Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.

Stochastic conformational search on the Lewis X (Lex) trisaccharide and three Lexanalogues

Biased stochastic conformational searches using the MMFF94 force field and the Born continuum solvation model were applied to the molecular modeling of the Lewis X (Lex) trisaccharide (β-D-Gal-(1,4)-[α-L-Fuc-(1,3)]-β-D-GlcNAc-OH) and three Lexanalogues, in which each of the three sugar units was replaced by another sugar residue, i.e., N-acetyl-glucosamine by glucose, galactose by glucose, and fucose by rhamnose. The stochastic search accurately identified a lowest energy conformation of the Lexdeterminant that corresponds to the reported conformations of Lexdeduced experimentally in the solid state by X-ray crystallography and in solution by NMR measurements. In this conformation stacking exists between the galactosyl and fucosyl residues. Five new local minima for the Lextrisaccharide were found within 3 kcal mol–1of the global minimum using the stochastic search and metric scaling. Modeling studies of the analogues showed that the stacking observed in the Lextrisaccharide was maintained when either galactosyl or N-acetylglucosamine were replaced by glucosyl residues. In contrast, substitution of the fucose residue by rhamnose led to two conformers in which stacking of the galactose and rhamnose residues was no longer maintained. These results indicate that the substitution of the non-reducing end galactosyl or N-acetyl-glucosaminyl residues by a glucose unit in the dimeric Lewis X (dimLex) tumour associated antigen could help in the development of a vaccine that cross-reacts with dimLexbut no longer displays Lexassociated three-dimensional epitopes also presented by non-cancerous cells. In contrast, an analogue in which the fucosyl residue is replaced by rhamnose does not constitute a good vaccine candidate, since our results indicate that this substitution will induce an important conformational change that is likely to abolish cross-reactivity with the natural dimLextumor associated antigen.Key words: molecular modeling, stochastic, conformational analysis, Lewis X, oligosaccharide.

Flexible alignment of small molecules

A method is presented for flexibly aligning small molecules. The method accepts a collection of small molecules with 3D coordinates as input and computes a collection of alignments. Each alignment is given a score, which quantifies the quality of the alignment both in terms of internal strain and overlap of molecular features. The results of several computational experiments on pairs of compounds with known binding conformations are used to systematically and objectively tune the parameters for the method. The results indicate the method's utility for the elucidation of pharmacophores and comparative field analysis.

A simple model for the prediction of blood-brain partitioning

We derived a simple model for the prediction of blood-brain barrier penetration using three descriptors. The model contains the calculated octanol-water partition coefficient, the number of hydrogen-bond acceptors in an aqueous medium and the polar surface area. It was validated using an extensive dataset, comprising 100 diverse drug molecules. The descriptors are easily calculated and the model is suitable for the rapid prediction of the blood-brain barrier partitioning of drugs.