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

We recently described a chemical strategy to pre-organize a trinucleotide subunit in a conformation suitable for Watson-Crick base pairing for modulating the binding kinetics of single-stranded oligonucleotides (ONs) using bis-phosphonate esters bridging hydrocarbon tethers to provide 11- and 15-membered macrocyclic analogues. In this manuscript, we describe the synthesis of all eight P-stereoisomers of macrocyclic 12-, 13-, 14-, and 16-membered hydrocarbon-bridged nucleotide trimers, their incorporation into ONs, and biophysical characterization of the modified ONs. The size of the macrocyclic tether and configuration at phosphorus had profound effects on hybridization kinetics. ONs containing 12- and 13-membered rings exhibited faster on-rates (up to 5-fold) and off-rates (up to 161-fold). In contrast, ONs using the larger ring size macrocycles generally exhibited smaller changes in binding kinetics relative to unmodified DNA. Interestingly, several of the analogues retained significant binding affinity for RNA based on their dissociation constants, despite being modestly destabilizing in the thermal denaturation experiments, highlighting the potential utility of measuring dissociation constants versus duplex thermal stability when evaluating novel nucleic acid analogues. Overall, our results provide additional insights into the ability of backbone-constrained macrocyclic nucleic acid analogues to modulate hybridization kinetics of modified ONs with RNA.

Systematic Investigation of Tether Length and Phosphorus Configuration in Backbone Constrained Macrocyclic Nucleic Acids to Modulate Binding Kinetics for RNA.

Potassium enolates of γ-alkoxy-α-methyl pentanoates can be alkylated with allylic and benzylic halides in solution and on solid phase with high 2,3- syn selectivity. Polypropionate units can be constructed on solid phase by a series of stereocontrolled conjugate additions and enolate hydroxylations relying on 1,2-induction.

Stereocontrolled Solution and Solid Phase Enolate Alkylations and Hydroxylations — Generation of Three and Four Contiguous Stereogenic Carbon Atoms in Acyclic Systems.

Cristallisation dans P2 1 2 1 2 1 avec a=10.636, b=12.759, c=18.185A, Z=4; affinement jusqu'a R=0.039. Ce compose est constitue d'un cyclohexane attache a un groupe phosphoryl de coordination tetraedrique. Un groupe phenylmethyl de configuration R ponte l'atome P et le cycle cyclohexanol. L'alcool tertiaire est dans une position axiale et le 4-t-butyl est dans une position equatoriale

Structure of a Chiral Bicyclic β‐Hydroxyphosphonamide ‐ An Asymmetric Olefination Intermediate, C25H41N2O2P.

Pentaerythritol (2,2-bis-hydroxymethyl-propane-1,3-diol) was converted into a series of mono-, di-, and trisubstituted derivatives, comprising allyl ethers and amino-alkyl ethers, by systematic che...

Synthesis of Chemically and Functionally Diverse Scaffolds from Pentaerythritol

A synthetic strategy towards tricholomic acid and acivicin has been established using the aldol condensation of N-pyruvilideneglycinatoaquocopper(II) and an optically active aldehyde derived from S-malic acid as the key bond-forming reaction. Although a viable strategy was developed, no asymmetric induction was observed.

Stephen Hanessian

Papers

Systematic Investigation of Tether Length and Phosphorus Configuration in Backbone Constrained Macrocyclic Nucleic Acids to Modulate Binding Kinetics for RNA.

Stereocontrolled Solution and Solid Phase Enolate Alkylations and Hydroxylations — Generation of Three and Four Contiguous Stereogenic Carbon Atoms in Acyclic Systems.

Structure of a Chiral Bicyclic β‐Hydroxyphosphonamide ‐ An Asymmetric Olefination Intermediate, C25H41N2O2P.

Synthesis of Chemically and Functionally Diverse Scaffolds from Pentaerythritol

A Synthetic Strategy for Tricholomic Acid and Acivicin.