Characterization of the putative active site of mycobacterium tuberculosis pyrazinamidase: An application of bioinformatics software for modeling, docking and testing of drug analogues

Pyrazinamide (PZA), a first-line pro-drug targeting Mycobacterium tuberculosis (Mtb), is a cornerstone in tuberculosis combined therapeutic management. It is converted to Pyrazinoic acid by Pyrazinamidase (PZAse), a 2kD enzyme encoded by pncA gene. Ongoing search for drug analogues of Pyrazinamide entails costly and labor-intensive in-vitro and in-vivo studies. This study presented a process to predict and characterize a putative active site of enzymes using free online softwares and databases. The developed platform was applied to Mycobacterium tuberculosis Pyrazinamidase to perform in-silico experiments such docking of its natural substrate and candidate drug analogues. Briefly, a molecular model of PZAse was constructed through online submission of wild type MTb (H37Rv) PZAse protein sequence to SwissProt Database. Conserved amino acids were identified through multiple sequence alignment of Mycobacterial strains 131, ten strains of Mycobacteria and five organisms expressing closely related nicotinamidase/pyrazinamidase. Conserved residues were plotted into the model supplemented by crevice and drug volume calculations coupled with mutation data from existing literature helped identify the putative active site. Drug docking using HEX software showed that amino acids D8, D49, C138, F13, W68, Y103, H71 and A134 interacted with PZA while residues F94 and Y95 stabilized PZA through non-polar interactions. Molecular docking of Nicotinamide and Morphazinamide revealed higher binding affinities to PZAse due to hydrophobic interactions at the binding site. Testing PZA analogues downloaded from PubChem database suggests Pyrazine-2,6-carboxamide fits the active site, shared similar proximity with PZA. This platform exhibits potential in exploring enzyme-substrate interactions that can be extended to other applications, such as exploring enzyme-substrate or receptor-drug interactions, putative active site identification, and testing candidate drugs in-silico as initial steps in rational drug desig

Towards developing science of survival (SOS) pamphlets for typhoon, flashflood, storm surge and tsunami for earthquakes and their aftermath: A pilot study

The catastrophic devastation from recent natural calamities in the Philippines such as Typhoon Yolanda and Central Visayas earthquake in 2013 had made disaster preparedness a primary concern in the country. Prompted by the critical need to use science to save lives, this study developed Science of Survival (SOS) pamphlets titled When the Wind Rages and Water Rises: A Science of Survival Pamphlet for Typhoon, Flashflood, Storm Surge and Tsunami and When the Earth Moves: A Science of Survival Pamphlet for Earthquakes and Their Aftermath (Liquefaction, Fire, Landslide and Tsunami). The study used the` developmental research design consisting of three phases: needs and context analysis phase, design, development and formative evaluation phase, and semi-summative evaluation phase. By carefully documenting the iterative process of analysis, design, evaluation and revision, insights were sought with regard to the development of pamphlets that provide useful and scientifically accurate information about surviving natural calamities such as typhoons and earthquakes. Experts from government agencies involved in disaster risk reduction and management, science experts in the university, and students who were victims of major disasters reviewed and evaluated the pamphlets. The results of the semi-summative quantitative evaluation showed that both pamphlets are highly acceptable as supplementary resourc

Characterization of Philippine drug-susceptible and multi-drug resistant mycobacterium tuberculosis isolates through combined 15-locus MIRU-VNTR genotyping and mutation analysis of drug resistance genes

Molecular genotyping, an important strategy to characterize bacterial strains infecting patients, allows identification of M. tuberculosis (MTb) complex members with varying responses to anti-mycobacterial therapy. M. tuberculosis Interspersed Repeating Units – Variable Number of Tandem Repeats (MIRU-VNTR) is a fast, reproducible and cost-effective PCR-based method capable of differentiating MTb strains. This study focused on evaluating the utility of MIRU-VNTRs to differentiate 54 MTB isolates from the Lung Center of the Philippines (LCP) through amplification of twelve MIRU-VNTRs and three Exact Tandem Repeats (ETRs). Digital codes were determined per isolate through calculation of VNTR repeats and analyzed using the MIRU-VNTRplus program (http://www.miruvntrplus.org/MIRU/index.faces). Values of the Hunter-Gaston discriminatory index (HGDI) suggest that five of fifteen (33.33%) MIRU-VNTRs are highly discriminating (\u3e0.75). All MIRU-VNTRs and ETRs except ETRC had HGDI values indicative of good resolving power (≥0.5). Among the LCP isolates, four Mtb clusters closely related to the East AfricanIndian strain family were identified on the basis of MIRU-VNTR profiles and mutation data on rpoB, katG and gyrA genes obtained through gene sequencing, which is consistent with previous reports regarding the existence of a distinct Manila family of MTb strains. The said four clusters have been designated as EAI-M1 through EAI-M4, in order of increasing propensity to develop drug resistance. Among these clusters, rpoB, katG and gyrA mutations were observed that are highly similar to those already reported in literature. Our results demonstrate that a 15-locus MIRU-VNTR genotyping strategy in combination with mutation profiling of drug resistance-related genes could serve as a molecular-epidemiology tool for characterizing and monitoring drug-susceptible and multi-drug resistant MTb strains in the Philippines

Initial validation of the chemistry MicroLab kit (Chem.µLab Kit) in facilitating learning of selected chemistry concepts for K-12 science

The introduction of the Chemistry MicroLab Kit (CμLK) aims to assist student learning of chemistry in a more interactive and practical way. Each kit was designed to address certain topics in chemistry that may otherwise be too abstract to do in a lecture-discussion set up. Among the many topics tackled in secondary school, 13 undergraduate students were hand- picked for this preliminary study. The test subjects for this initial phase of the research both majors and non-majors, were currently enrolled in a Chemistry course. It was also tried out at the Institute for Teaching and Learning (formerly Center for Teaching and Learning) with selected third year students. In this preliminary study, the students found three activities to be interesting and well-balanced: Gas Laws in a Box, Particulate Nature of Matter, and Solution Rules. In assessing the activities, they highly rated the easy language used for understanding the procedures, followed by setup of the experiments and a step-by-step presentation of the procedures. Initial results of the study find it a promising addition to the secondary level chemistry activities because CμLK enhances students’ attitudes and motivation toward chemistry laboratory work

LET as predictor of teaching performance: The case of PNU graduates across disciplines (2007-2010)

This study discusses the relationship between the performance in the Licensure Examination for Teachers (LET) taken by PNU graduates and their teaching performance. The LET scores, obtained from PRC, and teaching performance evaluation scores given by the Head, Peer and Self, were correlated. The results indicate that there is a negligible link between the scores in the LET and the teaching performance of the respondents. However, positive significant correlations, although weak, are found in the case of CLLL, COS, and 2007 examinees. The “Very Satisfactory” or “Outstanding” teaching performance evaluation rating earned by the respondents indicates the knowledge, skills, and philosophies learned during the pre‐service training. Finally, this research posits that an emerging paradigm of teaching performance must be progressively developed