Chemistry Reference
In-Depth Information
MOLECULAR SHAPE
According to Frank Lloyd Wright in 1908, form and function should be one,
joined in a spiritual union. Determination of molecular shape and changes in
properties can be important for understanding the molecules involved in chemical
reactions. Shape often determines the end-product as a result of molecular
interactions with preferred and non-preferred biological targets [239, 797-804].
Enzymes can use shape recognition to differentiate between functional groups in a
molecule. Shape recognition is also used by natural products (biosynthetic
pathways) for selective oxidation. At the molecular level, chiral recognition
involves mutually induced conformational adjustments. Ribozymes from
Escherichia coli
recognize cloverleaf-shape RNAs.
Chemical shape plays an important role in senses. These include olifactory
receptors (smell), receptors for perception of color (sight) as well as taste.
Addition of complementary electrostatic or steric interactions to molecular shape
should increase specificity.
Life, survival, targeting molecules with bioactivity are result of the
complementarity of binding in peptide-receptor, molecule-protein and antigen-
antibody and protein-protein interactions. Shape can be important in ligand
specificity, substrate recognition and antibody recognition
via
models of
quantitative structure-activity relationships, docking, similarity-search and
classification protocols.
Shape and shape-based descriptors can be useful molecular descriptors. One of the
problems of molecular docking involves predictions of the pose within the active
site of the receptor which is the result of hydrogen bonds, coulomb forces,
hydrophobic interactions and van der Walls forces. However, geometric
complementarity, apart from physical-chemical complementarity is not
understated. Geometric complementarity is taken into consideration in various
docking algorithms.
Among the state-of-the-art 3DVS techniques, molecular shape matching plays a
significant role in protein-ligand interactions. Molecules that share similar 3d
