Adnan Mannan

In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification

Plague is a major health concern and Yersinia pestis plays the central causal role in this disease. Yersinia pestis has developed resistance against the commonly available drugs. So, it is now a key concern to find a new drug target. Cysteine protease YopT enzyme is an important factor used by Yersinia pestis for pathogenesis in its host and it has the anti-phagocytic function of removal of C-termini lipid modification. The 3D structure of cysteine protease YopT of Yersinia pestis was determined by means of homology modeling through multiple alignments followed by intensive optimization and validation. The modeling was done by Phyre 2 and refined by ModRefiner. The obtained model was verified with structure validation programs such as PROCHECK, verify 3D and ERRAT for reliability. Interacting partners and active sites were also determined. PROCHECK analysis showed that 93% of the residues are in the most favored region, 5.9% are in the additional allowed region and 1.1% are in the generously allowed region of the Ramachandran plot. The verify 3D value of 0.78 indicates that the environmental profile of the model is good. SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT. Active site determination through CASTp proposes that this protein can be utilized as a potential drug target. However, these findings should further be confirmed by wet lab studies for a targeted therapeutic agent design against Yersinia pestis.

Identification of potential targets in Staphylococcus aureus N315 using computer aided protein data analysis.

Staphylococcus aureus is a gram positive bacterium, responsible for both community-acquired and hospital-acquired infection, resulting in a mortality rate of 39%. 43.2% resistance to methicilin and emerging resistance to Fluroquinolone and Oxazolidinone, have evoked the necessity of the establishment of alternative and effective therapeutic approach to treat this bacteria. In this computational study, various database and online software are used to determine some specific targets of Staphylococcus aureus N315 other than those used by Penicillin, Quinolone and Oxazolidinone. For this purpose, among 302 essential proteins, 101 nonhomologous proteins were accrued and 64 proteins which are unique in several metabolic pathways of S. aureus were isolated by using metabolic pathway analysis tools. Furthermore, 7 essentially unique enzymes involved in exclusive metabolic pathways were revealed by this research, which can be potential drug target. Along with these important enzymes, 15 non-homologous proteins located on membrane were identified, which can play a vital role as potential therapeutic targets for the future researchers.

Phytochemical, analgesic, antibacterial, and cytotoxic effects of Alpinia nigra (Gaertn.) Burtt leaf extract

This research evaluated the phytochemical contents as well as the analgesic, cytotoxic, and antimicrobial effects of the methanolic extract of Alpinia nigra leaf. Phytochemical analysis was carried out using established methods. The analgesic effects of the extract were measured with the formalin test and tail immersion test. The antibacterial activity of the extract was evaluated using the disc diffusion technique. Cytotoxicity was assessed with the brine shrimp lethality bioassay. Data were analyzed with one-way analysis of variance using statistical software (SPSS, Version 19.0). The qualitative phytochemical screening of A. nigra leaf extract showed the presence of medicinally active secondary metabolites such as alkaloids, glycosides, cardiac glycosides, flavonoids, steroids, tannins, anthraquinone glycosides, and saponins. The extract at a dose of 200 mg/kg revealed a prevailed central nociception increasing the reaction time in response to thermal stimulation. The extract also showed a response to chemical nociceptors, causing pain inhibition in the late phase. The leaf extract (2 mg/disc) showed mild antibacterial activity compared to tetracycline (50 μg/disc). In the brine shrimp lethality bioassay, the LC50 (lethal concentration 50) value of the extract was found to be 57.12 μg/mL, implying a promising cytotoxic effect. The results evidenced the moderate analgesic and antibacterial effects with pronounced cytotoxic capability.

Comparative assessment on in vitro antioxidant activities of ethanol extracts of Averrhoa bilimbi , Gymnema sylvestre and Capsicum frutescens

Background: Averrhoa bilimbi, Gymnema sylvestre and Capsicum frutescens are medicinal plants commonly used as traditional medicine for the treatment of various diseases. The present study was designed to investigate the antioxidant activities of Ethanolic extract of A. bilimbi, G. sylvestre and C. frutescens. Materials and Methods: The antioxidant activity of the extracts were evaluated using total phenolic and flavonoid contents, ferric reducing power and the free radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH). Results: Total phenolic and flavonoid contents were higher in G. sylvestre (53.63636 ± 0.454545 mg/g gallic acid equivalent) and C. frutescens (26.66667 ± 2.081666 mg/g quercetin equivalent) respectively. Reducing power of the crude ethanol extracts increased with the concentrations of the extracts and all the extracts showed moderate free radical scavenging activity against DPPH. The plant extract displayed moderate phenolic and flavonoid contents compared to gallic acid and quercetin equivalent respectively, whereas also exhibited significant scavenging of DPPH radical and reducing power compared with ascorbic acid as standard. Conclusion: Our study suggests that G. sylvestre has significant antioxidant activity. The antioxidant compound of this plant might be a therapeutic candidate against oxidative stress related diseases. Different sub-fraction of A. bilimbi and C. frutescens should be studied further to assess the effect. Further study is necessary for isolation and characterization of the active antioxidant agents for better treatment.

A cross sectional study on antibiotic resistance pattern of Salmonella typhi clinical isolates from Bangladesh

OBJECTIVE To investigate and compare the resistance and sensitivity of Salmonella typhi samples to commonly used antibiotics in three major divisions of Bangladesh and to evaluate the gradually developing resistance pattern. METHODS The antibiotic susceptibility of 70 clinical isolates collected from blood, sputum, urine and pus samples were identified by specific antisera and with standard biochemical tests. The patients were divided into 5 age groups. Susceptibility and resistance was also tested by Kirby-Bauer disc diffusion method using 12 regularly used antibiotics. RESULTS Antibiotic susceptibility test demonstrated that 64.28% isolates of Salmonella typhi were multidrug resistant. Present study suggests that the clinical samples were mostly resistant against nalidixic acid with all age groups and in all three divisions with similar resistance pattern. Resistance is more common among adult people (30-40 years) and children (0-10 years). Salmonella typhi was mostly sensitive against gentamycin, chloramphenicol and ciprofloxacin. CONCLUSIONS Although the population density of Dhaka region is markedly higher than Rajshahi and Chittagong regions, no significant difference in resistance pattern was found. The rate of multidrug resistance is a matter of concern. Physicians should reconsider before prescribing nalidixic acid and cefixime. Further molecular study is needed to reveal the genomic and proteomic basis of resistance.

Investigation of in vivo neuropharmacological effect of Alpinia nigra leaf extract

OBJECTIVE To analyze in vivo neuro-pharmacological effects of Alpinia nigra as anxiety is a particular form of behavioral inhibition that occurs in response to novel environmental events. METHODS In present study, the extract of Alpinia nigra was evaluated for its central nervous system depressant effect using mice behavioral models, such as hole cross, open field and thiopental sodium induced sleeping time tests for its sedative properties and an elevated plus-maze test for its anxiolytic potential, respectively. RESULTS In anxiolytic study, the extract displayed increased percentage of entry into open arm at the dose of 400 and 200 mg/kg. The extract produced a significant (P<0.01) increase in sleeping duration and reduction of onset of sleep compared to sodium thiopental at both doses (200 and 400 mg/kg). The extract (200 and 400 mg/kg) also showed a dose-dependent suppression of motor activity and exploratory activity of the mice in both open field and hole cross test. CONCLUSION This study demonstrates that the treated extract has significant central nervous system depressant effect. Further studies on active constituent of the extract can provide approaches for therapeutic intervention.

Computational analysis of bovine alpha-1 collagen sequences

Bovine collagen alpha-1 is a naturally occurring extracellular matrix protein found in tendons and other connective tissues. It plays a vital role in cell growth, differentiation, attachment, and migration. Recent findings have established that collagen alpha-1 is involved in osteogenesis imperfecta phenotype in cattle but deep information about other members of this large family is not available so far. So with a view to finding a new edge and attempt to figure out a correlation among the well attributed Bovine alpha-1 collagen sequences are executed and analyzed. To do so, comparative analysis among the 28 members of collagen family has been carried out using Computational tools. Consequently, based on the physico-chemical, secondary structural, functional and phylogenetic classifications, we have selected collagen 12, 14 and 20 as targets for pathological conditions. These proteins belong to the FACIT family and significantly showed low glycine and proline content, high instability and aliphatic index. Moreover, FACIT family collagens contain multiple triple helical domains and being members of the FACIT family, bovine collagen 12, 14, 20 do not form fibrils by themselves but they are associated to collagen 1 associated fibrils. These collagen molecules might be crucial candidates to detect and understand the process of matrix remodeling in diseases especially in the arena of cellular compartments.

A Computational analysis on Lectin and Histone H1 protein of different pulse species as well as comparative study with rice for balanced diet

The issue of balanced nutrition is of great concern to human. Meat and fish are the best sources of protein. The affordability of these resources for people in developing countries is less. Thus, there is an increasing interest in pulses and its derivates as an alternative to fish and meat. Lectin and histone H1 are the most common proteins in various pulses and our interest is in identifying the dominant essential amino acids in them for use as supplements. However, actin and lectin are common among Oryza Sativa and cicer arietinum. We describe the amount of lectin and histone H1 in cicer arietinum, Lens culinaris and Pisum sativum in a comparative manner. cicer arietinum was found to contain more essential amino acids than Lens culinaris and Pisum sativum. The secondary structures of lectin and histone H1 protein were analyzed to gain functional inferences in these species. The comparative study shows the relatively poor presence of the amino acid methionine in most pulses. However, Oryza Sativa was found to contain sufficient methionine. The study shows that pulses (especially cicer arietinum) were a suitable alternative source to meat and fish for Lectin and Histone H1 balance. Hence, pulses could be suggested with rice for balanced protein diet.