Affiliation:
1. Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras – MG, 37200-000,
Brazil
2. Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 500 03, Czech
Republic
Abstract
Abstract:
Since its early days in the 19th century, medicinal chemistry has concentrated its efforts
on the treatment of diseases, using tools from areas such as chemistry, pharmacology, and molecular
biology. The understanding of biological mechanisms and signaling pathways is crucial information
for the development of potential agents for the treatment of diseases mainly because they are such
complex processes. Given the limitations that the experimental approach presents, computational
chemistry is a valuable alternative for the study of these systems and their behavior. Thus, classical
molecular dynamics, based on Newton's laws, is considered a technique of great accuracy, when
appropriated force fields are used, and provides satisfactory contributions to the scientific community.
However, as many configurations are generated in a large MD simulation, methods such as Statistical
Inefficiency and Optimal Wavelet Signal Compression Algorithm are great tools that can
reduce the number of subsequent QM calculations. Accordingly, this review aims to briefly discuss
the importance and relevance of medicinal chemistry allied to computational chemistry as well as to
present a case study where, through a molecular dynamics simulation of AMPK protein (50 ns) and
explicit solvent (TIP3P model), a minimum number of snapshots necessary to describe the oscillation
profile of the protein behavior was proposed. For this purpose, the RMSD calculation, together
with the sophisticated OWSCA method was used to propose the minimum number of snapshots.
Publisher
Bentham Science Publishers Ltd.