A novel scoring function to estimate protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included: (1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce experimental binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, respectively) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.

/pdf/extra-precision-glide-docking-and-scoring-incorporating-a-2o3e7pl9pg.pdf

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

Structure-based virtual screening plays an important role in drug discovery and complements other screening approaches. In general, protein crystal structures are prepared prior to docking in order to add hydrogen atoms, optimize hydrogen bonds, remove atomic clashes, and perform other operations that are not part of the x-ray crystal structure refinement process. In addition, ligands must be prepared to create 3-dimensional geometries, assign proper bond orders, and generate accessible tautomer and ionization states prior to virtual screening. While the prerequisite for proper system preparation is generally accepted in the field, an extensive study of the preparation steps and their effect on virtual screening enrichments has not been performed. In this work, we systematically explore each of the steps involved in preparing a system for virtual screening. We first explore a large number of parameters using the Glide validation set of 36 crystal structures and 1,000 decoys. We then apply a subset of protocols to the DUD database. We show that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets. We provide examples illustrating the structural changes introduced by the preparation that impact database enrichment. While the work presented here was performed with the Protein Preparation Wizard and Glide, the insights and guidance are expected to be generalizable to structure-based virtual screening with other docking methods.

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

Metabolites are the end products of cellular regulatory processes, and their levels can be regarded as the ultimate response of biological systems to genetic or environmental changes. In parallel to the terms ‘transcriptome’ and ‘proteome’, the set of metabolites synthesized by a biological system constitute its ‘metabolome’. Yet, unlike other functional genomics approaches, the unbiased simultaneous identification and quantification of plant metabolomes has been largely neglected. Until recently, most analyses were restricted to profiling selected classes of compounds, or to fingerprinting metabolic changes without sufficient analytical resolution to determine metabolite levels and identities individually. As a prerequisite for metabolomic analysis, careful consideration of the methods employed for tissue extraction, sample preparation, data acquisition, and data mining must be taken. In this review, the differences among metabolite target analysis, metabolite profiling, and metabolic fingerprinting are clarified, and terms are defined. Current approaches are examined, and potential applications are summarized with a special emphasis on data mining and mathematical modelling of metabolism.

https://link.springer.com/content/pdf/10.1023%2FA%3A1013713905833.pdf

Metabolomics - the link between genotypes and phenotypes

N-Heterocyclic Carbenes in Late Transition Metal Catalysis

Cyclodextrin derivatives (I) comprising glucosidic subunits (a)-(c), are new. Cyclodextrin derivatives (I) comprising glucosidic subunits of formula (a)-(c), are new. R 1H or carbon chain; R 2amino group or azide; R 3OH, OR 4or halo; R 4carbon chain; and n : 4-6. [Image].

New cyclodextrin derivatives comprising glucosidic subunits useful for targeting, grafting and delivering a molecule of interest e.g. peptide from cyclodextrin platform

The addition of a chloroallyl phosphonamide anion to oximes has allowed the preparation of a variety of cis-disubstituted N-alkoxy aziridines in enantiomerically pure form. Oxidative cleavage of the chiral auxiliary followed by derivatization of the products has allowed the preparation of enantiopure N-alkoxy aziridines.

The Synthesis of Enantiomerically Pure Disubstituted Aziridines and N-Alkoxy Aziridines.

We report the synthesis and biophysical evaluation of an azabicycle dinucleotide with restricted γ, β, and e torsion angles, featuring the introduction of a piperidine ring that locks the conformation of the nucleoside into an RNA-type nucleic acid. The conceptual basis of the design is predicated upon the notion that the conformation of the phosphate group linking two RNA nucleotides can be approximated with an azabicyclic phosphoramidite which may also benefit from a unique stereoelectronic effect.

Design And Synthesis Of An Azabicyclic Nucleoside Phosphoramidite For Oligonucleotide Antisense Constructs.

A general and stereocontrolled synthesis of an azabicyclo[4.3.0]nonane amino acid template with an appended substitutent at C-5 was developed. The approach allows for stereochemical and functional variations that extend the utility of these rigid amino acid motifs as peptidomimetics. The synthesis of a weakly active but specific NK-2 receptor antagonist is described.

A Versatile Synthesis of a β‐Turn Peptidomimetic Scaffold: An Approach Towards a Designed Model Antagonist of the Tachykinin NK‐2 Receptor.

Radical-induced intramolecular Michael cyclization of a bromovinyl-type appendage onto a functionalized cyclohexene carboxylic acid derivative produces the corresponding oxahydrindanes which can be transformed into oxahydrindenes (hexahydrobenzofurans) related to the title compounds. (−)-Quinic acid is a useful optically active precursor.

Stephen Hanessian

Papers

New cyclodextrin derivatives comprising glucosidic subunits useful for targeting, grafting and delivering a molecule of interest e.g. peptide from cyclodextrin platform

The Synthesis of Enantiomerically Pure Disubstituted Aziridines and N-Alkoxy Aziridines.

Design And Synthesis Of An Azabicyclic Nucleoside Phosphoramidite For Oligonucleotide Antisense Constructs.

A Versatile Synthesis of a β‐Turn Peptidomimetic Scaffold: An Approach Towards a Designed Model Antagonist of the Tachykinin NK‐2 Receptor.

A Novel Synthetic Route to the Hexahydrobenzofuran Subunit of the Avermectins and Milbemycins.