Electrochemical and theoretical studies of the interaction between anticancer drug ponatinib and dsDNA
At a Glance
Section titled âAt a Glanceâ| Metadata | Details |
|---|---|
| Publication Date | 2024-01-27 |
| Journal | Scientific Reports |
| Authors | Sylwia Smarzewska, Anna Ignaczak, Kamila Koszelska |
| Institutions | University of ĆĂłdĆș |
| Citations | 9 |
| Analysis | Full AI Review Included |
Executive Summary
Section titled âExecutive Summaryâ- Core Objective: Investigated the interaction mechanism between the anticancer drug ponatinib (PNT), a third-generation tyrosine kinase inhibitor, and double-stranded DNA (dsDNA).
- Methodology: Combined electrochemical techniques (Square Wave Voltammetry, SWV) using a Boron-Doped Diamond Electrode (BDDE) with hierarchical quantum-chemical calculations (PM7 and DFT).
- Interaction Type: Voltammetric and theoretical results strongly suggest that the primary binding mechanism is groove binding, with intercalation largely excluded due to minimal peak potential shifts observed.
- Binding Site Preference (Theoretical): DFT calculations identified the dsDNA major groove (MaG) as the energetically preferred site for PNT complexation, regardless of the PNT conformer (stretched or lowest energy).
- Nucleobase Specificity: PNT interacts preferentially with electrochemically detectable nucleobases, specifically guanine (dGua) and adenine (dAdo) residues, confirmed by both pH-dependent voltammetry and hydrogen bonding analysis.
- Binding Strength: Computational analysis showed that hydrogen bonds formed between PNT and guanine residues are geometrically stronger than those formed with adenine.
- Electrode Kinetics: PNT oxidation on the BDDE was determined to be an irreversible process, controlled by adsorption in acetate buffer (pH 4.7) and a mixed diffusion-adsorption process in PBS (pH 7.4).
Technical Specifications
Section titled âTechnical Specificationsâ| Parameter | Value | Unit | Context |
|---|---|---|---|
| Working Electrode | Boron-Doped Diamond (BDDE) | 3 mm diameter | Conventional three-electrode system |
| Physiological pH | 7.4 | pH | Phosphate-Buffered Saline (PBS) |
| Acidic pH | 4.7 | pH | Acetate Buffer |
| SWV Amplitude | 30 | mV | Voltammetric interaction studies |
| SWV Frequency | 25 | Hz | Voltammetric interaction studies |
| SWV Step Potential | 4 | mV | Voltammetric interaction studies |
| CV Scan Rate Range | 50 to 500 | mV s-1 | Kinetics study |
| PNT Oxidation Peak 1 (Ep-pH slope) | 13 | mV pH-1 | Complex, multi-step reaction |
| PNT Oxidation Peak 2 (Ep-pH slope) | 51 | mV pH-1 | Suggests equal proton/electron participation |
| Log Ip - Log v Slope (PBS) | 0.71 | N/A | Mixed diffusion-adsorption control |
| Log Ip - Log v Slope (Acetate) | 0.97 | N/A | Adsorption control (close to 1.0) |
| Most Stable Ecompl (119D:PNT_ST) | -65.6 | kcal mol-1 | DFT, Major Groove (MaG) binding |
| Most Stable Ecompl (1BNA:PNT_LE) | -56.6 | kcal mol-1 | DFT, Major Groove (MaG) binding |
| Guanine OâŠH-N H-Bond Distance | 1.96 to 2.37 | Angstrom | Stronger hydrogen bonding |
| Adenine HâŠO H-Bond Distance | 2.20 | Angstrom | Weaker hydrogen bonding |
Key Methodologies
Section titled âKey MethodologiesâThe study employed a rigorous, three-stage hierarchical approach for computational modeling, coupled with advanced electrochemical analysis using a BDDE.
Electrochemical Analysis (SWV/CV)
Section titled âElectrochemical Analysis (SWV/CV)â- Electrode Preparation: BDDE surface was polished using alumina slurry, followed by thorough rinsing with distilled/deionized water to ensure a clean, active surface.
- PNT Characterization: Cyclic Voltammetry (CV) and Square Wave Voltammetry (SWV) were used to determine the irreversible oxidation behavior of PNT across a wide pH range (1.7-9.0).
- Interaction Study (Incubation): PNT (5.0 ”mol L-1) and dsDNA (80 mg L-1) were mixed in acetate buffer (pH 4.7) or PBS (pH 7.4) and incubated at room temperature for varying periods (10, 30, 60, 90 min).
- Concentration Variation Study: SWV was performed immediately after adding increasing amounts of dsDNA (10-80 mg L-1) to a fixed concentration of PNT, analyzing changes in peak current and potential shift.
Computational Modeling (Hierarchical Approach)
Section titled âComputational Modeling (Hierarchical Approach)â- Step 1: Molecular Mechanics (HyperChem):
- Initial models of dsDNA:PNT complexes were generated using two B-DNA dodecamers (1BNA and 119D).
- PNT conformers (PNT_LE and PNT_ST) were systematically rotated (30° increments around X, Y, Z axes) across four binding sites: External Binding (ExB), Major Groove (MaG), Minor Groove (MiG), and Intercalation (InC).
- Step 2: Semiempirical Optimization (MOPAC):
- All generated structures were optimized using the PM7 method, incorporating solvent effects via the Conductor-like Screening Model (COSMO) in water.
- Complexation enthalpies (Hcompl) were calculated to identify the most stable structure for each site.
- Step 3: DFT Calculation (Gaussian 16):
- The most stable structures from Step 2 underwent partial re-optimization (PNT relaxed, dsDNA frozen) using the high-accuracy M062X-GD3 functional with the 6-31G(d,p) basis set.
- Solvent effects were modeled using the Polarizable Continuum Model (PCM) in water.
- Final complexation energies (Ecompl) were computed to confirm binding stability and identify preferred sites.
Commercial Applications
Section titled âCommercial Applicationsâ- Electrochemical Drug Sensing: Utilizing the high sensitivity and stability of the BDDE for the trace analysis and quantification of tyrosine kinase inhibitors (TKIs) like PNT in complex biological matrices (plasma, urine), offering a âgreen chemistryâ alternative to traditional chromatographic methods.
- Genotoxicity Screening: Applying electrochemical biosensors (BDDE/DNA) to rapidly screen new drug candidates for potential DNA damage or interaction mechanisms (groove binding vs. intercalation), crucial for early-stage pharmaceutical safety assessment.
- Personalized Medicine & TKI Monitoring: Development of robust, portable electrochemical devices for clinical monitoring of TKI drug concentrations in cancer patients (e.g., CML, ALL), ensuring optimal therapeutic windows and minimizing toxic side effects.
- Advanced Biosensor Design: Leveraging the detailed structural and energetic data from DFT calculations to rationally design and optimize DNA-based biosensors that selectively recognize and bind specific drug molecules or metabolites based on groove geometry and nucleobase preference.
- Material Science for Electroanalysis: Confirms the utility of the BDDE as a stable, wide-potential-window platform for studying complex, irreversible redox processes involving large organic molecules and biomolecules, suitable for harsh or physiological environments.