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Crystal structure of the plasmid-encoded R67 dihydrofolate reductase complexed with Congo red an amyloid binding dye
Akshay N Narendra1, Elizabeth E Howell2, Narendra Narayana3
1UCHealth Parkview Medical Center, 400 West 16th street, Pueblo, CO, 81003, USA.
Scientific Reports
|February 12, 2025
Summary
Bacterial dihydrofolate reductase (DHFR) R67 mutant shows high resistance to Trimethoprim (TMP). Structural analysis reveals Congo Red (CGR) binding interactions, suggesting potential for developing novel inhibitors.
Area of Science:
- Biochemistry
- Structural Biology
- Drug Discovery
Background:
- Plasmid-encoded R67 dihydrofolate reductase (DHFR) confers antibiotic resistance.
- R67 DHFR is highly resistant to Trimethoprim (TMP), unlike its chromosomal counterpart.
- Understanding R67 DHFR structure-inhibitor interactions is crucial for developing new antibiotics.
Purpose of the Study:
- Determine the high-resolution crystal structure of the Q67H mutant of R67 DHFR.
- Investigate the binding mode of the non-specific inhibitor Congo Red (CGR) within the R67 DHFR active site.
- Propose strategies for designing specific and potent R67 DHFR inhibitors.
Main Methods:
- X-ray crystallography at 1.15 Å resolution.
- Complex formation between Q67H mutant R67 DHFR and Congo Red (CGR).
- Analysis of electron density maps (Fo-Fc) to visualize inhibitor binding.
- Preliminary computational modeling studies.
Main Results:
- The structure reveals one naphthalene moiety of CGR bound in the active site pore, with flexibility in other parts of the molecule.
- CGR binds asymmetrically, interacting with residues from all four protomers of the tetrameric enzyme.
- Specific interactions include ionic, van der Waals, stacking, and hydrogen bonding.
- Modeling suggests targeting Lys32 residues could lead to potent inhibitors.
Conclusions:
- The determined structure provides insights into the binding of CGR to R67 DHFR.
- The findings support the potential of CGR fragments as scaffolds for developing novel DHFR inhibitors.
- A model for CGR binding to cross-β amyloid is proposed based on observed protein-inhibitor interactions.
