Robust Strategy for Hit-to-Lead Discovery: NMR for SAR

Establishing robust structure-activity relationships (SARs) is key to successful drug discovery campaigns, yet it often remains elusive due to screening and hit validation artifacts (false positives and false negatives), which frequently result in unproductive downstream expenditures of time and resources. To address this issue, we developed an integrative biophysics-driven strategy that expedites hit-to-lead discovery, mitigates false positives/negatives and common hit validation errors, and provides a robust approach to obtaining accurate binding and affinity measurements. The advantage of this method is that it vastly improves the clarity and reproducibility for affinity-driven SAR by monitoring and eliminating confounding factors. We demonstrate the ease at which high-quality micromolar binders can be generated from the initial millimolar fragment screening hits against an "undruggable" protein target, HRas.

Discovery of Novel, Orally Bioavailable β-Amino Acid Azaindole Inhibitors of Influenza PB2

In our efforts to develop novel small-molecule inhibitors for the treatment of influenza, we utilized molecular modeling and the X-ray crystal structure of the PB2 subunit of the influenza polymerase to optimize a series of acyclic β-amino acid inhibitors, highlighted by compound 4. Compound 4 showed good oral exposure in both rat and mouse. More importantly, it showed strong potency versus multiple influenza-A strains, including pandemic 2009 H1N1 and avian H5N1 strains and showed a strong efficacy profile in a mouse influenza model even when treatment was initiated 48 h after infection. Compound 4 offers good oral bioavailability with great potential for the treatment of both pandemic and seasonal influenza.

Consumer palatability scores and volatile beef flavor compounds of five USDA quality grades and four muscles

Proximate data, consumer palatability scores and volatile compounds were investigated for four beef muscles (Longissimus lumborum, Psoas major, Semimembranosus and Gluteus medius) and five USDA quality grades(Prime, Upper 2/3 Choice, Low Choice, Select, and Standard). Quality grade did not directly affect consumer scores or volatiles but interactions (P < 0.05) between muscle and grade were determined. Consumer scores and volatiles differed (P < 0.05) between muscles. Consumers scored Psoas major highest for tenderness, juiciness, flavor liking and overall liking, followed by Longissimus lumborum, Gluteus medius, and Semimembranosus (P < 0.05). Principal component analysis revealed clustering of compound classes, formed by related mechanisms. Volatile n-aldehydes were inversely related to percent fat. Increases in lipid oxidation compounds were associated with Gluteus medius and Semimembranosus, while greater quantities of sulfur-containing compounds were associated with Psoas major. Relationships between palatability scores and volatile compound classes suggest that differences in the pattern of volatile compounds may play a valuable role in explaining consumer liking.

Identification of sensory attributes, instrumental and chemical measurements important for consumer acceptability of grilled lamb Longissimus lumborum

In this study, important eating quality attributes that influence consumer liking for grilled lamb loin have been identified using preference mapping techniques. The eating quality attributes identified as driving the consumer liking of lamb loin steaks were “tenderness”, “sweet flavour”, “meaty aftertaste”, “roast lamb flavour” and “roast lamb aftertaste”. In contrast, the texture attribute “rubbery” and the flavour attributes “bitter flavour” and "bitter aftertaste" had a negative influence on consumer perceptions. Associations were observed between eating quality and a number of instrumental and chemical measurements. Warner Bratzler Shear Force showed an association with “rubbery” texture and a negative association with “tenderness” and consumer liking scores. The compounds, glucose, glucose-6-phosphate, inosine, inosine monophosphate and adenosine monophosphate were associated with the attributes, “sweet flavour”,“meaty aftertaste”, “roast lamb flavour”, “roast lamb aftertaste” and with consumer scores for liking of lamb which is probably caused by the role some of these compounds play as precursors of flavour and as taste compounds.

Aza-retinoids as novel retinoid X receptor-specific agonists

A new structurally simple series of potent lipophilic aza-retinoids RXR agonists has been developed. SAR studies for the N-alkyl-azadienoic acids described here demonstrate that the RXR activity profile is sensitive to the N-alkyl chain length. Further, we have expanded the work to include azadienoic acids, which exhibited many accessible conformations leading to a better understanding of the SAR around the series.

Inhibitors of hepatitis C virus NS3.4A protease. Part 3: P2 proline variants

We recently described the identification of an optimized alpha-ketoamide warhead for our series of HCV NS3.4A inhibitors. We report herein a series of HCV protease inhibitors incorporating 3-alkyl-substituted prolines in P(2). These compounds show exceptional enzymatic and cellular potency given their relatively small size. The marked enhancement of activity of these 3-substituted proline derivatives relative to previously reported 4-hydroxyproline derivatives constitutes additional evidence for the importance of the S(2) binding pocket as the defining pharmacophore for inhibition of the NS3.4A enzyme.

Inhibitors of hepatitis C virus NS3.4A protease 2. Warhead SAR and optimization

The alpha-ketoamide warhead (e.g., 15) was found to be a practical replacement for aliphatic aldehydes in a series of HCV NS3.4A protease inhibitors. Structure-activity relationships and prime side optimization are discussed.

Inhibitors of hepatitis C virus NS3·4A protease 1. Non-Charged tetrapeptide variants

Tetrapeptide-based peptidomimetic compounds have been shown to effectively inhibit the hepatitis C virus NS3.4A protease without the need of a charged functionality. An aldehyde is used as a prototype reversible electrophilic warhead. The SAR of the P1 and P2 inhibitor positions is discussed.

Retinoic acid receptor ligands based on the 6-cyclopropyl-2,4-hexadienoic acid

A series of novel cyclopropanyl methyl hexadienoic acid retinoids was designed and prepared. These compounds exhibited either selective activity as RXR agonists or pan-agonists on one or more of each of the RAR and RXR isoforms. The most potent pan-agonist 5a (RAR's EC(50)=17-59 nM; RXR's EC(50)=6-14 nM) showed good antiproliferative properties in the in vitro cancer cell lines, ME 180 and RPMI 8226.

Effect of some fat replacers on the release of volatile aroma compounds from low-fat meat products

The effect of fat content and carbohydrate fat-replacers on the release of volatile odor compounds from beefburger, salami, and frankfurter has been investigated. The reduction in fat content in any of the three meat products studied resulted in a tendency toward an increase in the quantities of volatiles released in the headspace. Tapioca starch and maltodextrin appear to delay the release of certain classes of compounds selectively; for instance, tapioca starch appears to slow the release of some Maillard products while maltodextrin has a similar effect on terpenes. In contrast, oat fiber decreases the release of most of the compounds analyzed. Thus, the addition of carbohydrate fat-replacers to low-fat meat products could assist the flavor qualities of low-fat meat products by slowing down the release of odor compounds.

Identification of major volatile odor compounds in frankfurters

More than 100 volatile compounds have been identified in the headspace of frankfurter sausages. Most abundant were the terpene hydrocarbons, monoterpene alcohols, phenyl propanoids, and phenols. Separate analyses of solutions of spices and smoke demonstrated that most of the terpenes were derived from the spices, whereas the phenols originated mostly from the smoke ingredients. Many of the compounds contributing to the overall odor of the frankfurters have been identified. Some odors, characteristic of the smokiness and spiciness of frankfurters, were caused by phenols and terpenes, whereas others were due to compounds derived from the meat fraction; these compounds included aldehydes, ketones, furanthiols, and alicyclic sulfur compounds.

Release of volatile odor compounds from full-fat and reduced-fat frankfurters

The effect of fat content on the release of volatile aroma compounds from frankfurters has been investigated. Although the release of most n-alkanals, alcohols, ketones, and furans was little affected by changes in the fat content of frankfurters, that of monoterpene hydrocarbons, sesquiterpene hydrocarbons, terpenes containing oxygen, cyclopentenones, phenyl propanoids, and phenols was greatly increased when the fat content was decreased. Some odors were also detected more frequently in the low-fat than in the full-fat sausages. These included smoky odors, due to phenols, spicy, synthetic, and floral odors due to terpenes, and meaty, roasted odors caused by sulfur-containing heterocyclic compounds. The release of aroma compounds from frankfurters appears to be closely related to the solvation of these compounds in the lipid phase.

4-Alkyl- and 3,4-dialkyl-1,2,3,4-tetrahydro-8-pyridono[5,6-g]quinolines: potent, nonsteroidal androgen receptor agonists

A series of human androgen receptor (hAR) agonists based on 4-alkyl-; 4,4-dialkyl-; and 3,4-dialkyl-1,2,3,4-tetrahydro-8-pyridono[5,6-g]quinoline was synthesized and evaluated in competitive receptor binding assays and an androgen receptor cotransfection assay in a mammalian cell background. A number of compounds in this series demonstrated activity equal to or better than dihydrotestosterone in both assays and represent a novel class of compounds for use in androgen replacement therapy.

Nonsteroidal progesterone receptor antagonists based on a conformationally-restricted subseries of 6-aryl-1,2-dihydro-2,2,4-trimethylquinolines

A series of nonsteroidal human progesterone receptor (hPR) antagonists based on conformationally-restricted analogues of a 6-aryl-1,2-dihydro-2,2,4-trimethylquinoline pharmacophore were synthesized and evaluated for their ability to bind to the human progesterone receptor and inhibit progesterone-stimulated reporter gene expression in mammalian cells.

New nonsteroidal androgen receptor modulators based on 4-(trifluoromethyl)-2(1H)-pyrrolidino[3,2-g] quinolinone

A series of 2(1H)-pyrrolidino[3,2-g]quinolinones was prepared and tested for the ability to modulate the transcriptional activity of the human androgen receptor (hAR). The parent compound, 4-(trifluoromethyl)-2(1H)-pyrrolidino[3,2-g]quinolinone, displayed moderate interaction with hAR, but more substituted analogues, particularly 6,7-disubstituted compounds, were potent hAR agonists in vitro.

Synthesis and biological activity of a novel series of nonsteroidal, peripherally selective androgen receptor antagonists derived from 1,2-dihydropyridono[5,6-g]quinolines

A new nonsteroidal antiandrogenic pharmacophore has been discovered using cell-based cotransfection assays with human androgen receptor (hAR). This series of AR antagonists is structurally characterized by a linear tricyclic 1,2-dihydropyridono[5,6-g]quinoline core. Analogues inhibit AR-mediated reporter gene expression and bind to AR as potently as or better than any known AR antagonists. Several analogues also showed excellent in vivo activity in classic rodent models of AR antagonism, inhibiting growth of rat ventral prostate and seminal vesicles, without accompanying increases in serum gonadotropin and testosterone levels, as is seen with other AR antagonists. Investigations of structure-activity relationships surrounding this pharmacophore resulted in molecules with complete specificity for AR, antagonist activity on an AR mutant commonly observed in prostate cancer patients, and improved in vivo efficacy. Molecules based on this series of compounds have the potential to provide unique and effective clinical opportunities for treatment of prostate cancer and other androgen-dependent diseases.

Synthesis and biological activity of novel nonsteroidal progesterone receptor antagonists based on cyclocymopol monomethyl ether

A novel class of nonsteroidal progesterone receptor antagonists has been synthesized and was shown to exhibit moderate binding affinity for hPR-A, the ability to inhibit the transcriptional activity of human progesterone receptor (hPR) in cell-based assays, and anti-progestational activity in a murine model. Cyclocymopol monomethyl ether, a component of the marine alga Cymopolia barbata was weakly active in random screening against PR. Investigations into the SAR surrounding the core of this natural product lead structure resulted in improved in vitro activity. In contrast to the cross-reactivity profiles observed with known steroidal antiprogestins, compounds of the general structural class described display a high degree of selectivity for the progesterone receptor and no functional activity on the glucocorticoid receptor.

Discovery of novel intracellular receptor modulating drugs

Utilizing the co-transfection assay as a guide to determining structure activity relationships, we have been pursuing the discovery of non-steroidal hPR modulators. Small molecule, non-steroidal lead structures have been identified. Optimization of these structures has yielded more potent hPR modulators. Improved cross-reactivity profiles with other intracellular receptors are a feature of these compounds owing to their non-steroidal nature.

Observations on the pancreas of cattle deficient in copper

Lesions were found in the pancreas of clinically normal cattle of low copper status. In comparison with the pancreas of cattle with normal hepatic copper reserves, the abnormalities were an increase in the dry matter content and reduction in the concentrations of protein and copper in the wet tissue. Cytochrome oxidase activity and protein-to-RNA ratio were also reduced. Histologically, there were defects in acinar basement membranes, splitting and disorganization of acini, cellular atrophy and dissociation, and stromal proliferation. The pancreatic ductular system did not show atrophy or disorganization.