Hydrogen bonding plays an important role in the stabilization of complexes between HIV-1 protease (HIV-1 PR) and its inhibitors. The adequate treatment of the protease active site protonation state is important for accurate molecular simulations of the protonation state is important for accurate molecular simulations of the protease-inhibitor complexes. We have applied the free energy simulation/thermodynamic cycle approach to evaluate the relative binding affinities of the S vs R isomers of the U85548E inhibitor of the protease. Several mono- and diprotonation states of the catalytic aspartic acid residues of the protease active site were considered in the course of molecular simulations. The calculated difference in binding free energy of the S vs R isomers strongly depended on the location of proton(s), but in all cases the binding free energy of the S inhibitor was higher. On the basis of our calculations, we propose that in the HIV-1 PR-inhibitor complex only one catalytic aspartic acid residue is protonated and that the binding free energy of the S isomer is ca. 2.8 kcal/mol higher than that of the R isomer. The accuracy of these predictions shall be evaluated when binding affinities of both isomers become available.

The boronic acid functional group has been incorporated into various biologically important compounds. In order to study this class of compounds better with molecular mechanics, five alkyl-and arylboronic acids were calculated using ab initio methods (Spartan) at the RHF/6-31G * level. MM3 force field parameters were developed based on the theoretically calculated geometries, vibrational spectra, and torsional profiles.

The alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6-31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time-dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6-12 potential. The geometry of boronic acid moiety of the 6-31G* optimized methyl boronic acid was similar to that of the X-ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor-water and water-chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics forcefield parameters for alkyl boronic acids. 0 1994 by John Wiley & Sons, Inc.tease,3 and dihydro~rotase~ and of cell replicat i~n .~ Several side-chain derivatives of natural aamino acids such as leucine and phenylalanine, containing boronic acid moiety, were shown to be inhibitors of amino peptidases.6 ne c5 and c6 rofic acid derivatives of fie pyrimidine &splayed

Xylanase has been used in wood pulp bleaching in an effort to reduce chlorine release into the environment and pollution associated with paper production. The three-dimensional structure of xylanase is important to enable better understanding of the enzyme mechanism and to help design a more thermostable xylanase mutant. At the time this work was begun, there was no sequence homologous protein available for traditional sequence-based homology modeling. In order to circumvent this problem, the inverse protein folding approach was undertaken to find a suitable template structure. Model structures of Bacillus circuluns xylanase were built based on the database search results of related proteins. The model structures were refined and compared to the recently solved xylanase X-ray crystal structure. The overall structural similarity between the theoretical model and experimental structure demonstrate the usefulness of this approach. Disagreement in folding topology, however, warrants further research into the inverse protein folding approach.

Two series of thymidine analogs with a hydroxyalkylammonium(amine) moiety have been synthesized and evaluated for antitumor and antiviral activities. The hydroxyalkylammonium-(amine) group was introduced at the 5' position of the 2'-deoxyribose residue of thymidine or at a corresponding position in acyclic thymidine analogs. In order to increase the lipophilicity of these compounds and potentially enable them to cross the cell membrane, the free hydroxy group also was esterified with a long hydrocarbon chain. The hexadecanoyl analogs (compounds 1c, 1d, 7c, and 7d) showed moderate antitumor cytotoxicity against SV-28 and KB cell lines (IC50 approximately 20 microM). Compound 1d showed moderate anti-HIV activity (EC50 = 6.8 microM), while compound 5 showed weak anti-HIV activity (EC50 = 55 microM). None of the compounds showed antiherpes simplex virus activity.