BioDesign Research / 2022 / Article / Tab 3

Review Article

Design of Protein Segments and Peptides for Binding to Protein Targets

Table 3

Examples of the use of crosslinking strategy in designing peptide binders.

Starting pointTargetResults

Linear peptide known to bind in the pocketTLE1Kd as low as  nM [75]
Originally designed antagonistC5a receptorIC50 as low as 0.2 nM (cyclization combined with mutagenesis) [76]
Mutagenesis study of native protein-protein interactionsCK2 subunit interactionIC50 as low as 3.0 nM [77]
Antibody loopsInfluenza hemagglutininKd as low as  nM and IC50 as low as 30 nM (after mutagenesis) [74]
Original helical motifsNHR2-binding (N2B) motif of E-proteinsKd as low as 53 ± 20 μM [78]
Structure of B-hairpin at the binding siteCdiIKd of 13 ± 2 μM [79]
Structure of bovine immunodeficiency virus Tat with TAR RNAHIV TARKd as low as 1 nM (disulfide cyclization and mutations) [80]
Structure of LXXLL motif (NR box)Estrogen receptorKD as low as 0.075 μM for ER and 0.155 μM for ER [81]
Crystal structure of 14-3-3ζ in complex with ESp14-3-3Kd as low as 0.25 0.01 after stapling [82]
Structure of similar CYFIP1 to homologus WASF1CYFIP1Showed inhibition in cells [83]
EED binding domain of EZH2EEDKd as low as 264 nM after stapling [84]
Helical domain from Ras interaction with sosRasnucleotide-free Ras with a KD of μM and GDP-bound Ras with a KD of μM [85]
Previously known binder, StRIP3 [86]Rab8aKd as low as 7.8 μM after double stapling and mutagenesis [87]
Helical domain of HIF1a interacting with p300p300μM [88], kd as low as  nM [89]
Loop identified by LoopFinderStonin2 and Eps15 interactionsKd as low as μM and IC50 as low as μM by crosslinking the identified hot loop with Kd of μM and μM [68]
LC3 interacting regionLC3BKd of μM after stapling and mutational optimization [69]
10mer hot segment identified at the interfaceTLR4Synergistic activation of TLR signaling was observed for cyclized peptides [71]
Short helical segment from TRF1TRFH-Fbx4G structureUbiquitin E3 ligase SCFFbx4kD as low as μM and IC50 of 31.3 μM after mutagenesis [52]
BH3 domain mimicsBCL-2, Bcl-xLDissociation constants as low as  nM [90], Kd of 38.8 nM [91], IC50 as low as  nM with stapling and -amino acid [92]
BCL9 helix-CateninKi as low as μM [93]
Helix segment from HIV-1 gp41 structuregp41Kd as low as  nM after stapling [94], half life enhanced by an order of magnitude after double stapling [95], IC50 as low as 10 nM and Kd of 17 nM after stapling peptides containing the core binding residues [96]
Structure of p53 helical domain interacting with MDM2/MDMXMDM2/MDMXIC50 as low as 2 nM for MDM2 and  nM for MDMX [97], MDM2 ki as low as  nM [98], IC50 as low as  nM for MDM2 and as low as  nM for MDMX using a photoinduced cycloaddition [99], Kd of  nM for MDM2 [100]