Cyclic peptides can engage a single binding pocket through highly divergent modes

Abstract

Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.

Structure/Function Analysis of Truncated Amino-Terminal ACE2 Peptide Analogs That Bind to SARS-CoV-2 Spike Glycoprotein

“…Importantly, cyclized peptides have been efficacious in directing drug delivery and therapeutics due to their enhanced chemical and proteolytic stability and have shown more selective binding modes when compared to analogous sequences with unordered structure [ 68 , 69 , 70 ]. Historically, cyclic peptides have produced enhanced activity when examined in the context of naturally occurring linear peptide receptor ligands [ 71 ].…”

Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming

“…We initially performed a RaPID screen to identify cyclic peptide inhibitors of FXIIa (Figure A). Briefly, this entailed the use of a semirandom DNA library comprising an initial start codon (that was genetically reprogrammed during translation to encode N -chloroacetyl-tyrosine) flanked by 4–15 random codons (NNK with N = A, C, G, or T and K = G or T) and a final Cys codon, in addition to adjacent sequences required for transcription, ligation to puromycin, and PCR amplification. ,− …”

“…The crude cyclic peptide was purified by semipreparative RP-HPLC (0−30% B + 0.1% formic acid over 40 min). The appropriate fractions were combined and lyophilized to afford 30 as a white solid (9.4 Peptide (31) was synthesized via Fmoc-strategy SPPS as specified in general methods. The linear sequence N′-YLRFTLC-C′ was generated on the Rink amide resin (82 mg, 50 μmol, capacity: 0.52 mmolg −1 ) using manual SPPS as described in the general methods.…”

“…In contrast, the mRNA display libraries are typically >10 12 (one trillion) members, and genetic code reprogramming allows for the incorporation of nonproteogenic amino acids to further expand the chemical space accessible. mRNA display is therefore a powerful complementary technique for the in vitro selection of high-affinity peptides and proteins and has been used for the discovery of a number of tool molecules and medicinal chemistry leads over the past decade. − …”

De novo peptide grafting to a self-assembling nanocapsule yields a hepatocyte growth factor receptor agonist

“…X-ray structures of more than a dozen RaPID macrocycles cocrystallized with their target proteins have revealed that these pharmacophores can form a wide range of tertiary structures that interact with not only the specific binding pocket but also the shallow protein surfaces via a combination of hydrogen bonding and hydrophobic interactions ( Hazama et al., 2020 ; Kodan et al., 2014 ; McAllister et al., 2021 ; Patel et al., 2020 ; Zhang et al., 2020 ). Importantly, the macrocycles can also make such interaction networks within the macrocyclic scaffolds and spontaneously fold into the active conformation by themselves.…”