Ultrafast de novo docking combining pharmacophores and combinatorics

We report on a successful de novo design approach which relies on the combination of multi-million compound combinatorial docking under receptor-based pharmacophore constraints. Inspired by a rationale by A.R. Leach et al., we document on the unification of two steps into one for ligand assembly. In the original work, fragments known to bind in protein active sites were connected forming novel ligand compounds by means of generic skeleton linkers and following a combinatorial approach. In our approach, the knowledge of fragments binding to the protein has been expressed in terms of a receptor-based pharmacophore definition. The combinatorial linking step is performed in situ during docking, starting from combinatorial libraries. Three sample scenarios growing in size and complexity (combinatorial libraries of 1 million, 1.3 million, and 22.4 million compounds) have been created to illustrate the method. Docking could be accomplished between minutes and several hours depending on the outset; the results were throughout promising. Technically, a module compatibility between FlexX(C) and FlexX-Pharm has been established. The background is explained, and the crucial points from an information scientist's perspective are highlighted.     

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. HYDE reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes. The greatest benefit of HYDE is that it yields a very intuitive atom-based score, which can be mapped onto the ligand and protein atoms. This allows the direct visualization of the score and consequently facilitates analysis of protein-ligand complexes during the lead optimization process. In this study, we validated our new scoring function by applying it in large-scale docking experiments. We could successfully predict the correct binding mode in 93% of complexes in redocking calculations on the Astex diverse set, while our performance in virtual screening experiments using the DUD dataset showed significant enrichment values with a mean AUC of 0.77 across all protein targets with little or no structural defects. As part of these studies, we also carried out a very detailed analysis of the data that revealed interesting pitfalls, which we highlight here and which should be addressed in future benchmark datasets.     

Quantitative structure-property relationships in boron nitrides: the 15N- and 11B chemical shifts.

Nuclear Magnetic Resonance (NMR) chemical shifts(delta) for elements in solids may often be approached by ab initio cluster calculations. We employ this technique to investigate the influence of structural alterations on the 15N and 11B chemical shifts in boron nitrides--in both hexagonal and cubic modifications. Within a given class of connectivity, i.e., three- or fourfold coordinated nitrogen, for the first time, an almost linear correlation between the 15N chemical shift and N-B bond lengths could be established. Also, the 11B shifts in hexagonal boron nitride correlate with the B-N bond distance; however, the effect is less pronounced. For the value of the chemical shift (CS), the decisive property is the average bond length at the atom in focus. Variations of CS are predominantly caused by changes in the paramagnetic deshielding. Further, second-nearest neighbor effects on the shieldings at 15N nuclei are quantified by subtraction schemes. The present work is closely related to the verification of models for amorphous high-demand Si/B/N ceramics.     

FastGrow: on-the-fly growing and its application to DYRK1A

Journal of Computer-Aided Molecular Design - Fragment-based drug design is an established routine approach in both experimental and computational spheres. Growing fragment hits into viable ligands...     

Ab initio prediction of 15N-NMR chemical shift in α-boron nitride based on an analysis of connectivities

Hydrogen-saturated cut-outs of hexagonal boron nitride have been used to model the solid state. Model compounds have been geometry optimized by means of density functional theory, whereas chemical shift calculations have been carried out at the coupled-perturbed Hartree–Fock level of theory employing gauge-including atomic orbital (GIAO) basis sets. The reliability of results has been tested against experimental values for chemical shifts in stable molecules with similar structural elements. With increasing cluster size, viz. a vanishing influence of the saturating hydrogens on the innermost nitrogen atoms, we find a convergence of ¹⁵N chemical shifts. A classification scheme for the chemical environment of a nitrogen atom has been set up according to its bonding graph including the second coordination sphere. For a given connectivity, chemical shifts vary within a few parts per million, thus enabling us to predict a ¹⁵N-NMR chemical shift of −285 ± 5 ppm for solid α-boron nitride. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 716–725, 1998     

Simulation of the Solid State Vibrational Spectra of Aminodichloroborane and Ammonia Boron Trichloride

This is the second part of a quantum chemical investigation on the reaction between boron trichloride and ammonia. In part I [9] we focused on the energetic course of successive chlorine substitutions which are relevant for the chemical vapor deposition of BN. In this work we analyze in detail the vibrational spectra of reaction products accessible at room temperature. Regarding an experimental IR spectrum of the condensation product of the reaction between BCl₃ and NH₃ [10], there are more signals than expected for monomeric aminodichloroborane. Since this molecule shows the tendency to oligomerize, we have studied whether the presence of aminodichloroborane dimers or trimers or an impurity of the ammonia boron trichloride complex – an intermediate from which aminodichloroborane is formed – can explain the shape of the measured spectrum. To this end we have calculated the vibrational frequencies of monomeric, dimeric, and trimeric BCl₂NH₂, H₃N · BCl₃, and several van der Waals complexes at the level of a Møller‐Plesset second order perturbation theory. For the verification of the methodology, the vibrational frequencies of the dimethylaminodichloroborane molecule have been determined, in good accord with experimental gas phase spectra. Also the solid state spectrum of H₃N · BCl₃ is well reproduced by the computed vibrational spectrum of the monomeric adduct and a hydrogen‐bonded aggregate. Our studies concerning the spectrum of the condensation product of the reaction of boron trichloride with ammonia indicate that the substance investigated by Kwon and McGee had contained, besides monomeric aminodichloroborane, also its trimer and ammonia boron trichloride.     

Automated drawing of structural molecular formulas under constraints

In this paper, we present a new algorithm for automated drawing of 2D structural formulas of molecules. The algorithm is based on the classical scheme of a drawing queue placing the molecular fragments in a sequential way. We extend the concept of so-called prefabricated units developed for complex ring systems to automatically created drawing units for chains and rings which will then be assembled in a sequential fashion. The approach is fast and can be naturally extended to the problem of drawing molecules with common core structures. Further on, we present an algorithm that allows the drawing of 2D structural formulas under directional constraints assigned to a subset of bonds. Since no numerical optimization is necessary, the algorithm creates drawings of small organic molecules on the order of 500 structures per second. The new algorithm is relevant for all kinds of prediction and analysis software presenting a large number of probably similar molecular structures to the user of the software.