1
|
Sarker P, Mitro A, Hoque H, Hasan MN, Nurnabi Azad Jewel GM. Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Comput Biol Med 2023; 165:107436. [PMID: 37690289 DOI: 10.1016/j.compbiomed.2023.107436] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.
Collapse
Affiliation(s)
- Parth Sarker
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Arnob Mitro
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Hammadul Hoque
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - Md Nazmul Hasan
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - G M Nurnabi Azad Jewel
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh.
| |
Collapse
|
2
|
Ali H, Samad A, Ajmal A, Ali A, Ali I, Danial M, Kamal M, Ullah M, Ullah R, Kalim M. Identification of Drug Targets and Their Inhibitors in Yersinia pestis Strain 91001 through Subtractive Genomics, Machine Learning, and MD Simulation Approaches. Pharmaceuticals (Basel) 2023; 16:1124. [PMID: 37631039 PMCID: PMC10459760 DOI: 10.3390/ph16081124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Yersinia pestis, the causative agent of plague, is a Gram-negative bacterium. If the plague is not properly treated it can cause rapid death of the host. Bubonic, pneumonic, and septicemic are the three types of plague described. Bubonic plague can progress to septicemic plague, if not diagnosed and treated on time. The mortality rate of pneumonic and septicemic plague is quite high. The symptom-defining disease is the bubo, which is a painful lymph node swelling. Almost 50% of bubonic plague leads to sepsis and death if not treated immediately with antibiotics. The host immune response is slow as compared to other bacterial infections. Clinical isolates of Yersinia pestis revealed resistance to many antibiotics such as tetracycline, spectinomycin, kanamycin, streptomycin, minocycline, chloramphenicol, and sulfonamides. Drug discovery is a time-consuming process. It always takes ten to fifteen years to bring a single drug to the market. In this regard, in silico subtractive proteomics is an accurate, rapid, and cost-effective approach for the discovery of drug targets. An ideal drug target must be essential to the pathogen's survival and must be absent in the host. Machine learning approaches are more accurate as compared to traditional virtual screening. In this study, k-nearest neighbor (kNN) and support vector machine (SVM) were used to predict the active hits against the beta-ketoacyl-ACP synthase III drug target predicted by the subtractive genomics approach. Among the 1012 compounds of the South African Natural Products database, 11 hits were predicted as active. Further, the active hits were docked against the active site of beta-ketoacyl-ACP synthase III. Out of the total 11 active hits, the 3 lowest docking score hits that showed strong interaction with the drug target were shortlisted along with the standard drug and were simulated for 100 ns. The MD simulation revealed that all the shortlisted compounds display stable behavior and the compounds formed stable complexes with the drug target. These compounds may have the potential to inhibit the beta-ketoacyl-ACP synthase III drug target and can help to combat Yersinia pestis-related infections. The dataset and the source codes are freely available on GitHub.
Collapse
Affiliation(s)
- Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad 44000, Pakistan
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Amar Ajmal
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Amjad Ali
- Faculty of Biological Sciences, Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Ijaz Ali
- Centre for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, Hawally 32093, Kuwait;
| | - Muhammad Danial
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Masroor Kamal
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan; (A.S.); (A.A.); (M.D.); (M.K.)
| | - Midrar Ullah
- Department of Biotechnology, Shaheed Benazir Bhutto University Sheringal, Dir Upper 18050, Pakistan;
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy King Saud University, Riyadh 11451, Saudi Arabia;
| | - Muhammad Kalim
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
- Houston Methodist Cancer Center/Weill Cornel Medicine, Houston, TX 77030, USA
| |
Collapse
|
3
|
Kaur H, Modgil V, Chaudhary N, Mohan B, Taneja N. Computational Guided Drug Targets Identification against Extended-Spectrum Beta-Lactamase-Producing Multi-Drug Resistant Uropathogenic Escherichia coli. Biomedicines 2023; 11:2028. [PMID: 37509666 PMCID: PMC10377140 DOI: 10.3390/biomedicines11072028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most frequent bacterial infections in the world, both in the hospital and community settings. Uropathogenic Escherichia coli (UPEC) are the predominant etiological agents causing UTIs. Extended-spectrum beta-lactamase (ESBL) production is a prominent mechanism of resistance that hinders the antimicrobial treatment of UTIs caused by UPEC and poses a substantial danger to the arsenal of antibiotics now in use. As bacteria have several methods to counteract the effects of antibiotics, identifying new potential drug targets may help in the design of new antimicrobial agents, and in the control of the rising trend of antimicrobial resistance (AMR). The public availability of the entire genome sequences of humans and many disease-causing organisms has accelerated the hunt for viable therapeutic targets. Using a unique, hierarchical, in silico technique using computational tools, we discovered and described potential therapeutic drug targets against the ESBL-producing UPEC strain NA114. Three different sets of proteins (chokepoint, virulence, and resistance genes) were explored in phase 1. In phase 2, proteins shortlisted from phase 1 were analyzed for their essentiality, non-homology to the human genome, and gut flora. In phase 3, the further shortlisted putative drug targets were qualitatively characterized, including their subcellular location, broad-spectrum potential, and druggability evaluations. We found seven distinct targets for the pathogen that showed no similarity to the human proteome. Thus, possibilities for cross-reactivity between a target-specific antibacterial and human proteins were minimized. The subcellular locations of two targets, ECNA114_0085 and ECNA114_1060, were predicted as cytoplasmic and periplasmic, respectively. These proteins play an important role in bacterial peptidoglycan biosynthesis and inositol phosphate metabolism, and can be used in the design of drugs against these bacteria. Inhibition of these proteins will be helpful to combat infections caused by MDR UPEC.
Collapse
Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Vinay Modgil
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Naveen Chaudhary
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Neelam Taneja
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| |
Collapse
|
4
|
Islam J, Sarkar H, Hoque H, Hasan MN, Jewel GNA. In-silico approach of identifying novel therapeutic targets against Yersinia pestis using pan and subtractive genomic analysis. Comput Biol Chem 2022; 101:107784. [DOI: 10.1016/j.compbiolchem.2022.107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
|
5
|
Pereira de Araújo M, Sato MO, Sato M, Bandara WM KM, Coelho LFL, Souza RLM, Kawai S, Marques MJ. Unbalanced relationships: insights into the interaction between gut microbiota, geohelminths, and schistosomiasis. PeerJ 2022; 10:e13401. [PMID: 35539016 PMCID: PMC9080432 DOI: 10.7717/peerj.13401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/17/2022] [Indexed: 01/14/2023] Open
Abstract
Hosts and their microbiota and parasites have co-evolved in an adaptative relationship since ancient times. The interaction between parasites and intestinal bacteria in terms of the hosts' health is currently a subject of great research interest. Therapeutic interventions can include manipulations of the structure of the intestinal microbiota, which have immunological interactions important for modulating the host's immune system and for reducing inflammation. Most helminths are intestinal parasites; the intestinal environment provides complex interactions with other microorganisms in which internal and external factors can influence the composition of the intestinal microbiota. Moreover, helminths and intestinal microorganisms can modulate the host's immune system either beneficially or harmfully. The immune response can be reduced due to co-infection, and bacteria from the intestinal microbiota can translocate to other organs. In this way, the treatment can be compromised, which, together with drug resistance by the parasites makes healing even more difficult. Thus, this work aimed to understand interactions between the microbiota and parasitic diseases caused by the most important geohelminths and schistosomiasis and the consequences of these associations.
Collapse
Affiliation(s)
- Matheus Pereira de Araújo
- Institute of Biomedical Sciences, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil,Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Marcello Otake Sato
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, Niigata, Niigata, Japan
| | | | | | | | - Satoru Kawai
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Marcos José Marques
- Institute of Biomedical Sciences, Universidade Federal de Alfenas, Alfenas, Minas Gerais, Brazil
| |
Collapse
|
6
|
Hentschel V, Seufferlein T, Armacki M. Intestinal organoids in coculture: redefining the boundaries of gut mucosa ex vivo modeling. Am J Physiol Gastrointest Liver Physiol 2021; 321:G693-G704. [PMID: 34643092 DOI: 10.1152/ajpgi.00043.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
All-time preservation of an intact mucosal barrier is crucial to ensuring intestinal homeostasis and, hence, the organism's overall health maintenance. This complex process relies on an equilibrated signaling system between the intestinal epithelium and numerous cell populations inhabiting the gut mucosa. Any perturbations of this delicate cross talk, particularly regarding the immune cell compartment and microbiota, may sustainably debilitate the intestinal barrier function. As a final joint event, a critical rise in epithelial permeability facilitates the exposure of submucosal immunity to microbial antigens, resulting in uncontrolled inflammation, collateral tissue destruction, and dysbiosis. Organoid-derived intestinal coculture models have established themselves as convenient tools to reenact such pathophysiological events, explore interactions between selected cell populations, and assess their roles with a central focus on intestinal barrier recovery and stabilization.
Collapse
Affiliation(s)
- Viktoria Hentschel
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Milena Armacki
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| |
Collapse
|
7
|
Anis Ahamed N, Panneerselvam A, Arif IA, Syed Abuthakir MH, Jeyam M, Ambikapathy V, Mostafa AA. Identification of potential drug targets in human pathogen Bacillus cereus and insight for finding inhibitor through subtractive proteome and molecular docking studies. J Infect Public Health 2021; 14:160-168. [PMID: 33422858 DOI: 10.1016/j.jiph.2020.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Bacillus cereus is a gram-positive, anaerobic, spore-forming bacterium related to food poisoning in humans. Vomit and diarrhea are the symptoms of foodborne B. cereus infection caused by emetic toxins and three enterotoxins, respectively. This bacterium is broadly present in soil and foods such as vegetables, spices, milk, and meat. The antibiotics impenem, vancomycin, chloramphenicol, gentamicin, and ciprofloxacin are used for all susceptible strains of B. cereus. But these antibiotics cause side effects in the host due to the drug-host interaction; because the targeted proteins by the drugs are not pathogen specific proteins, they are similar to human proteins also. To overcome this problem, this study focused on identifying putative drug targets in the pathogen B. cereus and finding new drugs to inhibit the function of the pathogen. The identification of drug targets is a pipeline process, starting with the identification of targets non-homologous to human and gutmicrobiota proteins, finding essential proteins, finding other proteins that highly interact with these essential proteins that are also highly important for protein network stability, finding cytoplasmic proteins with a clear pathway and known molecular function, and finding non-druggable proteins. Through this process, two novel drug targets were identified in B. cereus. Among the various antibiotics, Gentamicin had showed good binding affinity with the identified novel targets through molecular modeling and docking studies using Prime and GLIDE module of Schrödinger. Hence, this study suggest that the identified novel drug targets may very useful in drug therapeutic field for finding inhibitors which are similar to Gentamicin and designing new formulation of drug molecules to control the function of the foodborne illness causing pathogen B. cereus.
Collapse
Affiliation(s)
- N Anis Ahamed
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia; Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia; Department of Botany and Microbiology, A.V.V.M. Sri Pushpam College (Autonomous), Poondi, Affiliated to Bharathidasan University, Thanjavur 620024, India.
| | - A Panneerselvam
- Department of Botany and Microbiology, A.V.V.M. Sri Pushpam College (Autonomous), Poondi, Affiliated to Bharathidasan University, Thanjavur 620024, India
| | - Ibrahim A Arif
- Prince Sultan Research Chair for Environment and Wildlife, Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia; Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| | | | - Muthusamy Jeyam
- Biochematics Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - V Ambikapathy
- Department of Botany and Microbiology, A.V.V.M. Sri Pushpam College (Autonomous), Poondi, Affiliated to Bharathidasan University, Thanjavur 620024, India
| | - Ashraf A Mostafa
- Department of Botany and Microbiology, College of Sciences, King Saud University (KSU), Riyadh, Saudi Arabia
| |
Collapse
|
8
|
Chakkyarath V, Shanmugam A, Natarajan J. Prioritization of potential drug targets and antigenic vaccine candidates against Klebsiella aerogenes using the computational subtractive proteome-driven approach. JOURNAL OF PROTEINS AND PROTEOMICS 2021; 12:201-211. [PMID: 34305354 PMCID: PMC8284688 DOI: 10.1007/s42485-021-00068-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/14/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Klebsiella aerogenes is a multidrug-resistant Gram-negative bacterium that causes nosocomial infections. The organism showed resistance to most of the conventional antibiotics available. Because of the high resistance of the species, the treatment of K. aerogenes is difficult. These species are resistant to third-generation cephalosporins due to the production of chromosomal beta-lactams with cephalosporin activity. The lack of better treatment and the development of therapeutic resistance in hospitals hinders better/new broad-spectrum-based treatment against this pathogen. This study identifies potential drug targets/vaccine candidates through a computational subtractive proteome-driven approach. This method is used to predict proteins that are not homologous to humans and human symbiotic intestinal flora. The resultant proteome of K. aerogenes was further searched for proteins, which are essential, virulent, and determinants of antibiotic/drug resistance. Subsequently, their druggability properties were also studied. The data set was reduced based on its presence in the pathogen-specific metabolic pathways. The subtractive proteome analysis predicted 13 proteins as potential drug targets for K. aerogenes. Furthermore, these target proteins were annotated based on their spectrum of activity, cellular localization, and antigenicity properties, which ensured that they are potent candidates for broad-spectrum antibiotic and vaccine design. The results open up new opportunities for designing and manufacturing powerful antigenic vaccines against K. aerogenes and the detection and release of new and active drugs against K. aerogenes without altering the gut microbiome. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-021-00068-9.
Collapse
Affiliation(s)
- Vijina Chakkyarath
- grid.411677.20000 0000 8735 2850Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
| | - Anusuya Shanmugam
- grid.444708.b0000 0004 1799 6895Department of Pharmaceutical Engineering, Vinayaka Mission’s Kirupananda Variyar Engineering College, Vinayaka Mission’s Research Foundation (Deemed to be University), Salem, Tamil Nadu 636308 India
| | - Jeyakumar Natarajan
- grid.411677.20000 0000 8735 2850Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
| |
Collapse
|
9
|
Metz P, Tjan MJH, Wu S, Pervaiz M, Hermans S, Shettigar A, Sears CL, Ritschel T, Dutilh BE, Boleij A. Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin. Front Cell Infect Microbiol 2019; 9:364. [PMID: 31709196 PMCID: PMC6823872 DOI: 10.3389/fcimb.2019.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/08/2019] [Indexed: 01/04/2023] Open
Abstract
Objective: The human intestinal microbiome plays an important role in inflammatory bowel disease (IBD) and colorectal cancer (CRC) development. One of the first discovered bacterial mediators involves Bacteroides fragilis toxin (BFT, also named as fragilysin), a metalloprotease encoded by enterotoxigenic Bacteroides fragilis (ETBF) that causes barrier disruption and inflammation of the colon, leads to tumorigenesis in susceptible mice, and is enriched in the mucosa of IBD and CRC patients. Thus, targeted inhibition of BFT may benefit ETBF carrying patients. Design: By applying two complementary in silico drug design techniques, drug repositioning and molecular docking, we predicted potential BFT inhibitory compounds. Top candidates were tested in vitro on the CRC epithelial cell line HT29/c1 for their potential to inhibit key aspects of BFT activity, being epithelial morphology changes, E-cadherin cleavage (a marker for barrier function) and increased IL-8 secretion. Results: The primary bile acid and existing drug chenodeoxycholic acid (CDCA), currently used for treating gallstones, cerebrotendinous xanthomatosis, and constipation, was found to significantly inhibit all evaluated cell responses to BFT exposure. The inhibition of BFT resulted from a direct interaction between CDCA and BFT, as confirmed by an increase in the melting temperature of the BFT protein in the presence of CDCA. Conclusion: Together, our results show the potential of in silico drug discovery to combat harmful human and microbiome-derived proteins and more specifically suggests a potential for retargeting CDCA to inhibit the pro-oncogenic toxin BFT.
Collapse
Affiliation(s)
- Paul Metz
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands.,Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands.,Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Martijn J H Tjan
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands.,Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Shaoguang Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mehrosh Pervaiz
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands
| | - Susanne Hermans
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands
| | - Aishwarya Shettigar
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tina Ritschel
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands
| | - Bas E Dutilh
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Annemarie Boleij
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center (Radboudumc), Nijmegen, Netherlands
| |
Collapse
|
10
|
Urusova DV, Kinsella RL, Salinas ND, Haurat MF, Feldman MF, Tolia NH. The structure of Acinetobacter-secreted protease CpaA complexed with its chaperone CpaB reveals a novel mode of a T2SS chaperone-substrate interaction. J Biol Chem 2019; 294:13344-13354. [PMID: 31320476 DOI: 10.1074/jbc.ra119.009805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
Members of the Acinetobacter baumannii-calcoaceticus complex are nosocomial pathogens frequently causing multidrug-resistant infections that are increasing at alarming rates. A. baumannii has become the Gram-negative bacterium with the highest rate of multidrug resistance. As such, it is categorized by the World Health Organization as a critical priority for the research and development of new antimicrobial therapies. The zinc-dependent metalloendopeptidase CpaA is a predominant substrate of the type II secretion system (T2SS). CpaA is also a virulence factor of medically relevant Acinetobacter strains that specifically degrade the human glycoprotein coagulation factor XII and not its deglycosylated form, but the mechanism for this specificity is unknown. CpaB is a membrane-anchored T2SS chaperone that interacts with CpaA and is required for its stability and secretion. Here, we report the crystal structure of the CpaAB complex at 2.6-Å resolution, revealing four glycan-binding domains in CpaA that were not predicted from its primary sequence and may explain CpaA's glycoprotein-targeting activity. The structure of the complex identified a novel mode for chaperone-protease interactions in which the protease surrounds the chaperone. The CpaAB organization was akin to zymogen inactivation, with CpaB serving as a prodomain that inhibits catalytically active CpaA. CpaB contains a C-terminal tail that appears to block access to the CpaA catalytic site, and functional experiments with truncated variants indicated that this tail is dispensable for CpaA expression and secretion. Our results provide new insight into the mechanism of CpaA secretion and may inform the future development of therapeutic strategies for managing Acinetobacter infections.
Collapse
Affiliation(s)
- Darya V Urusova
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, Saint Louis, Missouri 63110
| | - Rachel L Kinsella
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, Saint Louis, Missouri 63110
| | - Nichole D Salinas
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - M Florencia Haurat
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, Saint Louis, Missouri 63110
| | - Mario F Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, Saint Louis, Missouri 63110
| | - Niraj H Tolia
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, Saint Louis, Missouri 63110; Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892.
| |
Collapse
|
11
|
Hossain MU, Khan MA, Hashem A, Islam MM, Morshed MN, Keya CA, Salimullah M. Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration. Front Microbiol 2016; 7:1817. [PMID: 27920755 PMCID: PMC5118456 DOI: 10.3389/fmicb.2016.01817] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/28/2016] [Indexed: 11/13/2022] Open
Abstract
Background:Shigella flexneri is a gram negative bacteria that causes the infectious disease “shigellosis.” S. flexneri is responsible for developing diarrhea, fever, and stomach cramps in human. Antibiotics are mostly given to patients infected with shigella. Resistance to antibiotics can hinder its treatment significantly. Upon identification of essential therapeutic targets, vaccine and drug could be effective therapy for the treatment of shigellosis. Methods: The study was designed for the identification and qualitative characterization for potential drug targets from S. flexneri by using the subtractive proteome analysis. A set of computational tools were used to identify essential proteins those are required for the survival of S. flexneri. Total proteome (13,503 proteins) of S. flexneri was retrieved from NCBI and further analyzed by subtractive channel analysis. After identification of the metabolic proteins we have also performed its qualitative characterization to pave the way for the identification of promising drug targets. Results: Subtractive analysis revealed that a list of 53 targets of S. flexneri were human non-homologous essential metabolic proteins that might be used for potential drug targets. We have also found that 11 drug targets are involved in unique pathway. Most of these proteins are cytoplasmic, can be used as broad spectrum drug targets, can interact with other proteins and show the druggable properties. The functionality and drug binding site analysis suggest a promising effective way to design the new drugs against S. flexneri. Conclusion: Among the 53 therapeutic targets identified through this study, 13 were found highly potential as drug targets based on their physicochemical properties whilst only one was found as vaccine target against S. flexneri. The outcome might also be used as module as well as circuit design in systems biology.
Collapse
Affiliation(s)
- Mohammad Uzzal Hossain
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University Tangail, Bangladesh
| | - Md Arif Khan
- Department of Science and Humanities, Military Institute of Science and Technology, Mirpur Cantonment Dhaka, Bangladesh
| | - Abu Hashem
- Microbial Biotechnology Division, National Institute of Biotechnology Savar, Bangladesh
| | - Md Monirul Islam
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University Tangail, Bangladesh
| | - Mohammad Neaz Morshed
- Department of Science and Humanities, Military Institute of Science and Technology, Mirpur Cantonment Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University Bashundhara, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology Savar, Bangladesh
| |
Collapse
|
12
|
Abstract
PURPOSE OF REVIEW A diverse array of microbes colonizes the human intestine. In this review, we seek to outline the current state of knowledge on what characterizes a 'healthy' or 'normal' intestinal microbiome, what factors modify the intestinal microbiome in the healthy state and how the intestinal microbiome affects normal host physiology. RECENT FINDINGS What constitutes a 'normal' or 'healthy' intestinal microbiome is an area of active research, but key characteristics may include diversity, richness and a microbial community's resilience and ability to resist change. A number of factors, including age, the host immune system, host genetics, diet and antibiotic use, appear to modify the intestinal microbiome in the normal state. New research shows that the microbiome likely plays a critical role in the healthy human immune system and metabolism. SUMMARY It is clear that there is a complicated bidirectional relationship between the intestinal microbiota and host which is vital to health. An enhanced understanding of this relationship will be critical not only to maximize and maintain human health but also to shape our understanding of disease and to foster new therapeutic approaches.
Collapse
|
13
|
Chmiela M, Gajewski A, Rudnicka K. Helicobacter pylori vs coronary heart disease - searching for connections. World J Cardiol 2015; 7:187-203. [PMID: 25914788 PMCID: PMC4404374 DOI: 10.4330/wjc.v7.i4.187] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/16/2015] [Accepted: 02/09/2015] [Indexed: 02/07/2023] Open
Abstract
In this review, we discussed the findings and concepts underlying the potential role of Helicobacter pylori (H. pylori) infections in the initiation, development or persistence of atherosclerosis and coronary heart disease (CHD). This Gram-negative bacterium was described by Marshall and Warren in 1984. The majority of infected subjects carries and transmits H. pylori with no symptoms; however, in some individuals these bacteria may cause peptic ulcers, and even gastric cancers. The widespread prevalence of H. pylori infections and the fact that frequently they remain asymptomatic may suggest that, similarly to intestinal microflora, H. pylori may deliver antigens that stimulate not only local, but also systemic inflammatory response. Recently, possible association between H. pylori infection and extragastric disorders has been suggested. Knowledge on the etiology of atherosclerosis together with current findings in the area of H. pylori infections constitute the background for the newly proposed hypothesis that those two processes may be related. Many research studies confirm the indirect association between the prevalence of H. pylori and the occurrence of CHD. According to majority of findings the involvement of H. pylori in this process is based on the chronic inflammation which might facilitate the CHD-related pathologies. It needs to be elucidated, if the infection initiates or just accelerates the formation of atheromatous plaque.
Collapse
|
14
|
Abstract
The increasing emergence of antimicrobial multiresistant bacteria is of great concern to public health. While these bacteria are becoming an ever more prominent cause of nosocomial and community-acquired infections worldwide, the antibiotic discovery pipeline has been stalled in the last few years with very few efforts in the research and development of novel antibacterial therapies. Some of the root causes that have hampered current antibiotic drug development are the lack of understanding of the mode of action (MOA) of novel antibiotic molecules and the poor characterization of the bacterial physiological response to antibiotics that ultimately causes resistance. Here, we review how bacterial genetic tools can be applied at the genomic level with the goal of profiling resistance to antibiotics and elucidating antibiotic MOAs. Specifically, we highlight how chemical genomic detection of the MOA of novel antibiotic molecules and antibiotic profiling by next-generation sequencing are leveraging basic antibiotic research to unprecedented levels with great opportunities for knowledge translation.
Collapse
Affiliation(s)
- Silvia T Cardona
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and.,b Department of Medical Microbiology & Infectious Disease , University of Manitoba , Winnipeg , Canada
| | - Carrie Selin
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and
| | - April S Gislason
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and
| |
Collapse
|
15
|
Abstract
Although major advances in the care of cancer patients over the past several decades have resulted in improved survival, infectious complications remain a significant cause of morbidity and mortality. To successfully identify, treat, and prevent infections, a comprehensive understanding of risk factors that predispose to infection and of commonly encountered pathogens is necessary. In addition, clinicians must keep abreast of the changing epidemiology of infections in this population. As therapeutic modalities continue to evolve, as established pathogens become increasingly drug resistant, and as new pathogens are discovered, successful management of infections will continue to present challenges in the years to come.
Collapse
Affiliation(s)
- Valentina Stosor
- Div. Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois USA
| | - Teresa R. Zembower
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois USA
| |
Collapse
|
16
|
Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach. PLoS One 2013; 8:e59126. [PMID: 23527108 PMCID: PMC3602546 DOI: 10.1371/journal.pone.0059126] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/11/2013] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium abscessus, a non-tuberculous rapidly growing mycobacterium, is recognized as an emerging human pathogen causing a variety of infections ranging from skin and soft tissue infections to severe pulmonary infections. Lack of an optimal treatment regimen and emergence of multi-drug resistance in clinical isolates necessitate the development of better/new drugs against this pathogen. The present study aims at identification and qualitative characterization of promising drug targets in M. abscessus using a novel hierarchical in silico approach, encompassing three phases of analyses. In phase I, five sets of proteins were mined through chokepoint, plasmid, pathway, virulence factors, and resistance genes and protein network analysis. These were filtered in phase II, in order to find out promising drug target candidates through subtractive channel of analysis. The analysis resulted in 40 therapeutic candidates which are likely to be essential for the survival of the pathogen and non-homologous to host, human anti-targets, and gut flora. Many of the identified targets were found to be involved in different metabolisms (viz., amino acid, energy, carbohydrate, fatty acid, and nucleotide), xenobiotics degradation, and bacterial pathogenicity. Finally, in phase III, the candidate targets were qualitatively characterized through cellular localization, broad spectrum, interactome, functionality, and druggability analysis. The study explained their subcellular location identifying drug/vaccine targets, possibility of being broad spectrum target candidate, functional association with metabolically interacting proteins, cellular function (if hypothetical), and finally, druggable property. Outcome of the present study could facilitate the identification of novel antibacterial agents for better treatment of M. abscesses infections.
Collapse
|
17
|
Zhu Y, Wu H, Wang PP, Savas S, Woodrow J, Wish T, Jin R, Green R, Woods M, Roebothan B, Buehler S, Dicks E, Mclaughlin JR, Campbell PT, Parfrey PS. Dietary patterns and colorectal cancer recurrence and survival: a cohort study. BMJ Open 2013; 3:bmjopen-2012-002270. [PMID: 23396503 PMCID: PMC3586110 DOI: 10.1136/bmjopen-2012-002270] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE To examine the association between dietary patterns and colorectal cancer (CRC) survival. DESIGN Cohort study. SETTING A familial CRC registry in Newfoundland. PARTICIPANTS 529 newly diagnosed CRC patients from Newfoundland. They were recruited from 1999 to 2003 and followed up until April 2010. OUTCOME MEASURE Participants reported their dietary intake using a food frequency questionnaire. Dietary patterns were identified with factor analysis. Multivariable Cox proportional hazards models were employed to estimate HR and 95% CI for association of dietary patterns with CRC recurrence and death from all causes, after controlling for covariates. RESULTS Disease-free survival (DFS) among CRC patients was significantly worsened among patients with a high processed meat dietary pattern (the highest vs the lowest quartile HR 1.82, 95% CI 1.07 to 3.09). No associations were observed with the prudent vegetable or the high-sugar patterns and DFS. The association between the processed meat pattern and DFS was restricted to patients diagnosed with colon cancer (the highest vs the lowest quartile: HR 2.29, 95% CI 1.19 to 4.40) whereas the relationship between overall survival (OS) and this pattern was observed among patients with colon cancer only (the highest vs the lowest quartile: HR 2.13, 95% CI 1.03 to 4.43). Potential effect modification was noted for sex (p value for interaction 0.04, HR 3.85 for women and 1.22 for men). CONCLUSIONS The processed meat dietary pattern prior to diagnosis is associated with higher risk of tumour recurrence, metastasis and death among patients with CRC.
Collapse
Affiliation(s)
- Yun Zhu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Epidemiology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Hao Wu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Epidemiology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jennifer Woodrow
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Tyler Wish
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Rong Jin
- Department of Epidemiology, The First Affiliated Hospital of Wenzhou Medical College, Wenzhou, China
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Michael Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Barbara Roebothan
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Sharon Buehler
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - John R Mclaughlin
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Patrick S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| |
Collapse
|
18
|
Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog. Proc Natl Acad Sci U S A 2011; 108:1856-61. [PMID: 21233422 DOI: 10.1073/pnas.1012173108] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Enterotoxigenic Bacteroides fragilis is the most frequent disease-causing anaerobe in the intestinal tract of humans and livestock and its specific virulence factor is fragilysin, also known as B. fragilis toxin. This is a 21-kDa zinc-dependent metallopeptidase existing in three closely related isoforms that hydrolyze E-cadherin and contribute to secretory diarrhea, and possibly to inflammatory bowel disease and colorectal cancer. Here we studied the function and zymogenic structure of fragilysin-3 and found that its activity is repressed by a ∼170-residue prodomain, which is the largest hitherto structurally characterized for a metallopeptidase. This prodomain plays a role in both the latency and folding stability of the catalytic domain and it has no significant sequence similarity to any known protein. The prodomain adopts a novel fold and inhibits the protease domain via an aspartate-switch mechanism. The catalytic fragilysin-3 moiety is active against several protein substrates and its structure reveals a new family prototype within the metzincin clan of metallopeptidases. It shows high structural similarity despite negligible sequence identity to adamalysins/ADAMs, which have only been described in eukaryotes. Because no similar protein has been found outside enterotoxigenic B. fragilis, our findings support that fragilysins derived from a mammalian adamalysin/ADAM xenolog that was co-opted by B. fragilis through a rare case of horizontal gene transfer from a eukaryotic cell to a bacterial cell. Subsequently, this co-opted peptidase was provided with a unique chaperone and latency maintainer in the time course of evolution to render a robust and dedicated toxin to compromise the intestinal epithelium of mammalian hosts.
Collapse
|