopropyl nucleoside residues into point-substituted and fully modified oligomers does not decrease the affinity for complementary RNA compared to 2'-O-alkyl substituents of the same length. However, two APU residues placed at the 3'-terminus of an oligomer gives a 100-fold increase in resistance to exonuclease degradation, which is greater than observed for phosphorothioate oligomers. These structural and biophysical characteristics make the 2'-O-aminopropyl group a leading choice for incorporation into antisense therapeutics. A 20-mer phosphorothioate oligonucleotide capped with two phosphodiester aminopropyl nucleotides targeted against C-raf mRNA has been transfected into cells via electroporation. This oligonucleotide has 5-10-fold greater activity than the control phosphorothioate for reducing the abundance of C-raf mRNA and protein.

The structure and stability of a DNA triple helix was examined by molecular dynamics (MD) simulation using an all-atom force field. A 1.3 ns simulation was performed on a d(CG*G)7 triple helix in a 1 M saltwater solution. The Ewald method was used to calculate the electrostatic interactions of the system. The behavior of the DNA in the saltwater solution was determined by examining the structure, energetics, and mobility of water and ions in the system. The simulation results for the helical parameters support the validity of a model-built triplex -DNA structure. A low root mean square deviation of the dynamic structure from the initial structure demonstrates the stability of the triplex in the salt solution. The sugar pseudorotation, the backbone conformations, and the average helical parameters suggest that the conformation of strands I and III is strictly neither A-form nor B-form, whereas the conformation of strand II remains near the A-form. A higher mobility of both the cytosine strand and the triplexforming guanine strand and also a longer residence time of water molecules in the spine of hydration were observed and are consistent with available NMR results.