Background: Bovine mastitis is one of the major infectious diseases in dairy cattle, resulting in... more Background: Bovine mastitis is one of the major infectious diseases in dairy cattle, resulting in large economic loss due to decreased milk production and increased production cost to the dairy industry. Antibiotics are commonly used to prevent/treat bovine mastitis infections. However, increased antibiotic resistance and consumers’ concern regarding antibiotic overuse make it prudent and urgent to develop novel therapeutic protocols for this disease. Materials and methods: Potential druggable targets were found in 20 mastitis-causing pathogens and conserved and unique targets were identified. Bacterial strains Staphylococcus aureus (ATCC 29213, and two clinical isolates CI 1 and CI 2) and Staphylococcus epidermidis (ATCC 12228, and two clinical isolates CI 1 and CI 2) were used in the present study for validation of an effective drug combination. Results: In the current study, we identified the common and the unique druggable targets for twenty mastitis-causing pathogens using an i...
Fluoroquinolone (FQ) antibiotics are an important class of synthetic antibacterial agents. These ... more Fluoroquinolone (FQ) antibiotics are an important class of synthetic antibacterial agents. These are the most extensively used drugs for treating bacterial infections in the field of both human and veterinary medicine. Herein, the antibacterial and pharmacological properties of four fluoroquinolones: lomefloxacin, norfloxacin, ciprofloxacin, and ofloxacin have been studied. The objective of this study was to analyze the antibacterial characteristics of the different fluoroquinolones. Also, the pharmacological properties of the compounds including the Lipinski rule of five, absorption, distribution, metabolism, and excretion, LD50, drug likeliness, and toxicity were evaluated. We found that among all four FQ molecules, ofloxacin showed the highest antibacterial activity through in silico assays with a strong interaction (‒38.52 kJ/mol) with the antibacterial target protein (topoisomerase-II DNA gyrase enzyme). The pharmacological and pharmacokinetic analysis also showed that the comp...
Bovine Respiratory Disease (BRD) is a major problem in cattle production which causes substantial... more Bovine Respiratory Disease (BRD) is a major problem in cattle production which causes substantial economic loss. BRD has multifactorial aetiologies, is multi-microbial, and several of the causative pathogens are unknown. Consequently, primary management practices such as metaphylactic antimicrobial injections for BRD prevention are used to reduce the incidence of BRD in feedlot cattle. However, this poses a serious threat in the form of development of antimicrobial resistance and demands an urgent need to find novel interventions that could reduce the effects of BRD drastically and also delay/prevent bacterial resistance. We have employed a subtractive genomics approach that helps delineate essential, host-specific, and druggable targets in pathogens responsible for BRD. We also proposed antimicrobials from FDA green and orange book that could be repositioned for BRD. We have identified 107 putative targets that are essential, selective and druggable. We have also confirmed the susc...
Malignant melanoma (MM) is the most dangerous type of skin cancer, killing more than 1,100 people... more Malignant melanoma (MM) is the most dangerous type of skin cancer, killing more than 1,100 people each year in Canada. Prognosis for late stage and recurrent MM is extremely poor due to insensitivity to chemotherapy drugs, and thus many patients seek complementary and alternative medicines. In this study, we examined four commonly used anticancer herbs in traditional Chinese medicine, Hedyotis diffusa, Scutellaria barbata, Lobelia chinensis, and Solanum nigrum, for their in vitro antitumor effects toward human MM cell line A-375. The crude water extract of S. nigrum (1 g of dry herb in 100 mL water) and its 2-fold dilution caused 52.8%±13.0% and 17.3%±2.7% cytotoxicity in A-375 cells, respectively (P<0.01). The crude water extract of H. diffusa caused 11.1%±12.4% cytotoxicity in A-375 cells with no statistical significance (P>0.05). Higher concentrated formulation might be needed for H. diffusa to exert its cytotoxic effect against A-375 cells. No cytotoxicity was observed in ...
Metabolic network provides a unified platform to integrate all the biological information on gene... more Metabolic network provides a unified platform to integrate all the biological information on genes, proteins, metabolites, drugs and drug targets for a comprehensive system level study of the relationship between metabolism and disease. In recent times, drug-target identification by in silico methods has emerged causing a phenomenal achievement in the field of drug discovery. This paper focuses on describing how microbial drug target identification can be carried out using bioinformatic tools. Specifically, it highlights the use of metabolic 'choke point' and 'load point' analyses to understand the local and global properties of metabolic networks in Pseudomonas aeruginosa and allow us to identify potential drug targets. We also list out top 10 choke point enzymes based on the load point values and the number of shortest paths. A non-pathogenic bacterial strain Pseudomonas putida KT2440 and a related pathogenic bacteria P.aeruginosa PA01 was selected for the network ...
The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public h... more The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public health and emphasizes the need for new antimicrobial targets. The recent development of microbial genomics and the availability of genome sequences allows for the identification of essential genes which could be novel and potential targets for antibacterial drugs. However, these predicted targets need experimental validation to confirm essentiality. Here, we report on experimental validation of a two potential targets in the lipopolysaccharide (LPS) biosynthesis pathway of the pathogen Pseudomonas aeruginosa PAO1 using insertion duplication. Two genes, kdsA and waaG, from LPS encoding proteins 2-dehydro-3-deoxyphosphooctonate aldolase and UDP-glucose (heptosyl) LPS α-1,3-glucosyltransferase were selected as putative target candidates for the gene disruption experiments using plasmid insertion mutagenesis to determine essentiality. The introduction of a selectable ampicillin and kanamycin ...
International Journal of Systematic and Evolutionary Microbiology, 2005
Overlapping genes have been proposed as a means of achieving genome reduction by compressing the ... more Overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. In this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. The results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. The genomes of two closely related obligatory intracellular parasites –Rickettsia prowazekiiandRickettsia conorii– were investigated further. Detailed analyses of these two genomes revealed that mutations at the ends of coding regions and elimination of intergenic DNA are the main forces that determine overlapping of genes.
Background: Bovine mastitis is one of the major infectious diseases in dairy cattle, resulting in... more Background: Bovine mastitis is one of the major infectious diseases in dairy cattle, resulting in large economic loss due to decreased milk production and increased production cost to the dairy industry. Antibiotics are commonly used to prevent/treat bovine mastitis infections. However, increased antibiotic resistance and consumers’ concern regarding antibiotic overuse make it prudent and urgent to develop novel therapeutic protocols for this disease. Materials and methods: Potential druggable targets were found in 20 mastitis-causing pathogens and conserved and unique targets were identified. Bacterial strains Staphylococcus aureus (ATCC 29213, and two clinical isolates CI 1 and CI 2) and Staphylococcus epidermidis (ATCC 12228, and two clinical isolates CI 1 and CI 2) were used in the present study for validation of an effective drug combination. Results: In the current study, we identified the common and the unique druggable targets for twenty mastitis-causing pathogens using an i...
Fluoroquinolone (FQ) antibiotics are an important class of synthetic antibacterial agents. These ... more Fluoroquinolone (FQ) antibiotics are an important class of synthetic antibacterial agents. These are the most extensively used drugs for treating bacterial infections in the field of both human and veterinary medicine. Herein, the antibacterial and pharmacological properties of four fluoroquinolones: lomefloxacin, norfloxacin, ciprofloxacin, and ofloxacin have been studied. The objective of this study was to analyze the antibacterial characteristics of the different fluoroquinolones. Also, the pharmacological properties of the compounds including the Lipinski rule of five, absorption, distribution, metabolism, and excretion, LD50, drug likeliness, and toxicity were evaluated. We found that among all four FQ molecules, ofloxacin showed the highest antibacterial activity through in silico assays with a strong interaction (‒38.52 kJ/mol) with the antibacterial target protein (topoisomerase-II DNA gyrase enzyme). The pharmacological and pharmacokinetic analysis also showed that the comp...
Bovine Respiratory Disease (BRD) is a major problem in cattle production which causes substantial... more Bovine Respiratory Disease (BRD) is a major problem in cattle production which causes substantial economic loss. BRD has multifactorial aetiologies, is multi-microbial, and several of the causative pathogens are unknown. Consequently, primary management practices such as metaphylactic antimicrobial injections for BRD prevention are used to reduce the incidence of BRD in feedlot cattle. However, this poses a serious threat in the form of development of antimicrobial resistance and demands an urgent need to find novel interventions that could reduce the effects of BRD drastically and also delay/prevent bacterial resistance. We have employed a subtractive genomics approach that helps delineate essential, host-specific, and druggable targets in pathogens responsible for BRD. We also proposed antimicrobials from FDA green and orange book that could be repositioned for BRD. We have identified 107 putative targets that are essential, selective and druggable. We have also confirmed the susc...
Malignant melanoma (MM) is the most dangerous type of skin cancer, killing more than 1,100 people... more Malignant melanoma (MM) is the most dangerous type of skin cancer, killing more than 1,100 people each year in Canada. Prognosis for late stage and recurrent MM is extremely poor due to insensitivity to chemotherapy drugs, and thus many patients seek complementary and alternative medicines. In this study, we examined four commonly used anticancer herbs in traditional Chinese medicine, Hedyotis diffusa, Scutellaria barbata, Lobelia chinensis, and Solanum nigrum, for their in vitro antitumor effects toward human MM cell line A-375. The crude water extract of S. nigrum (1 g of dry herb in 100 mL water) and its 2-fold dilution caused 52.8%±13.0% and 17.3%±2.7% cytotoxicity in A-375 cells, respectively (P<0.01). The crude water extract of H. diffusa caused 11.1%±12.4% cytotoxicity in A-375 cells with no statistical significance (P>0.05). Higher concentrated formulation might be needed for H. diffusa to exert its cytotoxic effect against A-375 cells. No cytotoxicity was observed in ...
Metabolic network provides a unified platform to integrate all the biological information on gene... more Metabolic network provides a unified platform to integrate all the biological information on genes, proteins, metabolites, drugs and drug targets for a comprehensive system level study of the relationship between metabolism and disease. In recent times, drug-target identification by in silico methods has emerged causing a phenomenal achievement in the field of drug discovery. This paper focuses on describing how microbial drug target identification can be carried out using bioinformatic tools. Specifically, it highlights the use of metabolic 'choke point' and 'load point' analyses to understand the local and global properties of metabolic networks in Pseudomonas aeruginosa and allow us to identify potential drug targets. We also list out top 10 choke point enzymes based on the load point values and the number of shortest paths. A non-pathogenic bacterial strain Pseudomonas putida KT2440 and a related pathogenic bacteria P.aeruginosa PA01 was selected for the network ...
The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public h... more The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public health and emphasizes the need for new antimicrobial targets. The recent development of microbial genomics and the availability of genome sequences allows for the identification of essential genes which could be novel and potential targets for antibacterial drugs. However, these predicted targets need experimental validation to confirm essentiality. Here, we report on experimental validation of a two potential targets in the lipopolysaccharide (LPS) biosynthesis pathway of the pathogen Pseudomonas aeruginosa PAO1 using insertion duplication. Two genes, kdsA and waaG, from LPS encoding proteins 2-dehydro-3-deoxyphosphooctonate aldolase and UDP-glucose (heptosyl) LPS α-1,3-glucosyltransferase were selected as putative target candidates for the gene disruption experiments using plasmid insertion mutagenesis to determine essentiality. The introduction of a selectable ampicillin and kanamycin ...
International Journal of Systematic and Evolutionary Microbiology, 2005
Overlapping genes have been proposed as a means of achieving genome reduction by compressing the ... more Overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. In this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. The results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. The genomes of two closely related obligatory intracellular parasites –Rickettsia prowazekiiandRickettsia conorii– were investigated further. Detailed analyses of these two genomes revealed that mutations at the ends of coding regions and elimination of intergenic DNA are the main forces that determine overlapping of genes.
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