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Published on: December 4, 2017
The binding mechanism of nitroreductase fluorescent probe: Active pocket deformation and intramolecular hydrogen
Min Zhu1, Rui Rui Liu1, Hong Lin Zhai1
1College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China.
Abstract:
Nitroreductase (NTR), a member of the flavoenzyme family, could react with nicotinamide adenine dinucleotide by reducing nitro to amino at hypoxic tumor, which can be monitored by some fluorescent probes in vivo. Here, molecular docking and molecular dynamics simulation techniques were used to explore the molecular mechanisms between NTR and probes. The results showed that formation of hydrogen bond in 1F5V-13 between A@His215 and B@Ser41 with 74.53% occupancy might be the main reason for the decrease of probe fluorescence emission in experiment. Moreover, Probe 16 was rotated by nearly 60 degrees with respect to the position of other probes in protein binding pocket, deforming the protein active pocket, changing the hydrogen bond formation, which leads to the fluorescence performance of 16 with electron donor and electron acceptor groups was superior to other probes in experiment. The deformation of protein active pocket and the formation of intramolecular hydrogen bonds revealed the difference in performance of NTR fluorescent probe at molecular level, which provide theoretical guidance for latter design of fluorescent probes with better performance.
Insights
Nitroreductase enzymes catalyze reactions in hypoxic tumors, detectable with fluorescent probes. Molecular simulations reveal how probe interactions and protein pocket deformation influence probe performance for better diagnostic tool design.
Area of Science:
- Biochemistry
- Molecular Biology
- Biophysics
Background:
- Nitroreductase (NTR) is a flavoenzyme crucial for bioreductive drug activation and imaging in hypoxic tumors.
- Fluorescent probes are used in vivo to monitor NTR activity by detecting the reduction of nitro to amino groups.
Purpose of the Study:
- To elucidate the molecular mechanisms underlying the interaction between nitroreductase and fluorescent probes.
- To understand how these interactions affect probe performance and fluorescence emission.
- To provide theoretical guidance for designing improved NTR-targeting fluorescent probes.
Main Methods:
- Molecular docking simulations to predict binding modes and affinities.
- Molecular dynamics simulations to analyze binding stability and conformational changes.
- Analysis of hydrogen bond formation and occupancy.
- Correlation of simulation results with experimental fluorescence data.
Main Results:
- Hydrogen bond formation between NTR (A@His215) and a probe (B@Ser41) with 74.53% occupancy was identified as a key factor in fluorescence quenching.
- Probe 16 exhibited a distinct binding orientation, causing significant deformation of the NTR active pocket.
- This deformation altered hydrogen bonding patterns, leading to superior fluorescence performance of Probe 16 compared to others.
- Intramolecular hydrogen bonds within Probe 16 also contributed to its unique properties.
Conclusions:
- The study reveals the molecular basis for differential performance among NTR fluorescent probes.
- Active pocket deformation and specific hydrogen bonding interactions are critical determinants of probe efficacy.
- Findings offer a theoretical framework for the rational design of next-generation NTR-based fluorescent probes for tumor imaging.
