article Open Access (gold) EN 2020-12-30

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Outi M. H. Salo‐Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo V. Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela‐Kakkonen, Anders S. Larsen, Eveline Lescrinier, Parthiban Marimuthu, Muhammad Usman Mirza, Ghulam Mustafa, Ariane Nunes‐Alves, Tatu Pantsar, Atefeh Saadabadi, Kalaimathy Singaravelu, Michiel Vanmeert

Processes, Vol. 9, Issue 1, pp. 71–71 (2020)

Åbo Akademi University, Utrecht University, Uppsala University, University of Oulu, University of Eastern Finland, University of Copenhagen, Rega Institute for Medical Research, KU Leuven, German Cancer Research Center, Heidelberg University, DKFZ-ZMBH Alliance, Heidelberg Institute for Theoretical Studies, University of Tübingen, University of Turku

DOI: 10.3390/pr9010071

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Abstract

Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.

Topics

Protein Structure and Dynamics 1.00 Computational Drug Discovery Methods 1.00 Monoclonal and Polyclonal Antibodies Research 1.00

Field: Biochemistry, Genetics and Molecular Biology · Subfield: Molecular Biology

Keywords

Molecular dynamics,Drug development,Drug,Pharmaceutical sciences,Drug discovery,Nanotechnology,Drug delivery,Computational biology,Drug repositioning,Biochemical engineering

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APA

Outi M. H. Salo‐Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo V. Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela‐Kakkonen, Anders S. Larsen, Eveline Lescrinier, Parthiban Marimuthu, Muhammad Usman Mirza, Ghulam Mustafa, Ariane Nunes‐Alves, Tatu Pantsar, Atefeh Saadabadi, Kalaimathy Singaravelu, Michiel Vanmeert (2020). Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development. Processes, 9(1), 71–71. https://doi.org/10.3390/pr9010071

MLA

Outi M. H. Salo‐Ahen, et al. "Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development." Processes, vol. 9, no. 1, 2020, pp. 71–71. https://doi.org/10.3390/pr9010071

Chicago

Outi M. H. Salo‐Ahen, Ida Alanko, Rajendra Bhadane, Alexandre M. J. J. Bonvin, Rodrigo V. Honorato, Shakhawath Hossain, André H. Juffer, Aleksei Kabedev, Maija Lahtela‐Kakkonen, Anders S. Larsen, Eveline Lescrinier, Parthiban Marimuthu, Muhammad Usman Mirza, Ghulam Mustafa, Ariane Nunes‐Alves, Tatu Pantsar, Atefeh Saadabadi, Kalaimathy Singaravelu, Michiel Vanmeert. "Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development." Processes 9, no. 1 (2020): 71–71. https://doi.org/10.3390/pr9010071

BibTeX

@article{salo‐ahen2020,
  title = { Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development },
  author = { Outi M. H. Salo‐Ahen and Ida Alanko and Rajendra Bhadane and Alexandre M. J. J. Bonvin and Rodrigo V. Honorato and Shakhawath Hossain and André H. Juffer and Aleksei Kabedev and Maija Lahtela‐Kakkonen and Anders S. Larsen and Eveline Lescrinier and Parthiban Marimuthu and Muhammad Usman Mirza and Ghulam Mustafa and Ariane Nunes‐Alves and Tatu Pantsar and Atefeh Saadabadi and Kalaimathy Singaravelu and Michiel Vanmeert },
  journal = { Processes },
  year = { 2020 },
  volume = { 9 },
  number = { 1 },
  pages = { 71--71 },
  doi = { 10.3390/pr9010071 }
}

RIS

TY  - JOUR
TI  - Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
AU  - Outi M. H. Salo‐Ahen
AU  - Ida Alanko
AU  - Rajendra Bhadane
AU  - Alexandre M. J. J. Bonvin
AU  - Rodrigo V. Honorato
AU  - Shakhawath Hossain
AU  - André H. Juffer
AU  - Aleksei Kabedev
AU  - Maija Lahtela‐Kakkonen
AU  - Anders S. Larsen
AU  - Eveline Lescrinier
AU  - Parthiban Marimuthu
AU  - Muhammad Usman Mirza
AU  - Ghulam Mustafa
AU  - Ariane Nunes‐Alves
AU  - Tatu Pantsar
AU  - Atefeh Saadabadi
AU  - Kalaimathy Singaravelu
AU  - Michiel Vanmeert
JO  - Processes
PY  - 2020
VL  - 9
IS  - 1
SP  - 71
EP  - 71
DO  - 10.3390/pr9010071
ER  -

669

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