Scalable syntheses of both enantiomers of DNJNAc and DGJNAc from glucuronolactone: the effect of N-alkylation on hexosaminidase inhibition

The efficient scalable syntheses of 2-acetamido-1,2-dideoxy-D-galacto-nojirimycin (DGJNAc) and 2-acetamido-1,2-dideoxy-D-gluco-nojirimycin (DNJNAc) from D-glucuronolactone, as well as of their enantiomers from L-glucuronolactone, are reported. The evaluation of both enantiomers of DNJNAc and DGJNAc, along with their N-alkyl derivatives, as glycosidase inhibitors showed that DGJNAc and its N-alkyl derivatives were all inhibitors of α-GalNAcase but that none of the epimeric DNJNAc derivatives inhibited this enzyme. In contrast, both DGJNAc and DNJNAc, as well as their alkyl derivatives, were potent inhibitors of β-GlcNAcases and β-GalNAcases. Neither of the L-enantiomers showed any significant inhibition of any of the enzymes tested. Correlation of the in vitro inhibition with the cellular data, by using a free oligosaccharide analysis of the lysosomal enzyme inhibition, revealed the following structure-property relationship: hydrophobic side-chains preferentially promoted the intracellular access of iminosugars to those inhibitors with more-hydrophilic side-chain characteristics.     

Production of hygromycin A analogs in Streptomyces hygroscopicus NRRL 2388 through identification and manipulation of the biosynthetic gene cluster

Hygromycin A, an antibiotic produced by Streptomyces hygroscopicus NRRL 2388, offers a distinct carbon skeleton structure for development of antibacterial agents targeting the bacterial ribosomal peptidyl transferase. A 31.5 kb genomic DNA region covering the hygromycin A biosynthetic gene cluster has been identified, cloned, and sequenced. The hygromycin gene cluster has 29 ORFs which can be assigned to hygromycin A resistance as well as regulation and biosynthesis of the three key moieties of hygromycin A (5-dehydro-alpha-L-fucofuranose, (E)-3-(3,4-dihydroxyphenyl)-2-methylacrylic acid, and 2L-2-amino-2-deoxy-4,5-O-methylene-neo-inositol. The predicted Hyg26 protein has sequence homology to short-chain alcohol dehydrogenases and is assigned to the final step in production of the 5-dehydro-alpha-L-fucofuranose, catalyzing the reduction of alpha-L-fucofuranose. A hyg26 mutant strain was generated and shown to produce no hygromycin A but 5'-dihydrohygromycin A, 5'-dihydromethoxyhygromycin A, and a 5'-dihydrohygromycin A product lacking the aminocyclitol moiety. To the best of our knowledge, these shunt metabolites of biosynthetic pathway intermediates have not previously been identified. They provide insight into the ordering of the multiple unusual steps which compromise the convergent hygromycin A biosynthetic pathway.     

Determination of volatile compounds in foliage of Fraser fir (Abies fraseri) and balsam fir (Abies balsamea)

The Fraser fir (Abies fraseri) and balsam fir (Abies balsamea) are eastern North American conifers which have been infested by an exotic insect, the balsam woolly adelgid (BWA). BWA infestation has had particularly severe effects on Fraser fir, with up to 95% mortality rates at some sites, and is characterized by attack on mature trees only. The purpose of this research was to perform a chemosystematic study to evaluate whether differences in volatile chemical concentrations of various stands of fir were observed as a function of resistance to BWA infestation. The concentrations of volatiles were determined by a methylene chloride extraction procedure, followed by analysis by gas chromatography. First, comparisons were made of concentration levels of volatiles in Fraser and balsam fir foliage of seedlings, saplings, and mature trees. If a chemical provided resistance, one would expect higher volatile levels in the balsam foliage because of its greater resistance to BWA. Second, the volatile levels in Fraser fir saplings and mature trees at uninfested sites were compared to the levels in surviving Fraser fir saplings and mature trees at infested sites. For a compound that provided BWA-resistance, higher volatile levels would be expected at the infested site because of the greater resistance of the surviving trees. Lastly, the concentrations of volatiles in sapling foliage were compared to those in mature foliage, where higher levels of resistance-providing chemicals would be expected in the saplings. 3-Carene was shown to consistently follow the expected pattern for a compound that provides resistance against BWA and β-pinene followed the pattern for the majority of the comparisons. These results indicate that while maltol and total volatiles did not correlate with the expected pattern, 3-carene, and possibly β-pinene and sesquiterpenes may provide fir with defense against BWA infestation.     

Practical calculation of molecular acidity with the aid of a reference molecule

A set of linear free energy models are presented for determining the pK(a) values of amines, alcohols, and carboxylic acids. Models are determined from a series of pK(a) predictors, taken both from traditional natural atomic orbital analysis (NAO) and from a novel approach introduced here of using a reference molecule: an ammonium ion for amines and a hydrogen sulfide molecule for alcohols and carboxylic acids. Using these reference molecules, we calculate the barrier to proton transfer and show that a number of properties associated with the transition state are correlated with the pK(a). By considering 38 predictors, we obtain a four-variable model for amines and a three-variable model for oxygen-containing compounds. The model for amines is based on 145 compounds and has a root mean squared error (RMSE) of 0.45 and R(2) = 0.98. The oxygen set has 48 molecules: RMSE = 0.26, and R(2) = 0.993. Similar, linear, and multilinear models are constructed after separating the sets into chemically similar categories: alcohols, carboxylic acids, and primary, secondary, tertiary, and aromatic amines. This separation gives simpler models with relatively low RMSE values, where the most important predictor of the pK(a) is the difference in energy between transferring the proton from the reference molecular base to the conjugate acid from the data set.     

Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase

We investigate the effect of systematically applying molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) to docked poses in an attempt to improve the correspondence between theoretical prediction and experimental observation. The proposed scheme involves running a short time scale MD simulation on a docked ligand pose (and any known structurally important crystal structure waters in the active site), followed by QM/MM minimization. Both of these steps are relatively fast for moderately sized ligands; longer time scale MD involving the protein is not found to improve the results. The final binding energy is given in terms of the QM/MM total energy, a van der Waals correction, and a term to account for desolvation effects. This methodology is first tested with a trypsin inhibitor, for which we establish the importance of running MD before reoptimizing with QM/MM. The method is then applied to cytochrome c peroxidase using a set of binders and decoys. In this example, the proposed methodology affords much better discrimination between binders and decoys than the traditional docking approach used. For both systems presented, application of this protocol results in a significantly better energetic ranking and a smaller root mean squared deviation from known crystallographic ligand poses. This work highlights the importance of including polarization effects through QM/MM and of sampling with MD to refine a set of initial docked poses.     

Failure of the Weizs?cker kinetic energy functional for one-, two-, and three-electron distribution functions

Further progress in pair-density functional theory (sometimes called 2-DFT) hinges on the development of computationally facile and quantitatively accurate models for the kinetic energy functional. In this paper we perform computational tests for two of the simplest models, the generalized Weizs?cker kinetic energy functional and its spin-resolved extension. Both of these models perform very poorly for atoms. The higher-order Weizs?cker functionals (based on the three-electron distribution function) perform better, but are still not successful. This suggests that an alternative approach for designing kinetic energy functionals of the pair density is needed.     

Temperature-dependent approach to chemical reactivity concepts in density functional theory

The chemical reactivity concepts of density functional theory are studied through a unified view in the temperature-dependent approach provided by the grand canonical ensemble. This procedure leads to a more general perspective that enriches our understanding of the behavior of the average energy and its derivatives with respect to the average number of electrons, provides alternative definitions for those quantities that are “ill defined” at zero temperature, and allows one to determine the relationships among reactivity concepts at any temperature. In particular, it has been found that at high temperatures the parabolic model for reactivity indicators may be justified through the electronic entropy term in the Helmholtz free energy, and that at nonzero temperatures there is an electronic heat capacity contribution to the average energy. In summary, the unified view of the temperature-dependent approach is an important complement to the zero-temperature formulation that clarifies fundamental issues therein.     

Crystallization Force—A Density Functional Theory Concept for Revealing Intermolecular Interactions and Molecular Packing in Organic Crystals

Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short‐range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal‐growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self‐assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5‐methyl‐2‐[(2‐nitrophenyl)amino]‐3‐thiophenecarbonitrile, so‐called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.