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Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding
Preethi Parameswaran1, Yashaswina Arora1, Rajesh Patidar1
1Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India.
Biophysical Chemistry
|April 26, 2021
Summary
Bisamidines, like DAPI, show potential for targeting bacterial A-site RNA, crucial for developing new antibacterials. These compounds exhibit strong binding and base-stacking interactions, offering a promising avenue for novel drug development.
Area of Science:
- Biochemistry
- Molecular Biology
- Medicinal Chemistry
Background:
- Bacterial A-site RNA is a critical target for novel antibacterial drug development, particularly for tuberculosis treatment.
- The chemical motif bisamidines is explored for its potential in bacterial A-site RNA recognition.
Purpose of the Study:
- To investigate the potential of bisamidines, using DAPI as a prototype, for targeting bacterial A-site RNA.
- To characterize the binding interactions and affinity of DAPI to bacterial A-site RNA.
Main Methods:
- Thermal stabilization assays (ΔTm) to assess DAPI binding to bacterial A-site RNA.
- UV-vis and Circular Dichroism (CD) spectroscopy to analyze binding mechanisms.
- Scatchard analysis and Fluorescence Intensity Decay (FID) for binding affinity determination.
- Molecular docking studies to predict binding poses and interactions.
Main Results:
- DAPI binding demonstrated concentration-dependent thermal stabilization of bacterial A-site RNA (ΔTm = 9.9°C).
- Binding interactions involved base stacking, similar to intercalation, and were not pH-dependent.
- Scatchard analysis revealed a micromolar affinity (Ka = 1.14 × 106 M-1), corroborated by FID comparisons.
- Molecular docking confirmed polar and stacking interactions consistent with observed binding.
Conclusions:
- The study highlights the role of amidine groups in bacterial A-site RNA recognition.
- Bisamidines represent a promising chemical scaffold for developing aminoglycoside mimics.
- Further development of structural analogs is warranted for creating new antibacterial agents.
