Informatics resources for tuberculosis--towards drug discovery

Integration of biological data on gene sequence, genome annotation, gene expression, metabolic pathways, protein structure, drug target prioritization and selection, has resulted in several online bioinformatics databases and tools for Mycobacterium tuberculosis. Alongside there has been a growth in the list of cheminformatics databases for small molecules and tools to facilitate drug discovery. In spite of these efforts there is a noticeable lag in the drug discovery process which is an urgent need in the case of emerging and re-emerging infectious diseases. For example, more than 25 online databases are available freely for tuberculosis and yet these resources have not been exploited optimally. Informatics-centered drug discovery based on the integration and analysis of both bioinformatics and cheminformatics data could fill in the gap and help to accelerate the process of drug discovery. This article aims to review the current standing of developments in tuberculosis-bioinformatics and highlight areas where integration of existing resources could lead to acceleration of drug discovery against tuberculosis. Such an approach could be adapted for other diseases as well.     

Spectrum and Prevalence of Fungi Infecting Deep Tissues of Lower-Limb Wounds in Patients with Type 2 Diabetes

The prevalence rate and spectrum of fungi infecting deep tissues of diabetic lower-limb wounds (DLWs) have not been previously studied. Five hundred eighteen (382 male and 136 female) consecutive patients with type 2 diabetes hospitalized due to infected lower-limb wounds were enlisted in this study. Deep tissue (approximately 0.5- × 0.5-cm size) taken perioperatively from the wound bed was cultured for fungi. Fungi was found in 27.2% (141/518) of the study population. Candida parapsilosis (25.5%), Candida tropicalis (22.7%), Trichosporon asahii (12.8%), Candida albicans (10.6%), and Aspergillus species (5.0%) were the most predominant fungal isolates. Of the fungal isolates, 17.7% were resistant to itraconazole, 6.9% were resistant to amphotericin B, 6.9% were resistant to voriconazole, 3.9% were resistant to fluconazole, and 1.5% were resistant to flucytosine. Of the population, 79.7% (413/518) had bacterial infection in deep tissue. The predominant isolates were Enterococcus faecalis (14.1%), Staphylococcus aureus (12.2%), and Pseudomonas aeruginosa (10.8%). Mixed fungal and bacterial infections were seen in 21.4% of patients, while 5.8% had only fungal infection and 58.3% had only bacterial infections. Another 14.5% had neither bacteria nor fungi in the deep tissue. Patients with higher glycosylated hemoglobin levels had significantly more fungal infections. Our study reveals that deep-seated fungal infections are high in DLWs. In the context of delayed wound healing and amputation rates due to DLWs, it is important to study the pathogenicity of fungi in deep tissues of DLWs and their possible contribution to delayed wound healing. The role of antifungal agents in wound management needs to be evaluated further.Diabetes is now a worldwide epidemic. Among the 191 WHO member states, India has the highest number of people with diabetes (37). Fifteen percent of patients with diabetes develop lower-extremity ulcers during their lifetimes. Diabetes is the most common cause for nontraumatic amputation of lower extremities (1, 39). Eighty-five percent of these lower-limb amputations are preceded by polymicrobial infections of the wound (23, 26, 36). Despite proper surgical and antibacterial therapy for infected diabetic lower-limb wounds (DLWs), the global long-term outcome of patients was found to be poor; only <50% of these patients had global therapeutic success (16, 22).Fungal infections among immunocompromised patients are one of the major health concerns worldwide (5, 13, 19), but the spectrum of fungi infecting DLWs and their pathogenicity have not yet been studied thoroughly. Therefore, clinicians and surgeons treating diabetic foot wounds suspect only bacterial infections and treat them with antibacterial agents. They do not routinely send deep tissue from the wound bed for fungal culture and sensitivity, either due to lack of literature support or due to the assumption that there would not be any fungal infections in the DLWs. Surprisingly, our retrospective pilot study showed 27.9% positive fungal cultures in 318 diabetic patients with DLWs. We speculate that opportunistic fungi may invade deep into the wounds and contribute to delayed wound healing in some of the diabetic patients who are otherwise immunocompromised compared to nondiabetics.The magnitude of fungal infections in diabetic lower extremities in India has been previously studied in a limited number of patients. Hence, we undertook this study to estimate the prevalence of fungi in DLWs and also to describe the spectrum of these fungal infections.     

Design, synthesis and biological evaluation of some novel 3-cinnamoyl-4-hydroxy-2H-chromen-2-ones as antimalarial agents

A novel series of 3-cinnamoyl-4-hydroxy-2H-chromen-2-ones were designed, synthesized and screened for antiplasmodial activity. Eleven compounds of the series exhibited micromolar potency against chloroquine sensitive and chloroquine resistant strains. The most potent compound 4-hydroxy-3-(3-(4-nitrophenyl)acryloyl)-2H-chromen-2-one showed inhibitory potency (IC₅₀) of 3.1 and 4?μg/ml against chloroquine sensitive and chloroquine resistant strains, respectively. A structure activity relationship study was performed by correlating the effect of substituents with the antimalarial activity of the title compounds. The novel 3-cinnamoyl-4-hydroxy-2H-chromen-2-ones reported here should be good lead for further development of antimalarial agents that can overcome resistance.     

Pathotypes of diarrheagenic Escherichia coli in children attending a tertiary care hospital in South India

The prevalence of diarrheagenic Escherichia coli (DEC) in children under 5 years was studied in children with diarrhea and controls in South India. Four polymerase chain reaction (PCR) “schemes” were used to detect genes of the 6 pathotypes of DEC. In 394 children with diarrhea, 203 (52%) DEC infections were found. Among the 198 controls, 126 (63%) DEC infections were found. Enteroaggregative E. coli was the most common pathotype by multiplex PCR both in cases (58, 14.7%) and controls (47, 23.7%), followed by enteropathogenic E. coli seen in 10% cases and 8% of controls. Enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC), and diffusely adherent E. coli (DAEC) were found in 4.1%, 2.0%, 1.0%, and 0.5% of cases, respectively. ETEC was found in 2.5% of controls, but EHEC, EIEC, and DAEC were not detected. Overall, no single assay worked well, but by discounting genes with a pathogenicity index of less than 1, it was possible to use the PCR assays to identify DEC in 75/394 (19%) cases and 12/198 (6.1%) controls, while mixed infection could be identified in 8/394 (2%) cases and 2/198 (1%) controls.     

Anesthesia for deep brain stimulation in traumatic brain injury‐induced hemidystonia

Deep brain stimulation in an awake patient presents several unique challenges to the anesthesiologist. It is important to understand the various stages of the procedure and the complexities of anesthetic management in order to have a successful surgical outcome and provide a safe environment for the patient.     

Respiratory variation in peak aortic velocity accurately predicts fluid responsiveness in children undergoing neurosurgery under general anesthesia

The determination of fluid responsiveness in the critically ill child is of vital importance, more so as fluid overload becomes increasingly associated with worse outcomes. Dynamic markers of volume responsiveness have shown some promise in the pediatric population, but more research is needed before they can be adopted for widespread use. Our aim was to investigate effectiveness of respiratory variation in peak aortic velocity and pulse pressure variation to predict fluid responsiveness, and determine their optimal cutoff values. We performed a prospective, observational study at a single tertiary care pediatric center. Twenty-one children with normal cardiorespiratory status undergoing general anesthesia for neurosurgery were enrolled. Respiratory variation in peak aortic velocity (ΔVpeak ao) was measured both before and after volume expansion using a bedside ultrasound device. Pulse pressure variation (PPV) value was obtained from the bedside monitor. All patients received a 10 ml/kg fluid bolus as volume expansion, and were qualified as responders if stroke volume increased?>15% as a result. Utility of ΔVpeak ao and PPV and to predict responsiveness to volume expansion was investigated. A baseline ΔVpeak ao value of greater than or equal to 12.3% best predicted a positive response to volume expansion, with a sensitivity of 77%, specificity of 89% and area under receiver operating characteristic curve of 0.90. PPV failed to demonstrate utility in this patient population. Respiratory variation in peak aortic velocity is a promising marker for optimization of perioperative fluid therapy in the pediatric population and can be accurately measured using bedside ultrasonography. More research is needed to evaluate the lack of effectiveness of pulse pressure variation for this purpose.     

Ionophore A-23187- and thrombin-induced platelet aggregation: independence from cycloxygenase products.

Stimulation of platelets labeled with [14C]-arachidonate by ionophore A23187 or thrombin produces rapid degradation of specific membrane phospholipids. This is also reflected by the release of [14C]archidonate, which is immediately transformed into products of the cycloxygenase and lipoxygenase enzyme systems, and by increased labeling of phosphatidic acid. Arachidonate metabolism can be effectively prevented by preincubation with indomethacin and eicosatetraynoic acid, but platelet aggregation induced by ionophore A23187 or trombin is not blocked under these conditions. Nevertheless, in the virtually total absence of metabolism of arachidonate, platelet aggregation still occurs concomitantly with phospholipid breakdown and with increased labeling of phosphatidic acid. Increased levels of cyclic AMP block both phospholipase activation and aggregation induced by ionophore A23187 and trombin. These data suggest that some early consequence of phospholipase activation, independent of a metabolic product of arachidonate but possibly related to the production of phosphatidic acid, may play a central, causative role in mediating platelet aggregation.     

Virtual screening based on pharmacophoric features of known calpain inhibitors to identify potent inhibitors of calpain

Calpain, a member of the group of cysteine protease enzymes, has been recognized as a promising drug target for several diseases, including cataract. In the present study, an attempt was made to identify potential inhibitors of calpain by employing a pharmacophore-based virtual screening and docking approach. A knowledge-based 3D pharmacophore model was generated, based on the features of established calpain inhibitors SJA6017, MDL28170, E64D, SNJ 1715, calpastatin and CHEMBL 1921830, using the PHASE module of Schrödinger Suite. The best pharmacophore model (AAADH) derived consisted of five features, namely three hydrogen bond acceptors, one hydrogen bond donor and one hydrophobic region. This common pharmacophore hypothesis was then used to perform virtual screening against a binding database, with due consideration to the Lipinski ‘rule of five’ and absorption, distribution, metabolism, excretion properties were calculated using the Qikprop module, so as to obtain a pool of lead molecules. The short-listed lead molecules were then subjected to docking analysis with that of the mutated calpain 1 (1KXR) to reduce the false positive and false negative results against the target receptor. Interaction data and its corresponding interaction energy, along with binding energy calculated for the hit ligand (650709) and mutated receptor (1KXR) complex, suggest that compound 650709 has a more effective inhibitory potential than that of the other established calpain inhibitors.