Cell-Based Drug Discovery: Identification and Optimization of Small Molecules that Reduce c-MYC Protein Levels in Cells

Elevated expression of the c-MYC oncogene is one of the most common abnormalities in human cancers. Unfortunately, efforts to identify pharmacological inhibitors that directly target MYC have not yet yielded a drug-like molecule due to the lack of any known small molecule binding pocket in the protein, which could be exploited to disrupt MYC function. We have recently described a strategy to target MYC indirectly, where a screening effort designed to identify compounds that can rapidly decrease endogenous c-MYC protein levels in a MYC-amplified cell line led to the discovery of a compound series that phenocopies c-MYC knockdown by siRNA. Herein, we describe our medicinal chemistry program that led to the discovery of potent, orally bioavailable c-MYC-reducing compounds. The development of a minimum pharmacophore model based on empirical structure activity relationship as well as the property-based approach used to modulate pharmacokinetics properties will be highlighted.

High-Throughput Screening and Triage Assays Identify Small Molecules Targeting c-MYC in Cancer Cells

While c-MYC is well established as a proto-oncogene, its structure and function as a transcription factor have made c-MYC a difficult therapeutic target. To identify small-molecule inhibitors targeting c-MYC for anticancer therapy, we designed a high-throughput screening (HTS) strategy utilizing cellular assays. The novel approach for the HTS was based on the detection of cellular c-MYC protein, with active molecules defined as those that specifically decreased c-MYC protein levels in cancer cells. The assay was based on a dual antibody detection system using Förster/fluorescence resonance energy transfer (FRET) and was utilized to detect endogenous c-MYC protein in the MYC amplified cancer cell lines DMS273 and Colo320 HSR. The assays were miniaturized to 1536-well plate format and utilized to screen the GlaxoSmithKline small-molecule collection of approximately 2 million compounds. In addition to the HTS assay, follow-up assays were developed and used to triage and qualify compounds. Two cellular assays used to eliminate false-positive compounds from the initially selected HTS hits were (1) a cellular toxicity assay and (2) an unstable protein reporter assay. Three positive selection assays were subsequently used to qualify compounds: (1) 384-well cell cycle flow cytometry, (2) 384-well cell growth, and (3) c-MYC gene signature reverse transcription quantitative PCR (RT-qPCR). The HTS and follow-up assays successfully identified three compounds that specifically decreased c-MYC protein levels in cancer cells and phenocopied c-MYC siRNA in terms of cell growth inhibition and gene signatures. The HTS, triage, and three compounds identified are described.

Discovery of GSK2656157: An Optimized PERK Inhibitor Selected for Preclinical Development

We recently reported the discovery of GSK2606414 (1), a selective first in class inhibitor of protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK), which inhibited PERK activation in cells and demonstrated tumor growth inhibition in a human tumor xenograft in mice. In continuation of our drug discovery program, we applied a strategy to decrease inhibitor lipophilicity as a means to improve physical properties and pharmacokinetics. This report describes our medicinal chemistry optimization culminating in the discovery of the PERK inhibitor GSK2656157 (6), which was selected for advancement to preclinical development.

Discovery of 7-methyl-5-(1-{[3-(trifluoromethyl)phenyl]acetyl}-2,3-dihydro-1H-indol-5-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (GSK2606414), a potent and selective first-in-class inhibitor of protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK)

Protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK) is activated in response to a variety of endoplasmic reticulum stresses implicated in numerous disease states. Evidence that PERK is implicated in tumorigenesis and cancer cell survival stimulated our search for small molecule inhibitors. Through screening and lead optimization using the human PERK crystal structure, we discovered compound 38 (GSK2606414), an orally available, potent, and selective PERK inhibitor. Compound 38 inhibits PERK activation in cells and inhibits the growth of a human tumor xenograft in mice.

Acylprolinamides: a new class of peptide deformylase inhibitors with in vivo antibacterial activity

A new class of PDF inhibitor with potent, broad spectrum antibacterial activity is described. Optimization of blood stability and potency provided compounds with improved pharmacokinetics that were suitable for in vivo experiments. Compound 5c, which has robust antibacterial activity, demonstrated efficacy in two respiratory tract infection models.

Structure-based design of potent and selective 3-phosphoinositide-dependent kinase-1 (PDK1) inhibitors

Phosphoinositide-dependent protein kinase-1(PDK1) is a master regulator of the AGC family of kinases and an integral component of the PI3K/AKT/mTOR pathway. As this pathway is among the most commonly deregulated across all cancers, a selective inhibitor of PDK1 might have utility as an anticancer agent. Herein we describe our lead optimization of compound 1 toward highly potent and selective PDK1 inhibitors via a structure-based design strategy. The most potent and selective inhibitors demonstrated submicromolar activity as measured by inhibition of phosphorylation of PDK1 substrates as well as antiproliferative activity against a subset of AML cell lines. In addition, reduction of phosphorylation of PDK1 substrates was demonstrated in vivo in mice bearing OCl-AML2 xenografts. These observations demonstrate the utility of these molecules as tools to further delineate the biology of PDK1 and the potential pharmacological uses of a PDK1 inhibitor.

Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery

Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crystallography and follow-up screening led to the discovery of aminoindazole 19, a potent leadlike PDK1 inhibitor with high ligand efficiency. Well-defined structure-activity relationships and protein crystallography provide a basis for further elaboration and optimization of 19 as a PDK1 inhibitor.

N-borane-N-(trimethylsilyl)morpholine

The title compound, C7H20BNOSi, features an N,N-disubstituted six-membered morpholine ring in a chair conformation, with the trimethylsilyl group in the equatorial position and the borane group in the axial position. The least-squares plane formed by the four C atoms of the morpholine ring has a mean deviation of 0.013 (2) A. The O and N atoms are 0.672 (2) and 0.650 (2) A above and below the plane, respectively.

Idiopathic scoliosis instrumentation using the Lea Plaza sublaminar frame. A preliminary report

We reviewed 28 patients with idiopathic scoliosis operated on using the segmental sublaminar instrumentation devised by Lea Plaza. The results at 2 years show that the spine is rebalanced and normal alignment in the sagittal plane is obtained. The biplanar correction of double curves averaged 64% with a loss of 10% at 2 years. The upper and lower limits of the fusion area must be determined accurately in relation to the pattern of the curve. Combined anterior and posterior arthrodesis is advised in flexible or rigid curves of more than 60 degrees in skeletally immature or mature patients respectively. In double curves over-correction of the primary curve behind its flexibility index, and inclusion of the mobile transitional segments in the fusion area produce decompensation in the frontal plane. One case of total loosening of the frame occurred, but there was no protrusion of the frame, no fractures of the laminae, no sepsis, no pseudarthrosis and no permanent neural damage.

Very low frequency of latex and fruit allergy in patients with spina bifida from Venezuela: influence of socioeconomic factors

BACKGROUND

The prevalence of latex allergy appears to be substantially higher in certain high risk groups, particularly in children with spina bifida. The source of this increase is presently unknown and may be due either to increased infantile exposure or to an intrinsic predilection for atopy in this condition.

OBJECTIVE

We attempted to ascertain the prevalence of latex and tropical fruit allergy in children of lower socioeconomic strata with spina bifida from Caracas, Venezuela, who have limited operative and other medical exposure to latex.

METHODS

Ninety-three unselected patients with spina bifida from clinic and hospital populations were prick tested with commercial (Stallergenes-Pasteur) latex extract and crude glove (Baxter-Triflex, 1/5 wt/vol) latex extract as well as with standardized mite and cockroach, 1/10 wt/vol, extracts (Hollister-Stier). An array of tropical fruits were also included in the battery of skin test materials, using the prick by prick method. Careful family and personal history for allergy as well as any reactions to rubber products were noted, placing emphasis on intraoperative anaphylaxis, number of operations and use of bladder catheters.

RESULTS

Only four patients of the 93 skin tested (4.3%) were positive to latex. Atopy was not a predisposing factor for latex allergy and neither was the number of surgical interventions. No fruit allergy was found in this population and three of the four skin test-positive patients had facial angioedema when exposed to balloons.

CONCLUSIONS

The very low incidence of latex allergy found in our patients with spina bifida could very well be due to a low level of rubber exposure as best exemplified in the use of nonlatex bladder catheters, frequently washed and resterilized surgeon's gloves, and low number of operations per patient. The fact that atopy was no more prevalent in children with spina bifida than in the general population in Venezuela strongly supports exposure level as the major factor determining latex sensitization.

New delta 5,9 fatty acids in the phospholipids of the sea anemone Stoichactis helianthus

The diunsaturated fatty acids 5,9-heneicosadienoic acid, 5,9-docosadienoic acid and 5,9-tricosadienoic acid, the brominated fatty acids 6-bromo- 5,9-heneicosadienoic acid and 6-bromo-5,9-docosadienoic acid, and the polyunsaturated fatty acids 5,9,13-eicosatrienoic acid and 5,9,13-docosatrienoic acid, were identified for the first time in nature in the phospholipids (mainly phosphatidylethanolamine and phosphatidylserine) of the anemone Stoichactis helianthus. Structural elucidation was accomplished by means of mass spectrometry and chemical transformations such as pyrrolidide and dimethyldisulfide derivatization. Other delta 5,9 fatty acids such as 5,9-hexadecadienoic acid, 5,9-octadecadienoic acid, and 5,9-eicosadienoic acid were also identified in the anemone. Our results indicate that delta 5,9 phospholipid fatty acids are not unique to sponges, as previously recognized, but can be found in other marine invertebrates such as an anemone. 24-Methylated sterols predominated in the sterol composition of the anemone investigated.

Environmental pollution and malignant lymphomas: a tentative contribution to geographic pathology

The present study reports of the geographic distribution of 2,878 cases of uniformly classified malignant lymphomas and of 2,349 similar cases from the literature. Data on histological entities are compared with the geographic and socio-economic characteristics of the regions where they preferentially occur. The results provide three patterns in lymphoma distribution: small cell lymphocytic lymphomas are frequent among populations of European extraction and in farming rather than industrial regions. Lymphomas derived from cells of the germinal center are seen preferentially in so-called "underdeveloped countries", and large cell (immunoblastic) lymphomas appear rather characteristic of industrial areas. Besides genetic influences (rare chronic lymphocytic leukemia (CLL) in Asia as compared to Europe), the results suggest environmental cofactors in the pathogenesis of malignant lymphomas. CLL is more frequent in areas with rather low-dose chronic toxic influences such as from the use of fertilizers and pesticides in farming. Germinal center cell lymphomas tend to occur more frequently in countries with nutritional and hygienic deficiencies with frequent infectious diseases. Large cell high malignancy lymphomas apparently prefer highly industrialized regions with pollution of water supplies by more toxic and immunosuppressive substances.

A chromosomal linkage map of Azotobacter vinelandii

A chromosomal map of Azotobacter vinelandii strain UW was constructed. The map was based on measures of cotransfer of various markers mediated by plasmids R68.45 and pJB3JI, on results obtained from conjugal experiments with R-primes, and on recombinants obtained by chromosomal transfer mediated by RP4/Tn5-Mob.

The general stochastic model of nucleotide substitution

DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.

Variation in G + C-content and codon choice: differences among synonymous codon groups in vertebrate genes

The relationship between G + C-content and codon usage in genes of human, mus, rat, bovine and chicken nuclear genomes was investigated. Correlation and lineal regression analyses were carried out on plots that related the frequency of each codon within each synonymous codon group to the G + C-content of the coding sequence as a whole. Under GC pressure, in most of the quartet codon groups there is a preferential choice of the C-ending codon, except in leucine and valine codon groups where the choice of the G-ending codon is preferred. Among ducts, the choice of codons specifying phenylalanine and glutamate shows the strongest dependence on G + C-content. The relationship found between G + C-content and codon usage in these genomes correlate with taxonomic distance.

SDSE: a software package to simulate the evolution of a pair of DNA sequences

An algorithm to simulate DNA sequence evolution under a general stochastic model, including as particular cases all the previously used schemes of nucleotide substitution, is described. The stimulation is carried out on finite, variable length, DNA sequences through a strict stochastic process, according to the particular substitution rates imposed by each scheme. Five FORTRAN programs, running on an IBM PC and compatibles, carry out all the tasks needed for the simulation. They are menu driven and interfaced to the system through a principal menu. All sequence data files used and generated by the SDSE package conform to the standard GenBank database format, thus allowing the use of any sequence retrieved from this databank, as well as the application of other packages to analyse, manipulate or retrieve stimulated sequences.

Transfer of half the calcaneal tendon to the dorsum of the foot for paralytic equinus deformity

Transfer of half of the calcaneal tendon to the dorsum of the foot will maintain correction of a paralytic equinus deformity. We have used this procedure on 97 feet since 1967. Seventy-six were reviewed and the overall results were excellent or good in 69%. The outcome was better in children with cerebral palsy (85% excellent or good) than in those with poliomyelitis (only 13% excellent or good).

An effective mutagenic method in Azotobacter vinelandii

The acridine-like compound ICR-191 is an effective mutagenic agent in Azotobacter vinelandii. Selectable mutants, such as those resistant to chlorate, can be isolated without post-mutagenic segregation. Non selectable mutants, such as those unable to metabolize different sugars, can be easily isolated after twelve generations of post-mutagenic segregation.

Isolation of ntrA-like mutants of Azotobacter vinelandii

A number of chlorate-resistant mutants of Azotobacter vinelandii affected in a general control of nitrogen metabolism were isolated. These mutants could not utilize dinitrogen, nitrate, or nitrite as a nitrogen source. The reason for this inability is that they were simultaneously deficient in nitrogenase and nitrate and nitrite reductase activities. They were complemented by a cosmid carrying a DNA fragment of A. vinelandii able to complement ntrA mutants of Escherichia coli, so they seemed to be ntrA-like mutants.

Some comments on the variance of heterozygosity in finite populations

A new and more accurate formula for the variance of heterozygosity under genetic drift has been obtained. The variance can be partitioned into two components; the first comes from the dispersion of the allelic frequencies among populations, and the second from the dispersion of the actual heterozygosity, h, around their expected values, 2pq. A certain generation exists where the variance reaches a maximum; thus, the genetic drift can be split into two phases by this single maximum.

Non-Hodgkin's lymphomas: a simplified classification scheme

1,292 cases of malignant Non-Hodgkin's lymphomas were classified according to the Rappaport and Kiel classifications and to the New Working Formulation for Clinical Usage (NWF). Subsequently, all lymphoma entities were grouped together following the simple criteria of cell size and growth pattern (small cell, large cell, and mixed cellularity; nodular and diffuse growth). Supplementing these morphological criteria, were data from immunological and cytochemical cell marker studies. The accumulated information was correlated to clinical-prognostic parameters. The results show that using above simplified criteria, all Non-Hodgkin's lymphomas can be classified according to a simple scheme which is of clinical relevance. It can further be deduced from all currently used lymphoma classifications, avoids confusion, and offers abbreviated data useful for computer storage.

Epiglottitis due to ampicillin-tolerant Haemophilus influenzae type b

Tolerance to beta-lactam antibiotics has been described with staphylococci and enterococci, but this phenomenon and its clinical significance in Haemophilus influenzae has not been reported. We have reported a case of bacteremic epiglottitis due to an ampicillin-tolerant, beta-lactamase-negative strain of Haemophilus influenzae type b which was cured with ampicillin therapy alone. The organism was not tolerant to moxalactam, cefotaxime, or rifampin. Rifampin therapy eliminated pharyngeal carriage.

A new working formulation of non-Hodgkin's lymphomas. A retrospective study of the new NCI classification proposal in comparison to the Rappaport and Kiel classifications

Two hundred thirty cases of malignant non-Hodgkin's lymphomas were reclassified in a retrospective study according to the New Working Formulation for Clinical Usage of the NCI as compared to the Rappaport and Kiel classifications. The reproducibility for the individual schemes this study was 81% (Rappaport), 79% (Kiel), and 85% (New Working Formulation). In keeping with the results of the NCI international study, all lymphomas were subdivided into 3 prognostic groups: (1) low-grade malignancy (6.0 years median survival); (2) intermediate-grade malignancy (3.5 years median survival); and (3) high-grade malignancy (1.4 years median survival). The NCI-proposed New Working Formulation for Clinical Usage is thus recommended as practical and unprejudicing classification scheme for general application; however, its usefulness as tool for translating one classification scheme into another appears limited.

Male preference and family size

The influence on family size of the sex of the first children was studied in a sample of 1851 families of students in Sevilla University. Significantly more families limited family size to two or three children when the two or three children were of the same sex than in the opposite case. Significantly more families limited family size to three children when not all the three first children were females. The frequency of families having more than three children is not increased to a larger extent when the three first children are males than in the other cases.

Infected atrial myxoma

A patient with an infected atrial myxoma presented with clinical findings simulating bacterial endocarditis. The diagnosis was made with echocardiography, thus demonstrating the value of this rapid, noninvasive screening test. A ruptured mycotic aneurysm in the brain precluded early surgical excision of the tumor. The rapid evolution of this case to a fatal outcome underscores the need for prompt diagnosis.

Regional ventilation in the differential diagnosis of pulmonary embolism

In the diagnosis of pulmonary embolism by lung scanning, clinical errors of interpretation may arise. Diseases that affect the distribution of pulmonary blood flow, such as pulmonary emphysema and bronchial asthma, may be confused with pulmonary embolism.

With the addition of ventilation studies with 133 xenon to the perfusion scans, distinct differences appear between patients with emboli and those with obstructive lung disease. In patients with pulmonary emboli, ventilation is preserved in the areas of decreased perfusion, whereas patients with obstructive lung disease show both decreased ventilation and perfusion in the affected areas.

Immediate hemodynamic response of patients with atrioventricular block and cardiac failure to transvenous pacing

Immediate hemodynamic improvement in patients with complete heart block occurs when the ventricular rate is increased by electrical pacing. During pacing, there is reduction in the pulmonary artery wedge, right atrial, and left and right ventricular filling pressures. The mean rate of ejection, stroke volume, and stroke work decreased following pacing, whereas the ejection time per minute increased, and dye curves assumed a more normal configuration. Very little change was noted in the resting cardiac output.

The paced heart is able to obtain greater increases in cardiac output, stroke volume, and mean rate of ejection during exercise than when unpaced. In addition, pacing tends to return elevated exercising filling pressures in the right and left ventricles toward normal.