Case Studies of Minimizing Nonspecific Inhibitors in HTS Campaigns That Use Assay-Ready Plates

Identifying chemical lead matter by high-throughput screening (HTS) has been a common practice in early stage drug discovery. Evolution of small-molecule library composition to include more drug-like molecules with desirable physical chemical properties combined with improving assay technologies has vastly enhanced the capability of HTS. However, HTS campaigns can still be plagued by false positives arising from nonspecific inhibitors. The generation of assay-ready plates has permitted an incremental advancement to the speed and efficiency of HTS but has the potential to enhance the occurrence of nonspecific inhibitors. A subtle change in the order of reagent addition to the assay-ready plates can greatly alleviate false-positive inhibition. Our case studies with six different kinase and protease targets reveal that this type of inhibition affects targets regardless of enzyme class and is unpredictable based on protein construct or inhibitor chemical scaffold. These case studies support a model where a diversity set of compounds should be tested first for hit rates as a function of order of addition, carrier protein, and relevant mechanistic studies prior to launch of the HTS campaign.

A Phenotype-Based Model for Rational Selection of Novel Targeted Therapies in Treating Aggressive Breast Cancer

BackgroundGlobal transcriptional profiling has facilitated breast cancer research, and has led to analyses of breast cancer phenotypes and clinical outcomes. While gene expression signatures can identify patients with aggressive tumors who require chemotherapy, data that guide drug selection are relatively sparse, generally obtained in clinical trials that treat patients with standard therapies and often limited by small study size. We propose a method that incorporates genomic and in vitro and in vivo preclinical testing of patient tumors to identify optimal and novel therapeutic regimens for individual breast tumors.Methods and FindingsNine independent microarray datasets comprised of 1,723 breast cancer cases were used in a meta-analysis to examine patterns of drug sensitivity predictions. Drug sensitivity signatures were developed based on the Broad Institute Connectivity Map, and applied using binary regression to individual tumor gene expression data. These analyses provide probabilities for each individual tumor's sensitivity to specific drugs, and allows us to identify patterns of drug sensitivity for unique breast cancer phenotypes. We found consistent patterns of drug sensitivity that were specific to individual tumor subtypes. Notably, we discovered that over 80% of basal-like breast cancers were predicted to respond to inhibitors of the phosphatidylinositol 3-kinase pathway and that normal-like tumors were most likely to respond to a heat shock protein 90 inhibitor. Among the more aggressive breast cancer phenotypes, there was a high predicted response to valproic acid (VPA), a histone deacetylase inhibitor. Using a subset of targeted therapeutics that are currently in clinical trials with solid tumors and for which we have drug response signatures, we performed in vitro drug testing on a panel of 18 breast cancer cell lines and found significant correlation between predicted and actual drug sensitivity. Additionally, predicted sensitivity to VPA for specific patient breast tumors was confirmed in vitro and in vivo, using 3-D primary cell culture and orthotopic xenografts generated from the same human tumors for which the predictions were made. These studies highlight VPA as an effective therapy for aggressive breast cancer tumors, and underscore the suitability of our genomic approach to identify optimal targeted therapeutic strategies for women with breast cancer.ConclusionsWe provide a drug sensitivity prediction model using primary tumor gene expression profiles and offer preclinical examples of drug response based on this model. This approach can be used to personalize drug therapy for patients with breast cancer. This will hopefully improve clinical responses for patients while sparing them toxicity from agents that will have no effect on their tumors.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2007.

Oxime derivatives related to AP18: Agonists and antagonists of the TRPA1 receptor

AP18 1 was recently disclosed as an antagonist of the TRPA1 receptor by the research group of Patapoutian. However, no detailed structure-activity relationships around 1 have been disclosed. Thus, a small number of oximes related to AP18 were examined in order to characterize the determinants of TRPA1 activity. Congeners of AP18 were found to possess both agonist and antagonist activity, suggesting that AP18 may behave as a covalent antagonist of the TRPA1 ion-channel.

Third-body abrasive wear challenge of 32 mm conventional and 44 mm highly crosslinked polyethylene liners in a hip simulator model

Hip simulator studies have shown that wear in the polyethylene liners used for total hip replacements increased with the larger-diameter femoral balls and could also be exacerbated by third-body abrasion. However, they also indicated that the more highly cross-linked polyethylene (HXPE) bearings were more wear resistant than conventional polyethylene (CXPE) bearings. Unfortunately the HXPE bearings appeared to be particularly sensitive to adverse wear conditions. One simulator study in particular indicated that poly(methyl methacrylate) (PMMA) debris increased wear sixfold by means of two-body abrasive interactions rather than the supposed third-body abrasion or roughening effects of the Co-Cr surfaces. There has been no confirmation of such novel theories. Therefore the goal of this study was to investigate the sensitivity of large-diameter HXPE bearings to the third-body PMMA wear challenge in a hip simulator model. An orbital hip simulator was used in standard test mode with a physiological load profile. The 32 mm control liners were machined from moulded GUR1050 and gamma irradiated to 35 kGy under nitrogen (CXPE). The 44 mm liners were also from moulded blanks, gamma irradiated to 75 kGy, machined to shape, given a proprietary heat treatment, and sterilized by gas plasma (HXPE). As in the published simulator model, the study was conducted in three phases. In phase 1, all cups were run in standard ('clean') lubricant for 1.5 x 10(6) cycles duration. In phase 2, three CXPE cups and six HXPE cups were run for 2 x 10(6) cycles with a slurry of PMMA particles added to the lubricant. In phase 3, the implants were again run in 'clean' lubricant for 2 x 10(6) cycles duration. In addition, three HXPE cups were run as wear controls for 5.5 x 10(6) cycles duration in clean lubricant. In phase-1, the HXPE liners demonstrated twelvefold reduced wear compared with the CXPE controls. The 32 mm and 44 mm Co-Cr balls were judged of comparable roughnesses. However, the surface finish of HXPE liners was superior to that of CXPE liners. In phase-2 abrasion, wear rates increased sixfold and eighty-fold for CXPE and HXPE bearings respectively. These data confirmed that HXPE bearings were particularly sensitive to 'severe' test modes. The Co-Cr balls revealed numerous surface patches representing transferred PMMA with average transient roughness increased to 25 nm and 212 nm for the 32 mm and 44 mm balls respectively. These PMMA patches produced an aggressive two-body abrasion wear of the polyethylene. After cleaning, the ball roughness returned to near normal. Therefore the Co-Cr roughness was not an issue in this severe test mode. In phase 3, the wear decreased to near the index values of phase 1, while liner roughness dropped by more than 90 per cent. The control CXPE liners now demonstrated twice the wear of the HXPE, as would be predicted comparing the diameter and cross-linking algorithms. No previous study has correlated polyethylene roughness profiles to wear performance. In phase 2, PMMA abrasion created significant damage to the polyethylene surfaces. The average roughness Sa of CXPE liners increased to 3.6 microm, a twenty-four-fold increase with some scratches up to 40 microm deep. The HXPE roughness also increased but only to 1.5 microm, a ninefold increase. The scratch indices Sz and Sp for HXPE surfaces were also 50 per cent less severe than on CXPE surfaces. However, within 2 x 10(6) cycles duration of phase 3, all liners had recovered to virtually their original surface finish in phase 1. In all test phases, the surface finish of the HXPE liners remained superior to control liners. These experimental data confirmed many of the results from the previous simulator study with the PMMA abrasion models. Thus the 44 mm liners appeared an excellent clinical alternative to the smaller ball designs used in total hip replacements.

Myocardial scintigraphy as a supplementary diagnostic tool in heart disease

Myocardial scintigraphy with cesium-131 and thallium-201 was performed in 191 patients. Previous myocardial infarctions localized to the anterior and lateral wall of the left ventricle were correctly diagnosed with both radionuclides. Inferior and posterior infarctions were only detected when thallium was used. In patients with non-informative ECG changes like bundle branch block, non-specific ST-T changes or with atypical symptoms, myocardial imaging made an essential contribution to the establishment of a correct diagnosis. The potential value of myocardial imaging in patients with valvular heart disease and in cardiomyopathy is described.

Cardaic arrhythmias in chloral hydrate poisoning

In three patients admitted to hospital after ingestion of an overdose of chloral hydrate, the ECG showed supreventricular and ventricular tachyarrhythmias. The possible mechanism for the arrhythmias may be an enhanced automaticity of supraventricular and ventricular pacemaker cells caused by metabolites of chloral hydrate. The ventricular arrhythmia responded to i.v. treatment with lignocaine in one patient, and to phenytoin in another in whom lignocaine failed to restore a normal sinus rhythm.

The use of thallium-201 myocardial scintigraphy for the diagnosis of previous infarction

The ability of thallium-201 scintigraphy to detect previous infarction (greater than 6 months ago) was studied in 43 patients with coronary artery disease, 39 with valvular heart disease, and 5 with cardiomyopathy or myocarditis. All patients had undergone selective coronary arteriography and left ventricular angiography. Thallium-201 scintigraphy at rest proved a very sensitive method for detecting previous infarction, also clinically silent. Scintigraphy was more sensitive than a recent ECG. However, scintigraphy can give falsely positive results.

Diagnosis and management of acute aortic dissection, clinical and radiological follow-up

A clinical series of acute aortic dissections is presented. Twenty cases were of type A and 10 of type B. Acute severe chest pain was common, in type A also blood pressure difference between the arms and aortic regurgitation. The diagnosis was established by echocardiography, computerized tomography and/or aortography. Antihypertensive therapy was instituted immediately after diagnosis and was in type A cases followed by acute surgery unless definite contraindications existed. Of 14 surgically treated type A patients 13 survived the operation. On follow-up 1.5-3.5 years later, 12 patients were still alive and doing well, but the false channel remained open in all cases where it had not been resected totally. Only one of six conservatively treated type A patients survived. Type B dissections were operated on only if conservative therapy failed. Four of five conservatively and two of five surgically treated type B patients survived.

Reduced high density lipoproteins as a risk factor after acute myocardial infarction

In a group of normocholesterolemic, non-diabetic middle-aged males surviving an acute myocardial infarction for 4 +/- 2 years (mean +/- SD), we have previously described a low apolipoprotein A-I and a deficient fibrinolytic activity as two major characteristics. In the present study we have followed morbidity and mortality risk factors for five years in these males. Mortality was 40% in a hypertensive group and 16% in a normotensive group. In the normotensive group mortality was related to reinfarction. Furthermore, patients with a poor prognosis in the normotensive group had lower high density lipoprotein (HDL) cholesterol and lower apolipoprotein A-I concentration in plasma than patients with a good prognosis. Unexpectedly, in the hypertensive group death was related to a low (p less than 0.05) cortisol concentration in urine. It is concluded that a low HDL level may be a bad prognostic sign in males who have sustained an acute myocardial infarction and show no evidence of other risk factors, such as diabetes, hypercholesterolemia or hypertension.

Plasma lipoproteins and fatty acid composition during a moderate eicosapentaenoic acid diet

The effect of a diet rich in marine fatty acids, especially eicosapentaenoic acid, on plasma lipids (total plasma cholesterol, HDL cholesterol, total triglycerides and apolipoproteins A and B) and fatty acid composition in plasma phosphatidylcholine (PC) was studied in 10 healthy men. They were maintained for 11 weeks on their normal diet which was partly replaced by 150-200 g of fatty fish per day. In the same individuals this diet had previously caused a delay in primary haemostasis and a decrease in platelet aggregability similar to that caused by acetylsalicylic acid, a known inhibitor of thromboxane A2 formation. Apart from its effect on haemostasis, the fish diet substantially reduced serum triglycerides (by 43%, p less than 0.01) but caused no changes in total plasma or HDL cholesterol or apolipoproteins A and B. After three weeks on the diet the proportion of plasma PC omega-3 polyunsaturated fatty acids increased (C20:5 and C22:6) and omega-6 fatty acids decreased (C18:2 and C20:3). The relative plasma PC content of arachidonic acid was unaffected throughout. These alterations in plasma PC fatty acid composition were principally in accordance with those seen in platelet membrane PC. There was a linear correlation between the content of omega-3 and of omega-6 fatty acids in plasma PC with that of platelet PC as well as in predominate individual fatty acids of the two series. Six weeks after the volunteers had resumed their usual diet, total triglycerides and the fatty acid composition of plasma PC had returned to the original state.