Thioamide substitution to probe the hydroxyproline recognition of VHL ligands

Pedro Soares; Xavier Lucas; Alessio Ciulli

doi:10.1016/j.bmc.2018.03.034

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands

Pedro Soares, Xavier Lucas, Alessio Ciulli (Lead / Corresponding author)

Biological Chemistry and Drug Discovery

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

209 Downloads (Pure)

Abstract

Thioamide substitution influences hydrogen bond and n→π* interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n→π* interactions in fine-tuning hydroxyproline recognition by VHL.

Original language	English
Pages (from-to)	2992-2995
Number of pages	4
Journal	Bioorganic & Medicinal Chemistry
Volume	26
Issue number	11
Early online date	23 Mar 2018
DOIs	https://doi.org/10.1016/j.bmc.2018.03.034
Publication status	Published - 15 Jul 2018

Keywords

n → π interaction
PROTACs
Protein-ligand interactions
Thioamides
VHL ligands
Hydroxyproline/chemistry
Drug Stability
Humans
Von Hippel-Lindau Tumor Suppressor Protein/chemistry
Crystallography, X-Ray
Hydrogen Bonding
Protein Binding
Ligands
Thioamides/chemistry

ASJC Scopus subject areas

Drug Discovery
Molecular Medicine
Molecular Biology
Biochemistry
Clinical Biochemistry
Pharmaceutical Science
Organic Chemistry

Access to Document

10.1016/j.bmc.2018.03.034Licence: CC BY

Final Published VersionFinal published version, 1.01 MBLicence: CC BY

DrugE3CRL's: Probing Druggability of Multisubunit Complexes: E3 Cullin RING Ligases (ERC Starting Grant)
Ciulli, A. (Investigator)
COMMISSION OF THE EUROPEAN COMMUNITIES
1/05/13 → 30/04/18
Project: Research

Small-molecule approaches to interrogate the druggability of the VHL E3 Cullin RING Ubiquitin Ligase
Soares, P. (Author), Ciulli, A. (Supervisor), 2018
Student thesis: Doctoral Thesis › Doctor of Philosophy

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Ciulli, Alessio
- Centre for Targeted Protein Degradation - Professor of Chemical and Structural Biology
Person: Academic

Cite this

@article{7da032bb7f6f444e940bc3faadd9d8a1,

title = "Thioamide substitution to probe the hydroxyproline recognition of VHL ligands",

abstract = "Thioamide substitution influences hydrogen bond and n→π* interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n→π* interactions in fine-tuning hydroxyproline recognition by VHL.",

keywords = "n → π interaction, PROTACs, Protein-ligand interactions, Thioamides, VHL ligands, Hydroxyproline/chemistry, Drug Stability, Humans, Von Hippel-Lindau Tumor Suppressor Protein/chemistry, Crystallography, X-Ray, Hydrogen Bonding, Protein Binding, Ligands, Thioamides/chemistry",

author = "Pedro Soares and Xavier Lucas and Alessio Ciulli",

note = "This work was supported by the European Research Council ERC-2012-StG-311460 DrugE3CRLs (starting grant to A.C.), the European Commission (H2020-MSCA-IF-2015 806323 Marie Sk{\l}odowska-Curie Actions Individual Fellowship to X.L.), the strategic awards 100476/Z/12/Z for biophysics and drug discovery and 094090/Z/10/Z for structural biology and X-ray crystallography to BCDD and the Funda{\c c}{\~a}o para a Ci{\^e}ncia e Tecnologia FCT SFRH/BD/101598/2014 (PhD studentship to P.S.). We thank A. Testa for helpful discussions regarding the synthesis of compounds 2–4. We are thankful to P. Fife for the support with in-house X-ray facility, and to the Diamond Light Source for beamtime (BAG proposal MX10071) and beamline support at beamline I04-1.",

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month = jul,

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doi = "10.1016/j.bmc.2018.03.034",

language = "English",

volume = "26",

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journal = "Bioorganic & Medicinal Chemistry",

issn = "0968-0896",

publisher = "Elsevier",

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T1 - Thioamide substitution to probe the hydroxyproline recognition of VHL ligands

AU - Soares, Pedro

AU - Lucas, Xavier

AU - Ciulli, Alessio

N1 - This work was supported by the European Research Council ERC-2012-StG-311460 DrugE3CRLs (starting grant to A.C.), the European Commission (H2020-MSCA-IF-2015 806323 Marie Skłodowska-Curie Actions Individual Fellowship to X.L.), the strategic awards 100476/Z/12/Z for biophysics and drug discovery and 094090/Z/10/Z for structural biology and X-ray crystallography to BCDD and the Fundação para a Ciência e Tecnologia FCT SFRH/BD/101598/2014 (PhD studentship to P.S.). We thank A. Testa for helpful discussions regarding the synthesis of compounds 2–4. We are thankful to P. Fife for the support with in-house X-ray facility, and to the Diamond Light Source for beamtime (BAG proposal MX10071) and beamline support at beamline I04-1.

PY - 2018/7/15

Y1 - 2018/7/15

N2 - Thioamide substitution influences hydrogen bond and n→π* interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n→π* interactions in fine-tuning hydroxyproline recognition by VHL.

AB - Thioamide substitution influences hydrogen bond and n→π* interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n→π* interactions in fine-tuning hydroxyproline recognition by VHL.

KW - n → π interaction

KW - PROTACs

KW - Protein-ligand interactions

KW - Thioamides

KW - VHL ligands

KW - Hydroxyproline/chemistry

KW - Drug Stability

KW - Humans

KW - Von Hippel-Lindau Tumor Suppressor Protein/chemistry

KW - Crystallography, X-Ray

KW - Hydrogen Bonding

KW - Protein Binding

KW - Ligands

KW - Thioamides/chemistry

U2 - 10.1016/j.bmc.2018.03.034

DO - 10.1016/j.bmc.2018.03.034

M3 - Article

C2 - 29650462

SN - 0968-0896

VL - 26

SP - 2992

EP - 2995

JO - Bioorganic & Medicinal Chemistry

JF - Bioorganic & Medicinal Chemistry

IS - 11

ER -

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

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Projects

DrugE3CRL's: Probing Druggability of Multisubunit Complexes: E3 Cullin RING Ligases (ERC Starting Grant)

Student theses

Small-molecule approaches to interrogate the druggability of the VHL E3 Cullin RING Ubiquitin Ligase

Profiles

Ciulli, Alessio

Cite this