Chemistry Reference
In-Depth Information
Their bond lengths and angles fluctuate according to local environments. Crucial
for binding affinity/drug design they dictate the orientation in the receptor of the
binding ligand. The vdW term is known to be the primary origin of the
stabilization energy for stacking between aromatic rings.
The characteristics of halogen bonding are parallel with those of hydrogen
bonding in terms of directionality and strength. This type of bonding can be
important where the control of self-assembly and molecular recognition is
important. There are many structures in the Protein Data Bank with halogenated
ligands [790].
Boron (positioned just before carbon and nitrogen) has the potential to play an
important role in medicinal chemistry. The usage of transition metal-catalyzed
borylation reactions to prepare organo-boronates and the approval of Velcade
(bortezomib) by FDA (for myeloma/lymphoma treatment) has contributed to
borane chemistry. Boron compounds are in clinical and preclinical stages for
treatment of various diseases including diabetes, inflammation and cancer [804].
The binding interactions between proteins and carbohydrates (most abundant
biopolymers) are vital for life in nature. Both intrinsic protein-carbohydrate and
extrinsic chaperone-mediated mechanisms are used for covalent attached
carbohydrates in glycoprotein folding.
The immune system functions are directed by carbohydrates/carbohydrate-binding
proteins on proximal cells. Most membrane proteins on cell surfaces are
glycosylated with a variety of attached carbohydrate chains. Changes in their
patterns are associated with cancer growth and metastasis formation. A better
understanding
of
these
processes
could
improve
our
ability
to
design/tailor/stabilize protein-based therapeutics [286, 791, 805].
Transcription is responsible for construction of proteins and replication produces
copies of DNA. These vital processes can be targeted with the help of ligand-
DNA small binding molecules which can interact with DNA
via
intercalation or
minor groove binding. Intercalators with two or more fused rings forming a planar
structure and minor groove binding often possess crescent-shaped structures that
complements the shape of the minor groove [375, 806].
