with Tamiflu and mutations at the binding site can cause resistance
against the drug. Therefore, enhancing drug selectivity and search-
ing for novel binding sites are important research areas for influenza
treatment. In the search for new binding sites in Neuraminidase for
the H5N1 strain, Landon et al. combined extended explicit solvent
molecular dynamics (MD) and computational solvent mapping
(CS-Map) techniques to identify putative “hot-spots” within flexi-
ble binding regions of N1 neuraminidase. They used representative
conformations of the N1 binding region as extracted from the
clustering of 40 ns MD trajectories. They then employed CS-Map
to assess the ability of small solvent-sized molecules to bind close to
the sialic acid binding region. Mapping analyses of the dominant
MD conformations revealed the presence of additional hot spot
around binding region. Hot spot analysis provided further support
for the feasibility of developing high-affinity inhibitors that were
capable of binding to these regions, which appeared to be unique to
the N1 strain [62]. Furthermore, MD simulations also revealed the
function of crystal water molecules in the active site. Interestingly,
Landon et al. found that more potent ligands did not interact
strongly with these cocrystallized water molecules [61, 62]. They
were also able to study the effects of mutations on the interactions
with these compounds [63].3.2 An Allosteric Site
Problem: G-Protein
Coupled Receptor
(GPCR)
G-protein coupled receptors (GPCRs) are major targets for drug
development [64]. They are associated with approximately 30% of
current drugs and are linked to many diseases related to cardiovas-
cular and central nervous systems and cancer [31, 33, 64,
65 ]. GPCRs are transmembrane proteins with a conservative topol-
ogy composition, comprising of seven transmembrane alpha-
helixes, and highly dynamics structure [33, 66]. Ivetac and
McCammon used an ensemble-based approach combined with
the FTMAP algorithm to study binding sites in two different
GPCRs, namely, theβ 1 (β 1 AR) and theβ 2 (β 2 AR) adrenergic recep-
tors. They used Coarse-Grain MD simulations to rapidly assemble
the protein–lipid complexes. Then, they extracted a conformational
ensemble for the proteins from six independent 40 ns long conven-
tional MD simulations for each complex. The final protein struc-
tures involved 14 dominant conformations, representing the whole
240 ns MD simulation. Five allosteric binding sites, four of which
are conserved within the two complexes were detected through this
investigation. Site-1 and Site-4 were located at the extracellular and
intracellular mouth of the proteins and were exposed to the solvent
environment. On the other hand, the protein–lipid interface
contained site-2, site-3, and site-5. Site-5 was observed only in
the β 2 AR structure, which emphasized its value as a selective
β 2 AR-targeted pocket [31].98 Tianhua Feng and Khaled Barakat