2.3 Ligand Flexibility
Apart from the traditional approach to look for potential inhibitor as small molecules for proteins, small peptides can also be strategically designed to complement
interaction hot spots presented by receptor molecules, using knowledge about the
structure of receptor and its interacting partner molecules. In a recent article published in Science, Kadam et al. [72] have exemplified the approach. The study
focuses on influenza type 1 virus and their surface protein hemagglutinin (HA),
which is associated with virus invasion of host cells. HA is composed of two
domains HA1 and HA2, and functional unit is a homotrimer of HA. The interface
of HA1 and HA2 forms a hydrophobic pocket. This HA-binding site, which is near
the stem region of the HA membrane, is targeted by the broadly neutralizing
antibodies (bnAbs) of the host and blocks large conformational rearrangement
associated with membrane fusion and thus neutralize virus [72]. Structurally,
analyzing the epitopes, at HA1/HA2 interface, a highly conserved site was found.
This structural information allowed researches to synthesize novel proteins, e.g.,
HB80 and HB36, which could mimic bnAb paratope CR6261 and bind in the
conserved hydrophobic pocket, by placing amino acid side chains in appropriate
configuration and conformation. These proteins did show binding affinity comparable to CR6261 and inhibited low pH-induced conformational change in HA.
Further, optimizations lead to improved analogues of HB36, which were also
effective in protecting mice against lethal H1N1 infections [72].
Success of de novo designed protein inspired researcher to look for even smaller
peptide like inhibitors seeking better drug-like properties, e.g., availability in blood
stream with higher lifetime. Starting from the available structural and functional
information about bnAbs, e.g., CR9114, CR6261, F10, A06, FI6v3, HCDR3 was
selected which possesses major interactions as the starting point for design of
smaller HA inhibitory peptides. After creating a pool of potential HA inhibitory
peptides mimicking different structural features of the HCDR3 loop [72] and
characterization of each peptide in terms of its thermodynamic (K d ) and kinetic
parameters (k off and t 1/2 ), a combination of all distinct structural features of these
peptides into an 11-mercyclic peptide containing five non-proteinogenic residues
was synthesized. This peptide showed better affinity and longer residence time for
binding to HA. This study exemplified a novel approach, where compendium of
available structure is utilized with chemical intuition of structure and function to
yield a small cyclic peptide with better therapeutic prospect over existing inhibitory
proteins, e.g., HB36 and its variants [72].
Alternatively, another novel idea has been floated by Young et al. of stapling small
peptides to protect them from proteolytic cleavage and further designed a series of
stapled peptides among which mimic of a-helical peptide ATSP-7041 was reported to
be a potent and selective dual inhibitor of MDMX and MDM2 [73]. However, MDM2
and MDMX are suppressor of p53, thereby activates p53 pathway in tumors [74]. In a
recent in silico study, where Garima et al. tried to study the mechanistic aspect of
recognition of small stapled a-helical peptide ATSP-7041 with human serum albumin
122
S. K. Panday and I. Ghosh
Apart from the traditional approach to look for potential inhibitor as small molecules for proteins, small peptides can also be strategically designed to complement
interaction hot spots presented by receptor molecules, using knowledge about the
structure of receptor and its interacting partner molecules. In a recent article published in Science, Kadam et al. [72] have exemplified the approach. The study
focuses on influenza type 1 virus and their surface protein hemagglutinin (HA),
which is associated with virus invasion of host cells. HA is composed of two
domains HA1 and HA2, and functional unit is a homotrimer of HA. The interface
of HA1 and HA2 forms a hydrophobic pocket. This HA-binding site, which is near
the stem region of the HA membrane, is targeted by the broadly neutralizing
antibodies (bnAbs) of the host and blocks large conformational rearrangement
associated with membrane fusion and thus neutralize virus [72]. Structurally,
analyzing the epitopes, at HA1/HA2 interface, a highly conserved site was found.
This structural information allowed researches to synthesize novel proteins, e.g.,
HB80 and HB36, which could mimic bnAb paratope CR6261 and bind in the
conserved hydrophobic pocket, by placing amino acid side chains in appropriate
configuration and conformation. These proteins did show binding affinity comparable to CR6261 and inhibited low pH-induced conformational change in HA.
Further, optimizations lead to improved analogues of HB36, which were also
effective in protecting mice against lethal H1N1 infections [72].
Success of de novo designed protein inspired researcher to look for even smaller
peptide like inhibitors seeking better drug-like properties, e.g., availability in blood
stream with higher lifetime. Starting from the available structural and functional
information about bnAbs, e.g., CR9114, CR6261, F10, A06, FI6v3, HCDR3 was
selected which possesses major interactions as the starting point for design of
smaller HA inhibitory peptides. After creating a pool of potential HA inhibitory
peptides mimicking different structural features of the HCDR3 loop [72] and
characterization of each peptide in terms of its thermodynamic (K d ) and kinetic
parameters (k off and t 1/2 ), a combination of all distinct structural features of these
peptides into an 11-mercyclic peptide containing five non-proteinogenic residues
was synthesized. This peptide showed better affinity and longer residence time for
binding to HA. This study exemplified a novel approach, where compendium of
available structure is utilized with chemical intuition of structure and function to
yield a small cyclic peptide with better therapeutic prospect over existing inhibitory
proteins, e.g., HB36 and its variants [72].
Alternatively, another novel idea has been floated by Young et al. of stapling small
peptides to protect them from proteolytic cleavage and further designed a series of
stapled peptides among which mimic of a-helical peptide ATSP-7041 was reported to
be a potent and selective dual inhibitor of MDMX and MDM2 [73]. However, MDM2
and MDMX are suppressor of p53, thereby activates p53 pathway in tumors [74]. In a
recent in silico study, where Garima et al. tried to study the mechanistic aspect of
recognition of small stapled a-helical peptide ATSP-7041 with human serum albumin
122
S. K. Panday and I. Ghosh