Bioinformatics Applications on Cryptosporidium Research: A Review

The biology of Cryptosporidium has been studied increasingly since it was recognized as a pathogen of humans more than a century. Its recent recognition as a second leading cause of diarrhoea or cryptosporidiosis immunocompromised patients globally has led many researchers to study on this parasite. Many new technologies such as high-throughput omics and bioinformatics tools have been implemented to investigate this zoonotic parasite in a better approach. The aim of this review article is mainly to briefly describe recent applications of structural bioinformatics in order to reveal the potentiality of a suitable therapeutic target in Cryptosporidium. This review was written based on the search of cited publications in SCOPUS website with the combination of word ‘Cryptosporidium’ with other words like bioinformatics, protein structure, structural biology and homology modeling. The search results then were selected based on the relativeness of updated information needed to be prepared in this review. Several cited publications were used to elaborate the review accordingly despitelimitedreviewupdatesrelatedtoprotein bioinformation of thisparasite. As a conclusion, bioinformatics is a commonly known to be cutting-edge technology that has been recognised for its power to reveal the secret of parasite biology in silico including a neglected parasite, Cryptosporidium. Bangladesh Journal of Medical Science Vol. 21(1) 2022 Page : 8-18

Antibiotics Used in Covid-19 And Mucormycosis (Black Fungus)

Background: In late December 2019, Chinese health authorities reported an outbreak of pneumonia of unknown origin in Wuhan, Hubei Province. Summary: A few days later, the genome of a novel coronavirus was released. org/t/novel2019-coronavirus-genome/319; Wuhan- Hu-1, GenBank accession No. MN908947) and made publicly available to the scientific community. This novel coronavirus was provisionally named 2019-nCoV, now SARS-CoV-2 according to the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. SARS-CoV-2 belongs to the Coronaviridae family, Betacoronavirus genus, subgenus Sarbecovirus. Since its discovery, the virus has spread globally, causing thousands of deaths and having an enormous impact on our health systems and economies. In this review, we summarize the current knowledge about the epidemiology, phylogenesis, homology modeling, and molecular diagnostics of SARS-CoV-2. Phylogenetic analysis is essential to understand viral evolution, whereas homology modeling is important for vaccine strategies and therapies. Highly sensitive and specific diagnostic assays are key to case identification, contact tracing, identification of the animal source, and implementation of control measures. Keywords: COVID-19 · SARS-CoV-2 · Pandemic · Phylogenesis · Protein modeling · Real-time polymerase chain reaction

Bioethanol Production From Hassawi Rice Straw Wastes Assisted by Aspergillus sp. NAS51 Cellulosic Enzyme Under SSF and Saccharification Process With in Silico Enzyme Structural Homology Modeling

With the distribution of exploitable non-renewable energy resources, the use of lignocellulosic wastes to make bioethanol and biogas has drawn great attention from researchers. In our effort to find a potent cellulase-producing fungal strain, the fungus NAS51 was isolated from a sponge collected from the Red Sea, Jeddah, among eight isolates and selected as it displayed potent cellulolytic activity. The fungus was identified morphologically and genetically by sequencing its 18SrRNA gene as Aspergillus sp. NAS51. The cellulase activity of Aspergillus sp. NAS51 was optimized and maximum enzyme production was obtained at initial pH7, temp 30oC, incubation period 11 days, moisture content 70%, urea as a nitrogen source, and K2HPO4 (2g/L). The cellulase gene has been sequenced and the protein 3D structure was generated via in silico homology modeling. Determination of binding sites and biological annotations of the constructed protein was carried out via COACH and COFACTOR based on the I-TASSER structure prediction. To reach the maximum enzyme hydrolysis, the rice straw collected from Al-Ahsa, Kingdom of Saudi Arabia was pretreated with NaOH 1.5% to remove lignin and to enhance the saccharification process by cellulase enzyme. The saccharified product was measured using HPLC, fermented by S. cerevisiae and the bioethanol yield produced from the fermentation was 0.454 ml ethanol/g fermentable sugars.

Curcumin Analogues as a Potential Drug against Antibiotic Resistant Protein, β-Lactamases and L, D-Transpeptidases Involved in Toxin Secretion in Salmonella typhi: A Computational Approach

Typhoid fever caused by the bacteria Salmonella typhi gained resistance through multidrug-resistant S. typhi strains. One of the reasons behind β-lactam antibiotic resistance is -lactamase. L, D-Transpeptidases is responsible for typhoid fever as it is involved in toxin release that results in typhoid fever in humans. A molecular modeling study of these targeted proteins was carried out by various methods, such as homology modeling, active site prediction, prediction of disease-causing regions, and by analyzing the potential inhibitory activities of curcumin analogs by targeting these proteins to overcome the antibiotic resistance. The five potent drug candidate compounds were identified to be natural ligands that can inhibit those enzymes compared to controls in our research. The binding affinity of both the Go-Y032 and NSC-43319 were found against β-lactamase was −7.8 Kcal/mol in AutoDock, whereas, in SwissDock, the binding energy was −8.15 and −8.04 Kcal/mol, respectively. On the other hand, the Cyclovalone and NSC-43319 had an equal energy of −7.60 Kcal/mol in AutoDock, whereas −7.90 and −8.01 Kcal/mol in SwissDock against L, D-Transpeptidases. After the identification of proteins, the determination of primary and secondary structures, as well as the gene producing area and homology modeling, was accomplished. The screened drug candidates were further evaluated in ADMET, and pharmacological properties along with positive drug-likeness properties were observed for these ligand molecules. However, further in vitro and in vivo experiments are required to validate these in silico data to develop novel therapeutics against antibiotic resistance.

In vitro characterization of a nitro-forming oxygenase involved in 3-(trans-2’-aminocyclopropyl)alanine biosynthesis

In vitro characterization experiments revealed the formations of 3-(trans-2’-aminocyclopropyl)alanine ((3-Acp)Ala) and 3-(trans-2’-nitrocyclopropyl)alanine ((3-Ncp)Ala) are originated via two homologous proteins BelK and HrmI, which regioselectively catalyze Nε-nitration of L-lysine. The two enzymes belong to the emerging heme-oxygenase-like diiron oxidase and oxygenase (HDO) superfamily and the catalytic center of BelK is validated by homology modeling and site-directed mutations. Based on the in vitro characterization, the biosynthetic pathways of (3-Acp)Ala and (3-Ncp)Ala are first proposed.