Chemical Structural Novelty: On-Targets and Off-Targets.

Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding. A framework for combining multiple similarity computations is presented along with its systematic application to 358 drugs with overlapping pharmacology. Given a new molecule along with a set of molecules sharing some biological effect, … Continued

Toluidinesulfonamide Hypoxia-induced Factor 1 Inhibitors: Alleviating Drug-drug Interactions through Use of PubChem Data and Comparative Molecular Field Analysis Guided Synthesis

Inhibitors of hypoxia-inducible factor 1 (HIF-1) represent promising anticancer therapeutics. We have identified a series of potent toluidinesulfonamide HIF-1 inhibitors. However, the series was threatened by a potential liability to inhibit CYP2C9 which could cause dangerous drug-drug interactions when being coadministered with other drugs. We used structure-activity data from the PubChem database to develop a … Continued

Discovery of Novel GSK-3 β Inhibitors with Potent In Vitro and In Vivo Activities and Excellent Brain Permeability Using Combined Ligand- and Structure-based Virtual Screening

Dysregulation of glycogen synthase kinase (GSK-3β) is implicated in the pathophysiology of many diseases, including type-2 diabetes, stroke, Alzheimer’s, and others. A multistage virtual screening strategy designed so as to overcome known caveats arising from the considerable flexibility of GSK-3β yielded, from among compounds in our in-house database and two commercial databases, new GSK-3β inhibitors … Continued

Molecular Shape and Medicinal Chemistry: A Perspective

The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for “decoration” with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, … Continued

De Novo Design of a Picomolar Nonbasic 5-HT(1B) Receptor Antagonist

We describe herein the discovery of novel, de novo designed, 5-HT(1B) receptor antagonists that lack a basic moiety and that provide improved hERG and in vitro phospholipidosis profiles. We used a known 5-HT(1B) antagonist template as our starting point and focused on replacing the piperazine moiety. Pyrazole-based ideas were designed and synthesized among a small … Continued

Novel Organic Proteasome Inhibitors Identified by Virtual and In Vitro Screening

Proteasome inhibition is a promising strategy for treating cancers. Herein, we report the discovery of novel drug-like inhibitors of mammalian proteasome 20S using a multistep structure-based virtual ligand screening strategy. Sulfone- or piperazine-containing hits essentially belong to the under-represented class of noncovalent and nonpeptidic proteasome inhibitors. Several of our compounds act in the micromolar range … Continued

Physical Binding Pocket Induction for Affinity Prediction

Computational methods for predicting ligand affinity where no protein structure is known generally take the form of regression analysis based on molecular features that have only a tangential relationship to a protein/ligand binding event. Such methods have limited utility when structural variation moves beyond congeneric series. We present a novel approach based on the multiple-instance … Continued

Structure-based Design, Synthesis, and Biological Evaluation of a Series of Novel and Reversible Inhibitors for the Severe Acute Respiratory Syndrome-coronavirus Papain-like Protease

We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, nonpeptide inhibitors of SARS-CoV PLpro. Our initial lead compound was identified via high-throughput screening of a diverse chemical library. We subsequently carried out structure-activity relationship studies and optimized the lead structure to potent inhibitors that have shown antiviral … Continued

Novel Heteroaromatic Organofluorine Inhibitors of Fructose-1,6-bisphosphatase

A broad group of compounds including substituted pyrazoles, pyrroles, indoles, and carbazoles were screened to identify potential inhibitor lead compounds of fructose-1,6-bisphosphatase (FBPase). Best inhibitors are (1H-indol-1-yl)(4-(trifluoromethyl)phenyl)methanone, ethyl 3-(3,5-dimethyl-1H-pyrrol-2-yl)-4,4,4-trifluoro-3-hydroxybutanoate, 3,5-diphenyl-1-(3-(trifluoromethyl) phenyl)-1H-pyrazole, and ethyl 3,3,3-trifluoro-2-hydroxy-2-(1-methyl-1H-indol-3-yl)propanoate. The IC50values (3.1, 4.8, 6.1, and 11.9 µM) were comparable to that of AMP, the natural inhibitor of murine FBPase (IC50 … Continued

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