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Molecular dynamics simulations of ortho-carborane nano-diamond storage within the nonpolar channel cavities of a right-handed coiled-coil tetrabrachion nanotube
- Source :
- Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 3531-3541 (2021), Computational and Structural Biotechnology Journal
- Publication Year :
- 2021
- Publisher :
- Elsevier, 2021.
-
Abstract
- Graphical abstract Molecular dynamics simulations have been performed on a complex in which clusters of boron in the form of molecules of the nanodiamond ortho-carborane (C2B10H12) have been inserted into the four large nonpolar cavities of a nanotube of the right-handed coiled-coil RHCC. The techniques of multi-configurational thermodynamic integration, steered molecular dynamics and umbrella sampling have been combined to investigate the energetics of storage of ortho-carborane in the cavities and to map out the free energy landscape of the RHCC-tetrabrachion-ortho-carboranecomplex along the central channel and along directions transverse to the central channel. The purpose of the study was to explore potential pathways for the diffusion of ortho-carborane between the cavities and the solvent and to assess the stability of the complex as a possible drug delivery system for boron neutron capture therapy (BNCT). The investigation reveals a complex free energy landscape with a multitude of peaks and valleys, all of which can be related to specific architectural elements of the RHCC-nanotube, and the activation barriers for ortho-carborane capture and release support the requirements for rapid cargo uptake coupled with tight binding to the cavities.<br />Molecular dynamics simulations have been performed on a complex in which clusters of boron in the form of molecules of the nanodiamond ortho-carborane (C2B10H12) have been inserted into the four large nonpolar cavities of a nanotube of the right-handed coiled-coil (RHCC)tetrabrachion. The techniques of multi-configurational thermodynamic integration, steered molecular dynamics and umbrella sampling have been combined to investigate the energetics of storage of ortho-carborane in the cavities and to map out the free energy landscape of the RHCC-tetrabrachion-ortho-carboranecomplex along the central channel and along directions transverse to the central channel. The purpose of the study was to explore potential pathways for the diffusion of ortho-carborane between the cavities and the solvent and to assess the stability of the complex as a possible drug delivery system for boron neutron capture therapy (BNCT). The investigation reveals a complex free energy landscape with a multitude of peaks and valleys, all of which can be related to specific architectural elements of the RHCC-nanotube, and the activation barriers for ortho-carborane capture and release support the requirements for rapid cargo uptake coupled with tight binding to the cavities.
- Subjects :
- Steered molecular dynamics
Nanotube
Materials science
Biophysics
Thermodynamic integration
Ortho-carborane
Nonpolar cavities
Biochemistry
Right-handed coiled-coil tetrabrachion nanotube
Multi-configurational thermodynamic integration
Umbrella sampling
03 medical and health sciences
Molecular dynamics
Boron neutron capture therapy
0302 clinical medicine
Tight binding
Structural Biology
Genetics
Molecule
Double-decoupling
Free energy
030304 developmental biology
0303 health sciences
Molecular dynamics simulations
Energy landscape
Computer Science Applications
Crystallography
030220 oncology & carcinogenesis
Carborane
TP248.13-248.65
Research Article
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 20010370
- Volume :
- 19
- Database :
- OpenAIRE
- Journal :
- Computational and Structural Biotechnology Journal
- Accession number :
- edsair.doi.dedup.....fccf7af169e0dda2e139d08d1ff07f6e