1D 13C-NMR data as molecular descriptors in spectra--structure relationship analysis of oligosaccharides

Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the α or β anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1→2, 1→3, 1→4, or 1→6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1) classification of the anomeric configuration of the first unit, second unit and reducing end; (2) classification of the type of first and second linkages; (3) classification of the three residues: reducing end, middle and first residue; and (4) classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set-it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds) for the nine tasks, respectively, on the basis of unassigned chemical shifts.     

Portraying the selectivity of GSK-3 inhibitors towards CDK-2 by 3D similarity and molecular docking

Structural Chemistry - The striking structural resemblance between adenosine triphosphate (ATP) binding sites of glycogen synthase kinase-3 (GSK-3) and cyclin-dependent kinase-2 (CDK-2) raises...     

SHAFTS: a hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening

We developed a novel approach called SHAFTS (SHApe-FeaTure Similarity) for 3D molecular similarity calculation and ligand-based virtual screening. SHAFTS adopts a hybrid similarity metric combined with molecular shape and colored (labeled) chemistry groups annotated by pharmacophore features for 3D similarity calculation and ranking, which is designed to integrate the strength of pharmacophore matching and volumetric overlay approaches. A feature triplet hashing method is used for fast molecular alignment poses enumeration, and the optimal superposition between the target and the query molecules can be prioritized by calculating corresponding "hybrid similarities". SHAFTS is suitable for large-scale virtual screening with single or multiple bioactive compounds as the query "templates" regardless of whether corresponding experimentally determined conformations are available. Two public test sets (DUD and Jain's sets) including active and decoy molecules from a panel of useful drug targets were adopted to evaluate the virtual screening performance. SHAFTS outperformed several other widely used virtual screening methods in terms of enrichment of known active compounds as well as novel chemotypes, thereby indicating its robustness in hit compounds identification and potential of scaffold hopping in virtual screening.     

Conformational analysis of novel monoaryl substituted protoporphyrins by 1D NOE, 2D NOESY and molecular modeling studies

Porphyrins 1–4 are monoaryl protoporphyrins substituted on C-5 or C-15 by a phenyl group. One- and two-dimensional nOe experiments and molecular modeling studies allowed us to find the most favorable conformations for these compounds. In the four porphyrins, the exocyclic phenyl group adopts a non-coplanar disposition relative to the plane of the macrocycle and this is reflected in the ID nOe difference and 2D NOESY results. In porphyrins 1 and 3 the macrocycle is nearly planar while nonplanar saddle conformations were obtained for porphyrins 2 and 4.     

Fast 3D molecular superposition and similarity search in databases of flexible molecules

We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes the torsional flexibility of the database molecules fully into account, and can deal with an arbitrary number of conformation-dependent molecular features. The method utilizes a fragmentation-reassembly approach which allows for an efficient sampling of the conformational space. A fast clique-based pattern matching algorithm generates alignments of pairs of adjacent molecular fragments on the rigid query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups) we show that fFLASH is able to rapidly produce accurate alignments of medium-sized drug-like molecules. Experiments with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) have shown that average query processing times of the order of 0.1 seconds per molecule can be achieved on a PC.     

Combinatorial preferences affect molecular similarity/diversity calculations using binary fingerprints and Tanimoto coefficients

A combinatorial method was developed to calculate complete distributions of the Tanimoto coefficient (Tc) for binary fingerprint (FP) representations of specified length, regardless of the chemical parameters they reflect. Theoretical Tc distributions were calculated for FPs consisting of up to 67 bit positions which revealed significant statistical preferences of certain Tc values. Calculation of Tc distributions in a large compound database using different FPs mirrored the effects identified by our general analysis. On the basis of these findings, an average Tc is biased by statistically preferred values.     

SLIPPER-2001 -- software for predicting molecular properties on the basis of physicochemical descriptors and structural similarity

A new approach for predicting the lipophilicity (log P), solubility (log Sw), and oral absorption of drugs in humans (FA) is described. It is based on structural and physicochemical similarity and is realized in the software program SLIPPER-2001. Calculated and experimental values of log P, log Sw, and FA for 42 drugs were used to demonstrate the predictive power of the program. Reliable results were obtained for simple compounds, for complex chemicals, and for drugs. Thus, the principle of "similar compounds display similar properties" together with estimating incremental changes in properties by using differences in physicochemical parameters results in "structure - property " predictive models even in the absence of a precise understanding of the mechanisms involved.     

Structure elucidation and 3D solution conformation of the antibiotic enduracidin determined by NMR spectroscopy and molecular dynamics

Enduracidin and ramoplanin belong to the large family of cyclodepsipeptide antibiotics, highly effective against Gram-positive bacteria. The primary and 3D solution structure of ramoplanin is already well known, and the primary structure of enduracidin has been determined by a combination of chemical and NMR spectroscopic methods. Both antibiotics share a similar peptide core of 17 amino acids and differ mainly in the length of the acyl chain and the presence of two D-mannose moieties in ramoplanin. Based on the high sequence homology with ramoplanin, the structure in solution of enduracidin is modeled as a cyclic peptide. The tertiary structure thus obtained was refined through molecular dynamics (MD) simulation, in which the interatomic NOE-derived distance restraints were imposed. MD simulations yielded a family of representative 3D structures (RMSD = 0.89), which highlighted a backbone geometry similar to that of ramoplanin in its beta-hairpin arrangement. In contrast, enduracidin displays a different arrangement of the side-chain and of the residues forming the hydrophobic core.     

Structure determination of fexofenadine‐α‐cyclodextrin complex by quantitative 2D ROESY analysis and molecular mechanics studies

Complexation of fexofenadine with α‐cyclodextrin in aqueous medium was studied. The stoichiometry of the resulting inclusion complex was determined by ¹H NMR titration data. 2D ROESY data provided the evidence of formation of the complex by entry of the phenyl ring into the α‐cyclodextrin cavity probably from wider opening. Determination of relative peak intensities of intermolecular cross‐peaks for the most stable complexes obtained by molecular mechanics (MM2) studies and from 2D ROESY spectral data confirmed the presence of only one complex in solution that has been fully characterized. Copyright © 2012 John Wiley & Sons, Ltd.     

Laser ablation molecular isotopic spectrometry of water for 1D2/1H1 ratio analysis

Laser Ablation Molecular Isotopic Spectrometry (LAMIS) has been investigated for optical isotopic analysis of the deuterium to protium ratio in enriched water samples in ambient air at atmospheric pressure. Multivariate PLSR (Partial Least Squares Regression) based calibrations were carried out and validated using multiple statistical parameters. Comparisons of results are reported using two spectrometers having two orders of magnitude difference in spectral resolution. The accuracy and precision of isotopic analysis depends on the spectral resolution and the inherent isotope shift of the elements. The requirements for spectral resolution of the measurement system can be significantly relaxed when the isotopic abundance ratio is determined using chemometric processing of the spectra. Large isotopic shifts in the individual rotational branches of OH/OD molecular emission spectra were measured. Optimized temporal conditions for LAMIS measurements were established. Several sub-regions of spectra were used for PLSR calibration and the results demonstrate that both the emission intensity and degree of spectral differentiation affect the quality of the PLSR calibration. LAMIS results also were compared with traditional LIBS results obtained using PLSR and a spectral deconvolution method, demonstrating the advantages of LAMIS over LIBS with respect to isotopic composition determination.