A potential in silico antibody–antigen based diagnostic test for precise identification of Acinetobacter baumannii

Rahbar, Mohammad Reza; Rasooli, Iraj; Gargari, Seyed Latif Mousavi; Sandström, Gunnar; Amani, Jafar; Fattahian, Yaser; Jahangiri, Abolfazl; Jalali, Mohammad

doi:10.1016/j.jtbi.2011.10.026

Cited by 26 publications

(16 citation statements)

References 70 publications

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“…Baprelated proteins are outer membrane proteins, but it has also been suggested that Bap could be an extracellular protein [15] involved in intercellular adhesion within the mature biofilm and plays a significant role in bacterial infections processes. Bioinformatics studies suggested 15 potential linear B-cell epitopes within the primary sequence of the Bap subunit and homology search of these sequences returned mostly to A. baumannii [5]. Higher scores and the lowest BLAST hits for this subunit both belong to A. baumannii and shows the specificity of this region to the bacterium [9].…”

Section: Discussionmentioning

confidence: 99%

“…It causes nosocomial infections associated with morbidity and mortality [2] such as pneumonia, blood-stream and wound infections [3], secondary meningitis, urinary tract and burn infections [4]. Its resistance to many antimicrobial agents renders the treatment very difficult [5]. Its adherence to and persistence on abiotic and biotic surfaces as biofilm is the core pathogenicity factor of the bacteria [6].…”

Section: Introductionmentioning

confidence: 99%

“…Nucleotide sequence of this surface protein reveals a repetitive structure [7]. This protein contributes in bacterial stability at various environmental conditions [5]. Most strains of the bacteria can easily acquire various antibiotics resistance through different mechanisms, therefore the treatment could be a serious challenge [8].…”

Section: Introductionmentioning

confidence: 99%

“…These tests are based on detection of specific immunoglobulins in patient sera [9]. Rahbar et al [5]. reported potential antigenic structures in Bap subunit possessing various antigenic determinants that elicit antibody formation.…”

Section: Introductionmentioning

confidence: 99%

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A conserved region from biofilm associated protein as a biomarker for detection of Acinetobacter baumannii

Noori

Rasooli

Owlia

et al. 2014

Microbial Pathogenesis

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A conserved region from biofilm associated protein as a biomarker for detection of Acinetobacter baumannii

Noori

Rasooli

Owlia

et al. 2014

Microbial Pathogenesis

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“…Nowadays, bioinformatics is reliably employed in biology researches. It could be harnessed in vaccine design as well as epitope mapping purposes (Jahangiri et al 2011 F. Sefid et al Rahbar et al 2012;Hosseingholi et al 2014). In the present study we exploit bioinformatic tools to introduce the best regions of BauA as antigenic determinants in order to design (a) novel construct (s) as vaccine or diagnostics.…”

Section: Introductionmentioning

confidence: 99%

Functional Exposed Amino Acids of BauA as Potential Immunogen Against Acinetobacter baumannii

et al. 2015

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Multidrug-resistant Acinetobacter baumannii is recognized to be among the most difficult antimicrobial-resistant gram negative bacilli to control and treat. One of the major challenges that the pathogenic bacteria face in their host is the scarcity of freely available iron. To survive under such conditions, bacteria express new proteins on their outer membrane and also secrete iron chelators called siderophores. Antibodies directed against these proteins associated with iron uptake exert a bacteriostatic or bactericidal effect against A. baumanii in vitro, by blocking siderophore mediated iron uptake pathways. Attempts should be made to discover peptides that could mimic protein epitopes and possess the same immunogenicity as the whole protein. Subsequently, theoretical methods for epitope prediction have been developed leading to synthesis of such peptides that are important for development of immunodiagnostic tests and vaccines. The present study was designed to in silico resolving the major obstacles in the control or in prevention of the diseases caused by A. baumannii. We exploited bioinformatic tools to better understand and characterize the Baumannii acinetobactin utilization structure of A. baumannii and select appropriate regions as effective B cell epitopes. In conclusion, amino acids 26-191 of cork domain and 321-635 of part of the barrel domain including L4-L9, were selected as vaccine candidates. These two regions contain functional exposed amino acids with higher score of B cell epitopes properties. Majority of amino acids are hydrophilic, flexible, accessible, and favorable for B cells from secondary structure point of view.

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Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein

Leong

Lim

Ismail

et al. 2017

J of Molecular Recognition

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With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.

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A potential in silico antibody–antigen based diagnostic test for precise identification of Acinetobacter baumannii

Cited by 26 publications

References 70 publications

A conserved region from biofilm associated protein as a biomarker for detection of Acinetobacter baumannii

A conserved region from biofilm associated protein as a biomarker for detection of Acinetobacter baumannii

Functional Exposed Amino Acids of BauA as Potential Immunogen Against Acinetobacter baumannii

Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein

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