bound forms have provided greater insight into functioning and inhibitions [22].
Crystallography has helped in the structural characterization of many mutations
from HIV protease, where these mutations alter the active site and these mutants
reduce the drug efficacy. In case of HIV-RT, the structures helped in proposing
three mechanisms of drug resistance because of mutations, where these mutations
caused the alteration of the binding sites for the nucleoside analogue or
non-nucleoside inhibitors, mutations at the template DNA-binding site, and finally
mutations at active site region influencing the conformation of the enzyme [23–27].
Apart from individual laboratories trying to solve protein structures, there are
different structural consortium projects undertaken at higher level, which have also
been facilitated by the determination of genome sequences of most microorganism
and also humans. This has provided us with a great wealth of protein structures
which are crucial for pathogen survival and replication, thus chosen as targets in
designing new pharmaceutical importance. The role of crystallography in elucidating the advent of many genetic disorders is commendable and successful. For
instance, the understanding of sickle cell anemia, thalassemias, and other deficiencies of hemoglobin [28] is a well-known fact that has come out as consequence
of structure–function relationships.
The success of crystallography in the identification of inhibitors can be observed
in case of viral diseases, especially in the case of influenza virus by neuraminidase.
Numerous structures which are crucial drug targets of various bacteria have been
solved, and their function was understood using X-ray crystallography. In addition,
structural studies of a wide spectrum of target proteins from protozoa species such
as Plasmodium falciparum, Trypanosoma cruzi, and different Leishmania species
are carried out. Other phenomena such as detoxification, mutation, and enzyme
replacement mechanisms which lead to resistance are explained in molecular detail
which is possible largely by employing crystallography.
Role of synchrotron radiation in SBDD
As discussed earlier, crystallography helps in understanding the mode of binding of
ligand with target protein, and it provides detailed pattern of interactions of ligand
with which it inhibits or promotes the function of proteins. These interactions are
used as stepping stones in designing new class of ligands with better efficiency,
improving their specificity, physicochemical properties, reducing interactions
which might induce cross-interaction with protein leading to side effects [29].
The bottleneck problem arising at this situation is the availability of high-throughput
and pipelined techniques at different stages, of which high-energy synchrotron radiation
plays a crucial role. The high energetic, physically tunable wavelength X-ray radiation
helps in obtaining phases (using anomalous dispersion) relatively easily than any other
methods. Advent of improved detectors (CCD and pixel array detectors) and advanced
goniometers also play major roles in more structures being determined [30].
Pipelining helps in saving time and increased precision by least human intervention; they provide users with workflow to solve structures starting with data
collection, processing, structure determination, and finally with refinement with no
time and least intervention. This continuous workflow is important in understanding
Structure-Based Drug Design…
275
Crystallography has helped in the structural characterization of many mutations
from HIV protease, where these mutations alter the active site and these mutants
reduce the drug efficacy. In case of HIV-RT, the structures helped in proposing
three mechanisms of drug resistance because of mutations, where these mutations
caused the alteration of the binding sites for the nucleoside analogue or
non-nucleoside inhibitors, mutations at the template DNA-binding site, and finally
mutations at active site region influencing the conformation of the enzyme [23–27].
Apart from individual laboratories trying to solve protein structures, there are
different structural consortium projects undertaken at higher level, which have also
been facilitated by the determination of genome sequences of most microorganism
and also humans. This has provided us with a great wealth of protein structures
which are crucial for pathogen survival and replication, thus chosen as targets in
designing new pharmaceutical importance. The role of crystallography in elucidating the advent of many genetic disorders is commendable and successful. For
instance, the understanding of sickle cell anemia, thalassemias, and other deficiencies of hemoglobin [28] is a well-known fact that has come out as consequence
of structure–function relationships.
The success of crystallography in the identification of inhibitors can be observed
in case of viral diseases, especially in the case of influenza virus by neuraminidase.
Numerous structures which are crucial drug targets of various bacteria have been
solved, and their function was understood using X-ray crystallography. In addition,
structural studies of a wide spectrum of target proteins from protozoa species such
as Plasmodium falciparum, Trypanosoma cruzi, and different Leishmania species
are carried out. Other phenomena such as detoxification, mutation, and enzyme
replacement mechanisms which lead to resistance are explained in molecular detail
which is possible largely by employing crystallography.
Role of synchrotron radiation in SBDD
As discussed earlier, crystallography helps in understanding the mode of binding of
ligand with target protein, and it provides detailed pattern of interactions of ligand
with which it inhibits or promotes the function of proteins. These interactions are
used as stepping stones in designing new class of ligands with better efficiency,
improving their specificity, physicochemical properties, reducing interactions
which might induce cross-interaction with protein leading to side effects [29].
The bottleneck problem arising at this situation is the availability of high-throughput
and pipelined techniques at different stages, of which high-energy synchrotron radiation
plays a crucial role. The high energetic, physically tunable wavelength X-ray radiation
helps in obtaining phases (using anomalous dispersion) relatively easily than any other
methods. Advent of improved detectors (CCD and pixel array detectors) and advanced
goniometers also play major roles in more structures being determined [30].
Pipelining helps in saving time and increased precision by least human intervention; they provide users with workflow to solve structures starting with data
collection, processing, structure determination, and finally with refinement with no
time and least intervention. This continuous workflow is important in understanding
Structure-Based Drug Design…
275