Identification of biomarkers for the accurate and sensitive diagnosis of three bacterial pneumonia pathogens using in
Olalekan Olanrewaju Bakare1,2, Marshall Keyster3, Ashley Pretorius4
1Bioinformatics Research Group, Biotechnology Department, University of the Western Cape, Cape Town, 7535, South Africa. lekanbakare77@gmail.com.
Background:
Pneumonia ranks as one of the main infectious sources of mortality among kids under 5 years of age, killing 2500 a day; late research has additionally demonstrated that mortality is higher in the elderly. A few biomarkers, which up to this point have been distinguished for its determination lack specificity, as these biomarkers fail to build up a differentiation between pneumonia and other related diseases, for example, pulmonary tuberculosis and Human Immunodeficiency Infection (HIV). There is an inclusive global consensus of an improved comprehension of the utilization of new biomarkers, which are delivered in light of pneumonia infection for precision identification to defeat these previously mentioned constraints. Antimicrobial peptides (AMPs) have been demonstrated to be promising remedial specialists against numerous illnesses. This research work sought to identify AMPs as biomarkers for three bacterial pneumonia pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Acinetobacter baumannii using in silico technology. Hidden Markov Models (HMMER) was used to identify putative anti-bacterial pneumonia AMPs against the identified receptor proteins of Streptococcus pneumoniae, Klebsiella pneumoniae, and Acinetobacter baumannii. The physicochemical parameters of these putative AMPs were computed and their 3-D structures were predicted using I-TASSER. These AMPs were subsequently subjected to docking interaction analysis against the identified bacterial pneumonia pathogen proteins using PATCHDOCK.
Results:
The in silico results showed 18 antibacterial AMPs which were ranked based on their E values with significant physicochemical parameters in conformity with known experimentally validated AMPs. The AMPs also bound the pneumonia receptors of their respective pathogens sensitively at the extracellular regions.
Conclusions:
The propensity of these AMPs to bind pneumonia pathogens proteins justifies that they would be potential applicant biomarkers for the recognizable detection of these bacterial pathogens in a point-of-care POC pneumonia diagnostics. The high sensitivity, accuracy, and specificity of the AMPs likewise justify the utilization of HMMER in the design and discovery of AMPs for disease diagnostics and therapeutics.
Insights
Researchers identified 18 antimicrobial peptides (AMPs) as potential biomarkers for bacterial pneumonia. These AMPs show promise for accurate point-of-care diagnostics and therapeutics against pathogens like Streptococcus pneumoniae.
Area of Science:
- Biochemistry
- Computational Biology
- Infectious Diseases
Background:
- Pneumonia is a leading infectious cause of mortality in children under 5 and the elderly.
- Current pneumonia biomarkers lack specificity, failing to differentiate from diseases like tuberculosis and HIV.
- Antimicrobial peptides (AMPs) show therapeutic potential and are being explored as novel diagnostic biomarkers.
Purpose of the Study:
- To identify antimicrobial peptides (AMPs) as potential biomarkers for bacterial pneumonia.
- To target three key pneumonia pathogens: Streptococcus pneumoniae, Klebsiella pneumoniae, and Acinetobacter baumannii.
- To utilize in silico methods for efficient biomarker discovery.
Main Methods:
- Employed Hidden Markov Models (HMMER) to identify putative antibacterial AMPs against pathogen receptor proteins.
- Computed physicochemical parameters and predicted 3-D structures of identified AMPs using I-TASSER.
- Performed docking interaction analysis using PATCHDOCK to assess binding affinity to pathogen proteins.
Main Results:
- Identified 18 antibacterial AMPs with significant physicochemical properties comparable to validated AMPs.
- AMPs demonstrated sensitive binding to pneumonia pathogen receptors in extracellular regions.
- Results were ranked based on E values, indicating high confidence in the identified AMPs.
Conclusions:
- The identified AMPs are potential biomarkers for accurate point-of-care (POC) pneumonia diagnostics.
- AMPs' binding capabilities support their use in detecting bacterial pneumonia pathogens.
- HMMER is validated as an effective tool for designing and discovering AMPs for diagnostics and therapeutics.
More Related Videos
Related Concept Videos
01:30Pneumonia III: Complications and Assessment
01:28Methods of Classification and Identification