Development of an informatics platform for therapeutic protein and peptide analytics.

The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with biopolymers, including peptides, antibodies, and protein therapeutics programs. The program brings under a single user interface tools to filter, mine, and visualize data as well as those algorithms needed to organize sequences. As part of the data-analysis tools, we introduce two new concepts: mutation cliffs and invariant maps. Invariant maps show the variability of properties when a monomer is maintained constant in a position of the biopolymer. Mutation cliff maps draw attention to pairs of sequences where a single or limited number of point mutations elicit a large change in a property of interest. We illustrate the program and its applications using a peptide data set collected from the literature.

Molecular Diversity Assessment using Chemotypes.

BACKGROUND: Many techniques to design chemical libraries for screening have been put forward over time. General use libraries are still important when screening against novel targets, and their design has relied on the use of molecular descriptors. In contrast, chemotype or scaffold analysis has been used less often. OBJECTIVE: We describe a simple method to assess chemical diversity based on counts of the chemotypes that offers an alternative to model chemical diversity. We describe a simple method to assess chemical diversity based on counts of the chemotypes that offers an alternative to model chemical diversity based on computed molecular properties. We show how chemotype counts can be used to evaluate the diversity of a library and compare diversity selection algorithms. We demonstrate an efficient compound selection algorithm based on chemotype analysis. METHODS: We use automated chemotype perception algorithms and compare them to traditional techniques for diversity analysis to check their effectiveness in designing diverse libraries for screening. RESULTS: The best type of molecular fingerprints for diversity selection in our analysis are extended circular fingerprints, but they can be outperformed by the use of a chemotype diversity algorithm, which can be more intuitive than traditional techniques based on molecular descriptors. Chemotype- -based algorithms retrieve a larger share of the chemotypes contained in a library when picking a subset of the chemicals in a collection. CONCLUSIONS: Chemotype analysis offers an alternative for the generation of a general-purpose screening library as it maximizes the number of chemotypes present in a subset with the smallest number of compounds. The applications of methods based on chemotype analysis that does not resort to the use of molecular descriptors are a very promising but seldom explored area of chemoinformatics.

City Cancer Challenge: Changing the Future of Cancer in Urban Populations.

Incidence and mortality from cancer is increasing in most countries in the world, with the highest burden in developing countries. City Cancer Challenge (C/Can), an initiative launched in 2017, aims to improve access to quality cancer care in metropolitan areas (1 million inhabitants or more) in low- and upper-middle income countries by transforming the way stakeholders at the city, regional, and national levels collectively design, plan, and implement local cancer solutions. The approach is built on the core principle that local leaders in cities define their own needs and craft solutions with the support of a network of global, regional, and local partners that reflect an understanding of the unique local context. C/Can aims to build a collective movement of cities that can together deliver quality, equitable, and sustainable cancer control solutions for all.

Antegrade bowel intussusception after remote Whipple and Puestow procedures for treatment of pancreas divisum.

To date, antegrade intussusception involving a Roux-en-Y reconstruction has been reported only once. We report a case of acute bowel obstruction due to an intussusception involving two Roux-en-Y limbs in a 40-year-old woman with a history of chronic pancreatitis due to pancreas divisum. Four years preceding this event, the patient had undergone a Whipple procedure, and three years prior to that, a Puestow operation. The patient was successfully treated with bowel resection and a side-to-side anastomosis between the most distal aspect of the bowel and the most distal Roux-en-Y reconstruction, which preserved both Roux-en-Y reconstructions.

[Pulmonary mycobacteriosis in non HIV patients, Buenos Aires City, 2003-2004]. / Micobacteriosis pulmonar en pacientes HIV negativos en la Ciudad de Buenos Aires, años 2003-2004.

Pulmonary disease, due to Mycobacteria other than tuberculosis, is mainly suspected in HIV + patients, or underlying other diseases. In our country, there is no updated information on the prevalence of this pulmonary disease, its treatment and evolution in immucocompetent patients. We present 10 cases of pulmonary disease due to Mycobacteria other than tuberculosis in non HIV patients: clinical-bacteriological diagnosis, treatment and evolution.

Using NMR for ligand discovery and optimization.

Several recent technology-driven advances in the area of NMR have rekindled an interest in the application of the technology to problems in drug discovery and development. A unique aspect of NMR is that it has applicability in broadly different areas of the drug discovery and optimization processes. NMR techniques for screening aimed at the discovery of novel ligands or low molecular weight structures for fragment-based build up procedures are being applied commonly in the industry. Application of NMR in structure-guided drug design and metabonomics are also becoming routine. We present an overview of some of the most recent NMR developments in these areas.

Ring systems in mutagenicity databases.

The distribution of ring systems in public mutagenicity databases is analyzed. An automated enumeration of substructures permits determination of the occurrence of different scaffolds in data sets. The counts are used to perform population analysis via proportions and odds ratios of mutagenic compounds. Pairwise calculations of odds ratios between scaffolds allow comparison of ring systems for isostere replacement studies. These findings are presented in tables that readily show which scaffold is likely to occur in mutagenic compounds. Also, rings identified in public domain mutagenicity data sets are compared to rings in drugs data sets; unfortunately, public mutagenicity data sets do not reflect the types of scaffolds in drugs and those typically used in medicinal chemistry. The findings bring into question the utility of predictive models that were derived from public domain data sets. The automated ring identification and statistical approaches used here can be applied to other pharmacological properties to yield information about chemical scaffolds.

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox.

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.

Breast tissue accumulation of retinamides in a randomized short-term study of fenretinide.

PURPOSE: The synthetic retinoid N-(4-hydroxyphenyl)retinamide [4-HPR (or fenretinide)] has preclinical and clinical preventive activity in breast carcinogenesis. 4-HPR and its metabolites have been shown to accumulate in the mammary tissue of rodents. We assessed levels of 4-HPR and its major metabolite, N-(4-methoxyphenyl)retinamide (4-MPR), in plasma and in normal and neoplastic breast tissue obtained from women treated with 4-HPR. EXPERIMENTAL DESIGN: We randomly assigned 14 women with suspected or very recently diagnosed breast cancer to receive 100, 200, or 300 mg of 4-HPR daily for 3-12 days before scheduled biopsy, lumpectomy, or mastectomy. Using high-performance liquid chromatography, we measured post-4-HPR-treatment concentrations of 4-HPR and 4-MPR in plasma and breast tissue obtained during surgery. RESULTS: Breast tissue and plasma retinamide (4-HPR plus 4-MPR) concentrations increased significantly with short-term oral administration of 4-HPR. Retinamide levels increased in a linear and dose-related fashion in plasma, whereas they peaked and plateaued at 200 mg/day in breast tissue. The total retinamide concentration in breast tissue exceeded that in plasma at each 4-HPR dose. The highest mean tissue:plasma retinamide ratios were achieved at 200 mg/day: 639.5 +/- 253.8 to 190.6 +/- 91.9 ng/ml (4.8:1) for 4-HPR and 594.4 +/- 201.9 to 130.5 +/- 37.8 ng/ml (6.6:1) for 4-MPR. Plasma retinol levels decreased in association with increasing 4-HPR doses. Two patients experienced grade 1 toxicity at the 300 mg/day dose. CONCLUSIONS: These findings indicate that retinamides preferentially accumulate in human breast tissue (versus plasma). 4-HPR tissue concentrations at 200 mg/d were equivalent to those that inhibit growth and induce apoptosis of breast cancer cells in vitro. Previous clinical and correlative laboratory results suggest that 4-HPR may reduce risk in premenopausal women, who are more prone (than are postmenopausal women) to estrogen receptor (ER)-negative breast cancer development. The present results and previous data (including in vitro 4-HPR activity against ER-negative breast cancer) support further study of 4-HPR in the setting of premenopausal/ER-negative breast cancer prevention.

[High prevalence of beta hemolytic streptococci isolated from throat swabs in Buenos Aires]. / Aumento en la prevalencia de estreptococos beta hemoliticos en hisopados faríngeos en Buenos Aires.

Beta hemolytic streptococci, particulary group A, are the most frequently isolated pathogens in cases of pharyngoamigdalitis. Other beta hemolytic streptococci also produce this pathology. An increase of positive cultures for group A streptococci was detected during 2004 in relation to previous years. The aim of this study was to determine the isolation rates of beta hemolytic streptococci groups A, C and G during a period of 5 years. Pharyngeal exudates were obtained from children (aged 6 months to 18 years) and adults. Swabs were cultured on Columbia agar plates containing 5% sheep blood. Lancefield grouping was performed using a latex immunoagglutination test. Group A beta hemolytic streptococci were isolated significantly more frequently from pediatric population than from adults. Groups A, C and G beta hemolytic streptococci were isolated significantly more frequently during 2004 than in previous years. Group G beta hemolytic was more prevalent in adult population than in patients less than 18 years of age. Among the isolated beta hemolytic streptococci, in adults and children, 18.9% and 5.8% were non-group A streptococci, respectively. Therefore special attention should be paid not only to group A beta hemolytic streptococci but also to other groups. Throat culture is the most reliable method for detecting the presence of the beta hemolytic streptococci and should also be indicated in adult patients.

Chemoproteomics as a basis for post-genomic drug discovery.

The large number of small organic compounds now available for drug-lead screening has led to numerous methods for classifying molecular similarity and diversity, the aim being to restore a balance between the quantity and drug-like quality of compounds in small-molecule libraries. Whereas structural and physicochemical attributes continue to be emphasized in compound selection for drug-lead screening, chemoproteomics--the use of biological information to guide chemistry--offers a highly efficient alternative to small-molecule characterization that can accelerate drug discovery in the post-genomic era.

A path from primary protein sequence to ligand recognition.

A novel method to organize protein structural information based solely on sequence is presented. The method clusters proteins into families that correlate with the three-dimensional protein structure and the conformation of the bound ligands. This procedure was applied to nicotinamide adenine dinucleotide [NAD(P)]-utilizing enzymes to identify a total of 94 sequence families, 53 of which are structurally characterized. Each of the structurally characterized proteins within a sequence family correlates to a single protein fold and to a common bound conformation of NAD(P). A wide range of structural folds is identified that recognize NAD(P), including Rossmann folds and beta/alpha barrels. The defined sequence families can be used to identify the type and prevalence of NAD(P)-utilizing enzymes in the proteomes of sequenced organisms. The proteome of Mycobacterium tuberculosis was mined to generate a proteome-wide profile of NAD(P)-utilizing enzymes coded by this organism. This enzyme family comprises approximately 6% of the open reading frames, with the largest subgroup being the Rossmann fold, short-chain dehydrogenases. The preponderance of short-chain dehydrogenases correlates strongly with the phenotype of M. tuberculosis, which is characterized as having one of the most complex prokaryotic cell walls.

Novel cyclooxygenase-1 inhibitors discovered using affinity fingerprints.

We used protein affinity fingerprints to discover structurally novel inhibitors of cyclooxygenase-1 (COX-1) by screening a selected number of compounds, thus providing an alternative to extensive screening. From the affinity fingerprints of 19 known COX-1 inhibitors, a computational model for COX-1 inhibition was constructed and used to select candidate inhibitors from our compound library to be tested in the COX-1 assay. Subsequent refinement of the model by including affinity fingerprints of inactive compounds identified three molecules that were more potent than ibuprofen, a commonly used COX-1 inhibitor. These compounds are structurally distinct from those used to build the model and were discovered by testing only 62 library compounds. The discovery of these leads demonstrates the efficiency with which affinity fingerprints can identify novel bioactive chemotypes from known drugs.

Frequency and antibiotic susceptibility patterns of urinary pathogens in male outpatients in Argentina.

INTRODUCTION: Knowledge of the etiology and antimicrobial susceptibility patterns of uropathogens is important for determining the best treatment option. This study aimed to determine the distribution and antibiotic susceptibility patterns of bacterial strains isolated from adult male outpatients. METHODOLOGY: Between November 2012 and April 2013, 3,105 community urine samples were analyzed from adult male patients who attended the Laboratorio Hidalgo, Buenos Aires, Argentina. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method. Isolates resistant to third generation cephalosporin were tested for extended-spectrum beta-lactamase (ESBL) production using the double-disk synergy test. RESULTS: Of the 3,105 urine samples analyzed, 791 (25.5%) had significant bacteriuria. The frequency of positive urine cultures increased significantly with patient age. Escherichia coli was isolated most frequently (47.3%), followed by Enterococcus faecalis (13.6%), and Klebsiella pneumoniae (11.9%). Gram-negative organisms represented 78.8% of urinary pathogens. The highest activities against Gram-negative bacteria were found with imipenem (99.0%), amikacin (98.1%), ertapenem (94.2%), fosfomycin (90.7%), and piperacillin-tazobactam (90.1%). The frequencies of ESBLs among E. coli, K. pneumoniae, and P. mirabilis were 15.2 %, 22.3%, and 8%, respectively. Fosfomycin, piperacillin-tazobactam, and nitrofurantoin were most effective against Gram-positive organisms. CONCLUSIONS: Fosfomycin may be an excellent option for cystitis treatment in patients without risk factors, whereas piperacillin-tazobactam is preferred for the treatment of parenchymatous UTIs, complicated UTIs, and UTIs associated with risk factors. To ensure the optimal selection of antibiotics, physicians should have access to up-to-date information about the local prevalence of antimicrobial resistance.

[Emergence of high-level resistance to gentamicin and streptomycin in Streptococcus agalactiae in Buenos Aires, Argentina]. / Emergencia de Streptococcus agalactiae con resistencia de alto nivel a gentamicina y streptomicina en Buenos Aires, Argentina.

INTRODUCTION: Streptococcus agalactiae has become recognized as a cause of serious illness in newborns, pregnant women, and adults with chronic medical conditions. Optimal antimicrobial therapy for serious infections requires the use of synergistic combinations of a cell wall-active agent, such as a penicillin, with an aminoglycoside, which results in bactericidal activity against this organism. The synergistic effect is eliminated by the acquisition of high-level resistance (HLR) to aminoglycosides. The aim of our study was to determine the prevalence of HLR to gentamicin (GEN) and streptomycin (EST).The ability to detect HLR using a standard agar screen plate and high-content discs was investigated. METHODS: This study was conducted with 141 strains of S. agalactiae isolated from vaginal and rectal swabs of pregnant women at term. Minimum inhibitory concentrations (MICs) to GEN and STR were determined by the E-test method. Disks of GEN (120 µg) and STR (300 µg) were used to detect HLR. Agar screening plates were performed with GEN 100 mg/L, GEN 500 mg/L and STR 2000 mg/L. RESULTS: The HLR to GEN and STR was detected in 13.5% and 16.3% of the isolates respectively. Among 141 strains, 7.8% were simultaneously resistant to GEN and STR. With 120-µg GEN and 300-µg STR disks, strains for which MICs were ≥ 512 mg/L and ≥ 1024 mg/L had no zones of inhibition. Isolates with inhibitory zones for GEN and STR of ≥13 mm showed a MICs ≤ 64 mg/L and ≤ 512 mg/L. All the screening plates were negative for these isolates. HLR to aminoglycosides was associated (83.9%) with resistance to erythromycin and/or clindamycin. CONCLUSIONS: This study highlights the emergence of strains with HLR to aminoglycosides. The disk-agar diffusion test performed with high-content aminoglycoside disks and screening plates can provide laboratories with a convenient and reliable method for detecting S. agalactiae isolates that are resistant to aminoglycoside-betalactam synergy.

Faecal carriage of ESBL-producing Enterobacteriaceae and carbapenem-resistant Gram-negative bacilli in community settings.

INTRODUCTION: The aim of this study was to determine the prevalence of intestinal carriage of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Gram-negative bacilli in the community in Buenos Aires, Argentina. METHODOLOGY: Faecal samples from 164 non-hospitalized patients were cultured on CHROMagar KPC and CHROMagar ESBL plates. Isolates resistant to third-generation cephalosporins or carbapenems were selected for further study. The minimal inhibitory concentration (MIC) of the isolates was determined using the E-test method. The phenotypic detection of ESBLs and carbapenemases was performed using the double-disc synergy test. RESULTS: The rate of faecal carriage of Enterobacteriaceae resistant to third-generation cephalosporins was 26.8%. Escherichia coli represented a large majority (75%) of the isolates recovered. Thirty-three ESBL-producing isolates were detected from 31 faecal samples (18.9% of the collected specimens). Eight carbapenem-resistant Gram-negative bacilli were recovered from eight specimens (4.9%). CONCLUSIONS: This study revealed a high prevalence of faecal carriage of multidrug-resistant Gram-negative bacteria, including ESBLs, in Buenos Aires. Therefore, the use of surveillance cultures will be helpful for tracking and monitoring the spread of ESBL-producing Enterobacteriaceae within community settings.

Maternal carriage of extended-spectrum beta-lactamase-producing Escherichia coli isolates in Argentina.

The aim of this study was to determine the prevalence of vaginal Escherichia coli colonization and perianal carriage of Enterobacteriaceae resistant to third generation cephalosporins in pregnant women. Vaginal and perianal samples from 259 pregnant women were studied. Vaginal swabs were inoculated onto MacConkey agar plates and perianal swabs were inoculated onto CHROMagar extended-spectrum beta-lactamase (ESBL) plates. The minimal inhibitory concentration of the isolates was determined using the Epsilometer test method. The phenotypic detection of ESBLs was performed by the combined disc method using cefotaxime versus cefotaxime plus clavulanate. The prevalence of vaginal E. coli colonization during pregnancy was 14.3%. The resistance rate to ampicillin, gentamicin, and cefotaxime was 48.6, 10.8, and 0.8%, respectively. Enterobacteriaceae resistant to third generation cephalosporins were recovered in 7.3% of all perianal specimens. Among them, 5.4% of pregnant women were colonized with E. coli ESBL-producer strains. The present study revealed that colonization with Enterobacteriaceae resistant to third generation cephalosporins is significant in pregnancy. ESBL-producing E. coli were the most prevalent organisms. Screening strategies designed to monitor for ESBL-producing E. coli could be useful in endemic areas to prevent perinatal transmission and the introduction of multiresistant strains to the maternity ward.