Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods

Alexander Maksimenko

doi:doi:10.11648/j.ccr.20200404.19

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Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods

Alexander Maksimenko

Published in Cardiology and Cardiovascular Research (Volume 4, Issue 4)

Received: 9 December 2020 Accepted: 24 December 2020 Published: 31 December 2020

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Abstract

Computational methods have proved to be sometimes a single tool available for investigation of glycosaminoglycan-protein interactions. A two-stage process including molecular docking with its subsequent detalization using the methods of molecular dynamics is a prospective approach to theoretical modeling of protein-glycosaminoglycan complexes. This review deals with specific features of protein-glycosaminoglycan interactions studied by computational methods, docking and scoring function algorithms, and the use of molecular dynamics results with short-time (ps and ns) changes for processes developing within much longer time scales (ranging over several orders of magnitude). The data obtained with help of computational methods contribute the disclosure of biological interaction mechanism, elaboration of enzyme activity control and grounding of rational recommendations for novel therapeutic means development of high-molecular sort. The results of molecular docking of heparanase, chondroitinlyase ABC, chondroitinase B, and hyaluronidase were shown. The approach to productive design of molecules of compounds (regulating enzyme activity for novel drug derivative obtaining) is representative. The investigations of such kind are directed on ascertainment of action mechanism of these agents in biosystems for production of high efficacy of drug preparations of enzyme nature. It is shown that the molecular dynamics method provides modeling of all degrees of freedom in a protein-ligand complex and draws special attention to protein structure flexibility as a considerable challenge in the development of molecular docking. Computational data are reviewed in the aspect of complex formation between proteins and glycosaminoglycan ligands.

Published in	Cardiology and Cardiovascular Research (Volume 4, Issue 4)
DOI	10.11648/j.ccr.20200404.19
Page(s)	220-230
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Hyaluronidase, Glycosaminoglycan Ligands, Docking, Scoring Function, 3D Model of Enzyme Structure

References

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Alexander Maksimenko. (2020). Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods. Cardiology and Cardiovascular Research, 4(4), 220-230. https://doi.org/10.11648/j.ccr.20200404.19

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ACS Style

Alexander Maksimenko. Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods. Cardiol. Cardiovasc. Res. 2020, 4(4), 220-230. doi: 10.11648/j.ccr.20200404.19

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AMA Style

Alexander Maksimenko. Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods. Cardiol Cardiovasc Res. 2020;4(4):220-230. doi: 10.11648/j.ccr.20200404.19

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@article{10.11648/j.ccr.20200404.19,
  author = {Alexander Maksimenko},
  title = {Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods},
  journal = {Cardiology and Cardiovascular Research},
  volume = {4},
  number = {4},
  pages = {220-230},
  doi = {10.11648/j.ccr.20200404.19},
  url = {https://doi.org/10.11648/j.ccr.20200404.19},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ccr.20200404.19},
  abstract = {Computational methods have proved to be sometimes a single tool available for investigation of glycosaminoglycan-protein interactions. A two-stage process including molecular docking with its subsequent detalization using the methods of molecular dynamics is a prospective approach to theoretical modeling of protein-glycosaminoglycan complexes. This review deals with specific features of protein-glycosaminoglycan interactions studied by computational methods, docking and scoring function algorithms, and the use of molecular dynamics results with short-time (ps and ns) changes for processes developing within much longer time scales (ranging over several orders of magnitude). The data obtained with help of computational methods contribute the disclosure of biological interaction mechanism, elaboration of enzyme activity control and grounding of rational recommendations for novel therapeutic means development of high-molecular sort. The results of molecular docking of heparanase, chondroitinlyase ABC, chondroitinase B, and hyaluronidase were shown. The approach to productive design of molecules of compounds (regulating enzyme activity for novel drug derivative obtaining) is representative. The investigations of such kind are directed on ascertainment of action mechanism of these agents in biosystems for production of high efficacy of drug preparations of enzyme nature. It is shown that the molecular dynamics method provides modeling of all degrees of freedom in a protein-ligand complex and draws special attention to protein structure flexibility as a considerable challenge in the development of molecular docking. Computational data are reviewed in the aspect of complex formation between proteins and glycosaminoglycan ligands.},
 year = {2020}
}

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TY  - JOUR
T1  - Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods
AU  - Alexander Maksimenko
Y1  - 2020/12/31
PY  - 2020
N1  - https://doi.org/10.11648/j.ccr.20200404.19
DO  - 10.11648/j.ccr.20200404.19
T2  - Cardiology and Cardiovascular Research
JF  - Cardiology and Cardiovascular Research
JO  - Cardiology and Cardiovascular Research
SP  - 220
EP  - 230
PB  - Science Publishing Group
SN  - 2578-8914
UR  - https://doi.org/10.11648/j.ccr.20200404.19
AB  - Computational methods have proved to be sometimes a single tool available for investigation of glycosaminoglycan-protein interactions. A two-stage process including molecular docking with its subsequent detalization using the methods of molecular dynamics is a prospective approach to theoretical modeling of protein-glycosaminoglycan complexes. This review deals with specific features of protein-glycosaminoglycan interactions studied by computational methods, docking and scoring function algorithms, and the use of molecular dynamics results with short-time (ps and ns) changes for processes developing within much longer time scales (ranging over several orders of magnitude). The data obtained with help of computational methods contribute the disclosure of biological interaction mechanism, elaboration of enzyme activity control and grounding of rational recommendations for novel therapeutic means development of high-molecular sort. The results of molecular docking of heparanase, chondroitinlyase ABC, chondroitinase B, and hyaluronidase were shown. The approach to productive design of molecules of compounds (regulating enzyme activity for novel drug derivative obtaining) is representative. The investigations of such kind are directed on ascertainment of action mechanism of these agents in biosystems for production of high efficacy of drug preparations of enzyme nature. It is shown that the molecular dynamics method provides modeling of all degrees of freedom in a protein-ligand complex and draws special attention to protein structure flexibility as a considerable challenge in the development of molecular docking. Computational data are reviewed in the aspect of complex formation between proteins and glycosaminoglycan ligands.
VL  - 4
IS  - 4
ER  -

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Author Information

Alexander Maksimenko

Department of Bioengineering Technologies and Support of Scientific Researches, Institute of Experimental Cardiology, National Medical Research Center for Cardiology, Moscow, Russia

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APA Style

Alexander Maksimenko. (2020). Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods. Cardiology and Cardiovascular Research, 4(4), 220-230. https://doi.org/10.11648/j.ccr.20200404.19

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ACS Style

Alexander Maksimenko. Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods. Cardiol. Cardiovasc. Res. 2020, 4(4), 220-230. doi: 10.11648/j.ccr.20200404.19

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AMA Style

Alexander Maksimenko. Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods. Cardiol Cardiovasc Res. 2020;4(4):220-230. doi: 10.11648/j.ccr.20200404.19

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@article{10.11648/j.ccr.20200404.19,
  author = {Alexander Maksimenko},
  title = {Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods},
  journal = {Cardiology and Cardiovascular Research},
  volume = {4},
  number = {4},
  pages = {220-230},
  doi = {10.11648/j.ccr.20200404.19},
  url = {https://doi.org/10.11648/j.ccr.20200404.19},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ccr.20200404.19},
  abstract = {Computational methods have proved to be sometimes a single tool available for investigation of glycosaminoglycan-protein interactions. A two-stage process including molecular docking with its subsequent detalization using the methods of molecular dynamics is a prospective approach to theoretical modeling of protein-glycosaminoglycan complexes. This review deals with specific features of protein-glycosaminoglycan interactions studied by computational methods, docking and scoring function algorithms, and the use of molecular dynamics results with short-time (ps and ns) changes for processes developing within much longer time scales (ranging over several orders of magnitude). The data obtained with help of computational methods contribute the disclosure of biological interaction mechanism, elaboration of enzyme activity control and grounding of rational recommendations for novel therapeutic means development of high-molecular sort. The results of molecular docking of heparanase, chondroitinlyase ABC, chondroitinase B, and hyaluronidase were shown. The approach to productive design of molecules of compounds (regulating enzyme activity for novel drug derivative obtaining) is representative. The investigations of such kind are directed on ascertainment of action mechanism of these agents in biosystems for production of high efficacy of drug preparations of enzyme nature. It is shown that the molecular dynamics method provides modeling of all degrees of freedom in a protein-ligand complex and draws special attention to protein structure flexibility as a considerable challenge in the development of molecular docking. Computational data are reviewed in the aspect of complex formation between proteins and glycosaminoglycan ligands.},
 year = {2020}
}

Copy | Download

TY  - JOUR
T1  - Theoretical Research of Interactions Between Glycosidases and Glycosaminoglycan Ligands with Molecular Docking and Molecular Dynamics Methods
AU  - Alexander Maksimenko
Y1  - 2020/12/31
PY  - 2020
N1  - https://doi.org/10.11648/j.ccr.20200404.19
DO  - 10.11648/j.ccr.20200404.19
T2  - Cardiology and Cardiovascular Research
JF  - Cardiology and Cardiovascular Research
JO  - Cardiology and Cardiovascular Research
SP  - 220
EP  - 230
PB  - Science Publishing Group
SN  - 2578-8914
UR  - https://doi.org/10.11648/j.ccr.20200404.19
AB  - Computational methods have proved to be sometimes a single tool available for investigation of glycosaminoglycan-protein interactions. A two-stage process including molecular docking with its subsequent detalization using the methods of molecular dynamics is a prospective approach to theoretical modeling of protein-glycosaminoglycan complexes. This review deals with specific features of protein-glycosaminoglycan interactions studied by computational methods, docking and scoring function algorithms, and the use of molecular dynamics results with short-time (ps and ns) changes for processes developing within much longer time scales (ranging over several orders of magnitude). The data obtained with help of computational methods contribute the disclosure of biological interaction mechanism, elaboration of enzyme activity control and grounding of rational recommendations for novel therapeutic means development of high-molecular sort. The results of molecular docking of heparanase, chondroitinlyase ABC, chondroitinase B, and hyaluronidase were shown. The approach to productive design of molecules of compounds (regulating enzyme activity for novel drug derivative obtaining) is representative. The investigations of such kind are directed on ascertainment of action mechanism of these agents in biosystems for production of high efficacy of drug preparations of enzyme nature. It is shown that the molecular dynamics method provides modeling of all degrees of freedom in a protein-ligand complex and draws special attention to protein structure flexibility as a considerable challenge in the development of molecular docking. Computational data are reviewed in the aspect of complex formation between proteins and glycosaminoglycan ligands.
VL  - 4
IS  - 4
ER  -

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