Stereoselective deuterium labeling of proRβ‐protons in the NMR structure determination of a helix‐turn‐helix turn peptide mimic

Abstract

The NMR structure of a small, side-chain-cyclized tripeptide mimic of the turn in the helix-turn-helix (HTH) motif was determined. The four beta-protons were stereospecifically assigned by stereoselective deuterium replacement of only the proR beta-protons. All 24 of 30 NOESY cross-peaks not involving chemically defined or freely rotating protons, and six of seven coupling constants from the P.COSY were used as distance and angle constraints in molecular modeling. MacroModel found 33/1000 structures in the NMR constrained search and 263/1000 structures in the unconstrained search, indicating meaningful constraint by the NMR data. However, the 10 lowest-energy structures from the unconstrained and constrained searches are very similar, so modeling alone was able to find the experimentally determined structure.

Design and Synthesis of Peptides with Hybrid Helix-Turn-Helix (HTH) Motif and Their Conformational Study

“…The type II and II′ β-turns have sequence chiralities that make them particularly facile targets for de novo design . Etzkorn et al reported a peptidomimetic of the turn in the HTH motif of DNA-binding proteins. The conformational constraint in this system was achieved by an unusual linking of two amino acids with a side chain C–C bond and determined the structure.…”

Design and Synthesis of a Potent Histone Deacetylase Inhibitor

“…Combining the cyclic peptide mimic with the hydroxamic acid functionality not only retained the hydrophobic property of the cyclic peptide mimic, but also introduced the linker and zinc-binding functional group into the targeted molecule 1 . The three-dimensional structure of the cyclic peptide mimic was determined by NMR in previous work . In the molecular modeling, the known 3-D structure of the cyclic peptide mimic 26 was attached to the linker and hydroxamic acid of SAHA from the cocrystal structure with the bacterial histone deacetylase-like protein (HDLP), which is similar to class I HDACs .…”

“…Long coupling times using HATU or PyAOP produced no product. Steric hindrance was not a problem in previous cyclizations with Ala in the position of the α-aminosuberic acid . The instability of the hydroxamic acid functionality may have contributed to the low yield of 10 .…”

“…The three-dimensional structure of the cyclic peptide mimic was determined by NMR in previous work. 26 In the molecular modeling, the known 3-D structure of the cyclic peptide mimic 26 was attached to the linker and hydroxamic acid of SAHA from the cocrystal structure with the bacterial histone deacetylase-like protein (HDLP), 27 which is similar to class I HDACs. 28 Compound 1 was docked manually by superposition onto SAHA in the HDLP active site.…”

“…Steric hindrance was not a problem in previous cyclizations with Ala in the position of the R-aminosuberic acid. 26 The instability of the hydroxamic acid functionality may have contributed to the low yield of 10. Hydrogenolysis of 10 to expose the key hydroxamic Inhibition of HDAC activity in HeLa nuclear extracts by compound 1 was measured using a fluorescence-based assay.…”