20 research outputs found
Systems Biology And The Development Of Vaccines And Drugs For Malaria Treatments
The sequencing race has ended and the functional race has already
begun. Microarray technology enables simultaneous gene expression
analysis of thousands of genes, enabling a snapshot of an organisms'
transcriptome at an unprecedented resolution. The close correlation
between gene transcription and function, allow the inference of
biological processes from the assessed transcriptome profile. Among the
sophisticated analytical problems in microarray technology at the front
and back ends respectively, are the selection of optimal DNA oligos and
computational analysis of the genes expression. In this review paper,
we analyse important methods in use today in customized oligos design.
In the course of executing this, we discovered that the oligos designer
algorithm hanged on gene PFA0135w of chromosome 1, while designing
oligos for the gene sequences of Plasmodium falciparum . We do not
know the reason for this yet, as the algorithm runs on other sequences
like the yeast ( Saccharomyces cervisiae ) and Neurospora crassa . We
conclude the paper highlighting the procedures encompassing the back
end phase and discuss their application to the development of vaccines
and drugs for malaria treatment. Note that, malaria is the cause of
significant global morbidity and mortality with 300-500 million cases
annually. Our aims are not ends, but a means to achieve the following:
Iterate the need for experimental biologists to (i) know how to design
their customized oligos and (ii) have some idea about gene expression
analysis and the need for cooperation between experimental biologists
and their counterpart, the computational biologists. These will help
experimental biologists to coordinate very well the front and the back
ends of the system biology analysis of the whole genome effectively
Recent advances in functionalized quinoline scaffolds and hybridsâExceptional pharmacophore in therapeutic medicine
Quinoline is one of the most common nitrogen-containing heterocycles owing to its fascinating pharmacological properties and synthetic value in organic and pharmaceutical chemistry. Functionalization of this moiety at different positions has allowed for varying pharmacological activities of its derivative. Several publications over the last few decades have specified various methods of synthesis. This includes classical methods of synthesizing the primary quinoline derivatives and efficient methods that reduce reaction time with increased yield employing procedures that fulfill one of the twelve green chemistry principles, âsafer solventâ. The metal nanoparticle-catalyzed reaction also serves as a potent and effective technique for the synthesis of quinoline with excellent atom efficiency. The primary focus of this review is to highlight the routes to synthesizing functionalized quinoline derivatives, including hybrids that have moieties with predetermined activities bound to the quinoline moiety which are of interest in synthesizing drug candidates with dual modes of action, overcoming toxicity, and resistance amongst others. This was achieved using updated literature, stating the biological activities and mechanisms through which these compounds administer relief. The ADMET studies and Structure-Activity Relationship (SAR) of novel derivatives were also highlighted to explore the drug-likeness of the quinoline-hybrids and the influence of substituent characteristics and position on the biological activity of the compounds
Synthesis, in silico and in vitro antimicrobial efficacy of substituted arylidene-based quinazolin-4(3H)-one motifs
Introduction: Quinazolin-4(3H)-one derivatives have attracted considerable attention in the pharmacological profiling of therapeutic drug targets. The present article reveals the development of arylidene-based quinazolin-4(3H)-one motifs as potential antimicrobial drug candidates.Methods: The synthetic pathway was initiated through thermal cyclization of acetic anhydride on anthranilic acid to produce 2-methyl-4H-3,1-benzoxazan-4-one 1, which (upon condensation with hydrazine hydrate) gave 3-amino-2-methylquinazolin-4(3H)-one 2. The reaction of intermediate 2 at its amino side arm with various benzaldehyde derivatives furnished the final products, in the form of substituted benzylidene-based quinazolin-4(3H)-one motifs 3aâl, and with thiophene-2-carbaldehyde to afford 3Â m. The purified targeted products 3aâm were effectively characterized for structural authentication using physicochemical parameters, microanalytical data, and spectroscopic methods, including IR, UV, and 1H- and 13C-NMR, as well as mass spectral data. The substituted arylidene-based quinazolin-4(3H)-one motifs 3aâm were screened for both in silico and in vitro antimicrobial properties against selected bacteria and fungi. The in silico studies carried out consisted of predicted ADMET screening, molecular docking, and molecular dynamics (MD) simulation studies. Furthermore, in vitro experimental validation was performed using the agar diffusion method, and the standard antibacterial and antifungal drugs used were gentamicin and ketoconazole, respectively.Results and discussion: Most of the compounds possessed good binding affinities according to the molecular docking studies, while MD simulation revealed their levels of structural stability in the proteinâligand complexes. 2-methyl-3-((thiophen-2-ylmethylene)amino) quinazolin-4(3H)-one 3Â m emerged as both the most active antibacterial agent (with an minimum inhibitory concentration (MIC) value of 1.95Â ÎŒg/mL) against Staphylococcus aureus and the most active antifungal agent (with an MIC value of 3.90Â ÎŒg/mL) against Candida albicans, Aspergillus niger, and Rhizopus nigricans
Ten Simple Rules for Organizing a Virtual ConferenceâAnywhere
Etienne P. de Villiers and Sheila C. Ommeh are ILRI author
Development of Bioinformatics Infrastructure for Genomics Research in H3Africa
Background: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNetâs role has evolved in response to changing needs from the consortium and the African bioinformatics community.
Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis.
Methods and Results: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training.
Conclusions: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa
Extracting common motifs under the levenshtein measure: Theory and experimentation
Abstract. Using our techniques for extracting approximate non-tandem repeats[1] on well constructed maximal models, we derive an algorithm to find common motifs of length P that occur in N sequences with at most D differences under the Edit distance metric. We compare the effectiveness of our algorithm with the more involved algorithm of Sagot[17] for Edit distance on some real sequences. Her method has not been implemented before for Edit distance but only for Hamming distance[12, 20]. Our resulting method turns out to be simpler and more efficient theoretically and also in practice for moderately large P and D.
Recent advances in functionalized quinoline scaffolds and hybrids âExceptional pharmacophore in therapeutic medicine
Quinoline is one of the most common nitrogen-containing heterocycles owing to its
fascinating pharmacological properties and synthetic value in organic and
pharmaceutical chemistry. Functionalization of this moiety at different positions
has allowed for varying pharmacological activities of its derivative. Several
publications over the last few decades have specified various methods of
synthesis. This includes classical methods of synthesizing the primary quinoline
derivatives and efficient methods that reduce reaction time with increased yield
employing procedures that fulfill one of the twelve green chemistry principles, âsafer
solventâ. The metal nanoparticle-catalyzed reaction also serves as a potent and
effective technique for the synthesis of quinoline with excellent atom efficiency. The
primary focus of this review is to highlight the routes to synthesizing functionalized
quinoline derivatives, including hybrids that have moieties with predetermined
activities bound to the quinoline moiety which are of interest in synthesizing drug
candidates with dual modes of action, overcoming toxicity, and resistance amongst
others. This was achieved using updated literature, stating the biological activities
and mechanisms through which these compounds administer relief. The ADMET
studies and Structure-Activity Relationship (SAR) of novel derivatives were also
highlighted to explore the drug-likeness of the quinoline-hybrids and the
influence of substituent characteristics and position on the biological activity of
the compounds