TY - JOUR
T1 - Current tools and methods in Molecular Dynamics (MD) simulations for drug design
AU - Hernández-Rodríguez, Maricarmen
AU - Rosales-Hernández, Martha C.
AU - Mendieta-Wejebe, Jessica E.
AU - Martínez-Archundia, Marlet
AU - Basurto, José Correa
N1 - Publisher Copyright:
© 2016 Bentham Science Publishers.
PY - 2016/10/1
Y1 - 2016/10/1
N2 - Molecular Dynamics (MD) simulations is a computational method that employs Newton's laws to evaluate the motions of water, ions, small molecules, and macromolecules or more complex systems, for example, whole viruses, to reproduce the behavior of the biological environment, including water molecules and lipid membranes. Specifically, structural motions, such as those that are dependent of the temperature and solute/solvent are very important to study the recognition pattern of ligandprotein or protein-protein complexes, in that sense, MD simulations are very useful because these motions can be modeled using this methodology. Furthermore, MD simulations for drug design provide insights into the structural cavities required to design novel structures with higher affinity to the target. Also, the employment of MD simulations to drug design can help to refine the three-dimensional (3D) structure of targets in order to obtain a better sampling of the binding poses and more reliable affinity values with better structural advantages, because they incorporate some biological conditions that include structural motions compared to traditional docking procedures. This work analyzes the concepts and applicability of MD simulations for drug design because molecular structural motions are considered, and these help to identify hot spots, decipher structural details in the reported protein sites, as well as to eliminate sites that could be structural artifacts which could be originated from the structural characterization conditions from MD. Moreover, better free energy values for protein ligand recognition can also be obtained, and these can be validated under experimental procedures due to the robustness of the MD simulation methods.
AB - Molecular Dynamics (MD) simulations is a computational method that employs Newton's laws to evaluate the motions of water, ions, small molecules, and macromolecules or more complex systems, for example, whole viruses, to reproduce the behavior of the biological environment, including water molecules and lipid membranes. Specifically, structural motions, such as those that are dependent of the temperature and solute/solvent are very important to study the recognition pattern of ligandprotein or protein-protein complexes, in that sense, MD simulations are very useful because these motions can be modeled using this methodology. Furthermore, MD simulations for drug design provide insights into the structural cavities required to design novel structures with higher affinity to the target. Also, the employment of MD simulations to drug design can help to refine the three-dimensional (3D) structure of targets in order to obtain a better sampling of the binding poses and more reliable affinity values with better structural advantages, because they incorporate some biological conditions that include structural motions compared to traditional docking procedures. This work analyzes the concepts and applicability of MD simulations for drug design because molecular structural motions are considered, and these help to identify hot spots, decipher structural details in the reported protein sites, as well as to eliminate sites that could be structural artifacts which could be originated from the structural characterization conditions from MD. Moreover, better free energy values for protein ligand recognition can also be obtained, and these can be validated under experimental procedures due to the robustness of the MD simulation methods.
KW - Docking studies
KW - Drug design
KW - Drug discovery
KW - Molecular Dynamics simulations
KW - Protein motions
KW - Sampling several protein conformations
UR - http://www.scopus.com/inward/record.url?scp=84979702836&partnerID=8YFLogxK
U2 - 10.2174/0929867323666160530144742
DO - 10.2174/0929867323666160530144742
M3 - Artículo de revisión
SN - 0929-8673
VL - 23
SP - 3909
EP - 3924
JO - Current Medicinal Chemistry
JF - Current Medicinal Chemistry
IS - 34
ER -