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Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations.

ABSTRACT: The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.

SUBMITTER: Yamamoto S

PROVIDER: S-EPMC7761175 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations.

Yamamoto Shohei S Saito Ryosuke R Nakamura Shunya S Sogawa Haruki H Karpov Pavel P Shulga Sergey S Blume Yaroslav Y Kurita Noriyuki N

Antibiotics (Basel, Switzerland) 20201126 12

The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of <i>Mycobacteria</i>. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific ...[more]

PMID: 33256135

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Project description:We investigated excess electron solvation dynamics in (NH3)n- ammonia clusters in the n = 8-32 size range by performing finite temperature molecular dynamics simulations. In particular, we focused on three possible scenarios. The first case is designed to model electron attachment to small neutral ammonia clusters (n ≤ ∼10) that form hydrogen-bonded chains. The excess electron is bound to the clusters via dipole bound states, and persists with a VDE of ∼160 meV at 100 K for the n = 8 cluster. The coupled nuclear and electronic relaxation is fast (within ∼100 fs) and takes place predominantly by intermolecular librational motions and the intramolecular umbrella mode. The second scenario illustrates the mechanism of excess electron attachment to cold compact neutral clusters of medium size (8 ≤ n ≤ 32). The neutral clusters show increasing tendency with size to bind the excess electron on the surface of the clusters in weakly bound, diffuse, and highly delocalized states. Anionic relaxation trajectories launched from these initial states provide no indication for excess electron stabilization for sizes n < 24. Excess electrons are likely to autodetach from these clusters. The two largest investigated clusters (n = 24 and 32) can accommodate the excess electron in electronic states that are mainly localized on the surface, but they may be partly embedded in the cluster. In the last 500 fs of the simulated trajectories, the VDE of the solvated electron fluctuates around ∼200 meV for n = 24 and ∼500 meV for n = 32, consistent with the values extrapolated from the experimentally observed linear VDE-n-1/3 trend. In the third case, we prepared neutral ammonia cluster configurations, including an n = 48 cluster, that contain possible electron localization sites within the interior of the cluster. Excess electrons added to these clusters localize in cavities with high VDEs up to 1.9 eV for n = 48. The computed VDE values for larger clusters are considerably higher than the experimentally observed photoelectric threshold energy for the solvated electron in bulk ammonia (∼1.4 eV). Molecular dynamics simulations launched from these initial cavity states strongly indicate, however, that these cavity structures exist only for ∼200 fs. During the relaxation the electron leaves the cavity and becomes delocalized, while the cluster loses its initial compactness.

Dataset Information

Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations.

Publications

Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations.

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