همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

In Silico Design of DNA G-Quadruplex Aptamers Targeting Lipopolysaccharide Core and Capsular Polysaccharide in Multidrug-Resistant Klebsiella pneumoniae

نویسندگان :

Aida Arezoumandchafi¹ Maryam Azimzadeh Irani² Hamidreza Mollasalehi³

1- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran 2- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran 3- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran

کلمات کلیدی :

SELEX،G-quadruplex،Molecular diagnostics،Glycans،Aptamers

چکیده :

Klebsiella pneumoniae is linked to serious infections such as pneumonia, urinary tract infections (UTIs), and sepsis, particularly affecting immunocompromised and hospitalized individuals (Paniagua-Contreras and Bautista-Cerón, 2023). The increasing prevalence of multidrug-resistant (MDR) strains, including extended-spectrum beta-lactamase (ESBL) and carbapenemase producers, has significantly elevated mortality rates and posed treatment challenges (Paniagua-Contreras and Bautista-Cerón, 2023). Although traditional detection methods remain effective, they typically require specialized equipment, limiting accessibility in resource-limited environments. Research has identified conserved regions in lipopolysaccharides (LPS) (Kim and Jang, 2022) and capsular polysaccharides (CPS) as promising targets for biosensor development (Kaszowska and Majkowska-Skrobek, 2021). This study used in silico techniques to design a library and potential specific DNA aptamers for cost-effective detection of K. pneumoniae, circumventing the experimental SELEX process. To identify G-quadruplex-forming sequences, six K. pneumoniae gene sequences were obtained from NCBI GenBank (Benson and Cavanaugh, 2013): KPHS_37010, KPHS_20120, KPHS_51230, KPHS_47480, KPHS_51270, and KPHS_20620. These sequences were used to construct an initial nucleotide pool. Molecular models of LPS core oligosaccharides, which link the lipid A component to the O-antigen, and Type 1 CPS, a polysaccharide capsule aiding immune evasion, were generated using CHARMM-GUI (Jo and Kim, 2008). QGRS Mapper (Kikin and D'Antonio, 2006) identified 44 DNA G-quadruplex sequences between 20 and 40 nucleotides in length, each with a G-score above 15, indicating stability and specificity. Aptasuite (Hoinka and Backofen, 2018) clustered these sequences into four structural groups with consensus sequences of 38 nucleotides. The 3D structures of the top five G-quadruplexes with G-scores above 30 were modeled using AlphaFold (Abramson and Adler, 2024), along with the four clusters, and docked to LPS and CPS glycan targets using HADDOCK2.4 (Honorato and Trellet, 2024). Among these, the Optimal G-quadruplex—identical in sequence to the Final Selected Cluster—demonstrated strong binding to both LPS and CPS. Docking analysis revealed that the Optimal G-quadruplex exhibited the highest binding affinity for CPS (HADDOCK score 1.9 ± 5.1; vdW energy -28.3 ± 1.9; electrostatic energy -34.1 ± 3.9), while the Final Selected Cluster showed superior scores for LPS (HADDOCK score 16.4 ± 1.6; vdW energy -20.4 ± 0.7; electrostatic energy -31.7 ± 11.2). Both structures achieved negative binding energies, highlighting their stability and suitability for biosensing applications. This study provides a foundation for developing stable, specific DNA G-quadruplex aptamers for the rapid detection of K. pneumoniae. The structurally conserved LPS core oligosaccharides represent a universal target, making the findings applicable to both clinical and field biosensor development. Experimental validation is needed to confirm the diagnostic potential and optimize efficacy.