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

An overview is given of various strategies aimed at the total synthesis of natural products, with particular emphasis on some clinically important molecules. Of necessity, total synthesis must also incorporate the elements of absolute stereochemistry, and the ultimate objective of obtaining enantiomerically pure or enriched products. In this regard, the Chiron Approach which capitalizes on the recognition and eventual use of readily available, chiral non-racemic starting materials, has been very successful over the years. A number of examples from the author's laboratory are illustrated and discussed.

Reflections on the Total Synthesis of Natural Products: Art, Craft, Logic, and the Chiron Approach

Total Synthesis of A-315675: A Potent Inhibitor of Influenza Neuraminidase. [J. Am. Chem. Soc. 2002, 124 (17), 4716−4721].

On the basis of the knowledge that the proline-rich hot spot PPPRPP region of P(151)PSNPPPRPP(160), an oligopeptide derived from the cytosolic portion of p22phox (p22), binds to the single functional bis-SH3 domain of the regulatory protein p47phox (p47), we designed a mimetic of the tripeptide PPP based on NMR and X-ray crystallographic data for the p22(151-161) peptide PPSNPPPRPPA with a peptide construct. Incorporation of the synthetic pseudo-triproline mimetic Pro-Pro-Cyp in a molecule derived from molecular modeling studies led to only a 7-fold diminution in activity in a surface plasmon resonance assay relative to the same molecule containing the natural Pro-Pro-Pro tripeptide. The alternative sequence corresponding to a Pro-Cyp-Pro insertion was inactive. This is a first example of the use of a triproline mimetic to interfere with the formation of the p47-p22 complex, which is critical for the activation of NOX, leading to the production of reactive oxygen species as superoxide anions.

Targeting NOX2 via p47/phox-p22/phox Inhibition with Novel Triproline Mimetics.

The Synthesis of Enantiopure ω‐Methanoprolines and ω‐ Methanopipecolic Acids by a Novel Cyclopropanation Reaction: The “ Flattening” of Proline.

Hydroxamic acid derivatives (I) are new. Hydroxamic acid derivatives of formula (I) and their acid and base addition salts are new. R1 = 1-6C alkyl (optionally substituted by at least one OH, halo, 1-6C alkoxy, mercapto, 1-6C alkylthio, aryl, 1-6C acyl or amino (optionally substituted by one or two 1-6C alkyl, cycloalkyl or aryl)), 1-6C acyl, cycloalkyl, aryl, heterocyclic group or aminocarbonyl-1-6C alkyl (with amino optionally substituted by one 1-6C alkyl (optionally substituted by at least one aryl, 1-6C arylalkyl, cycloalkyl or 1-6C alkylaminocarbonyl; R2 = 1-4C alkylene; R3 = X or T-U'-V'- X = 1-6C alkyl, 1-6C acyl, 1-6C alkoxycarbonyl, 1-6C aminoalkyl (amino optionally substituted by one or two 1-6C alkyl), 1-6C hydroxyalkyl, 1-6C carboxyalkyl, 1-6C aminocarbonylalkyl, 1-6C mercaptoalkyl, cycloalkyl, aryl or heterocyclic; T = aryl or heterocyclic; U' = single bond, S, O, NH, carbonyl, -R8O-, -R8S-, -R8NH-, -R8OR9-, -R8-NH-R9-, -R8-CO-R9- or -R9- (with R8 bound to T and R9 bound to V'); R8 = 1-6C alkylene; R9 = arylene or heteroarylene; V' = 1-6C alkylene; R4 = biaryl, arylheteroaryl, heteroarylaryl, 1-6C alkyl (optionally substituted by one heterocyclic group), cycloalkyl, aryl, 1-6C arylalkyl, cycloalkyl-1-6C alkyl or heterocyclic; and provided that R4 is 1-6C alkyl (optionally substituted by one heterocyclic group), cycloalkyl, aryl, 1-6C arylalkyl, cycloalkyl-1-6C alkyl or heterocyclic, when R3 is T-U'-V'-. An Independent claim is also included for the preparation of (I).

Stephen Hanessian

Papers

Reflections on the Total Synthesis of Natural Products: Art, Craft, Logic, and the Chiron Approach

Total Synthesis of A-315675: A Potent Inhibitor of Influenza Neuraminidase. [J. Am. Chem. Soc. 2002, 124 (17), 4716−4721].

Targeting NOX2 via p47/phox-p22/phox Inhibition with Novel Triproline Mimetics.

The Synthesis of Enantiopure ω‐Methanoprolines and ω‐ Methanopipecolic Acids by a Novel Cyclopropanation Reaction: The “ Flattening” of Proline.

Hydroxamic acid derivatives, process for their preparation and pharmaceutical compositions containing them