show a remarkable flexibility upon ligand binding, making this
simple model inadequate to describe correctly the association and
dissociation process of high-affinity drugs. It appears that proteins
need to change their conformation, essentially near the pocket
region, during compound binding [1–3]. Proteins are dynamic
entities that are in constant motion and their structural dynamics
are dependent on the amino acid composition and folding. Their
conformations depend on physiological factors like temperature,
pH, but also on direct factors, such as interactions with other
entities (proteins, peptides, DNA, membrane, molecules, hor-
mone, etc.). This ability of conformation changing in response to
its environment is a key step in biological processes such as pro-
tein–ligand interactions, enzyme catalysis, protein–protein interac-
tion, protein transport, and signal transduction. The inherent
flexibility of proteins could involve important part of the 3D struc-
ture, or just few amino acids side chains, which results in large-scale
movement through transition intermediates [4, 5]. A complete
understanding of the protein function necessarily implies a struc-
tural description and an energetic quantification of the dynamic
events of interest. The consideration of these structural mechan-
isms is very important for the design and development of new drugs
and constitutes a fundamental step in our knowledge of key
biological processes.
Protein flexibility is an important biological phenomenon that
must be taken into account in structure-based drug design (SBDD)
strategies. The structural and dynamics events occurring during the
process of drug–receptor complex formation and dissociation con-
siderably affect the binding kinetics, thermodynamics and affinity of
the drug. This binding kinetics, especially the dissociation kinetic
(directly associated to drug residence time) has acquired over a
period of 10 years, a considerable importance in drug design
[6, 7], because of its significant impact on drug in vivo efficacy
[8, 9]. Understanding these structural changes related to transition
state(s) formation along the association and/or dissociation path-
way is crucial and can provide considerable insights for further
optimization of drugs.
Beyond traditional approaches (such as X-ray crystallography
and nuclear magnetic resonance (NMR) spectroscopy), consider-
able efforts were made in the development of new experimental
methods to investigate the dynamics and flexibility of biomolecules.
Time-resolved studies, solution X-ray scattering, and new detectors
for cryo-electron microscopy have pushed the limits of structural
investigation of flexible systems but still remain expensive and time
consuming. In addition, they could be used only on a limited set of
protein conformers and are not always applicable to the biological
system of interest [10]. Moreover, the increasing complexity of the
studied biomolecule including, for example, large transient protein404 Sonia Ziada et al.