List of works - Alessio Ciulli

3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation

scientific article published on 12 July 2018

A Fragment-Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry

scientific article

Allosteric Targeting of the Fanconi Anemia Ubiquitin-Conjugating Enzyme Ube2T by Fragment Screening.

scientific article published on 24 April 2017

Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase

scientific article

Application of fragment screening and merging to the discovery of inhibitors of the Mycobacterium tuberculosis cytochrome P450 CYP121

scientific article

BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

scientific article published on 10 June 2019

Biophysical tools to monitor enzyme-ligand interactions of enzymes involved in vitamin biosynthesis.

scientific article

Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery

scientific article published in 2011

Chemical genetics approaches for selective intervention in epigenetics

scientific article

Correction to "3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation"

scientific article published on 24 April 2019

Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate bound: substrate recognition, conformational change, and cooperativity

scientific article

Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions

scientific article

Design and Characterization of SGK3-PROTAC1, an Isoform Specific SGK3 Kinase PROTAC Degrader

scientific article published on 05 September 2019

Development of BromoTag: A “Bump-and-Hole”–PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins

scientific article published on 17 October 2021

Development of NanoLuc-targeting protein degraders and a universal reporter system to benchmark tag-targeted degradation platforms

scientific article published on 19 April 2022

Dissecting Fragment-Based Lead Discovery at the von Hippel-Lindau Protein:Hypoxia Inducible Factor 1α Protein-Protein Interface

scientific article

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones

scientific article published on 03 November 2020

Gram-Scale Laboratory Synthesis of TC AC 28, a High-Affinity BET Bromodomain Ligand

scientific article published on 08 August 2017

Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-

scientific article published on 30 August 2017

Highly Selective PTK2 Proteolysis Targeting Chimeras to Probe Focal Adhesion Kinase Scaffolding Functions

scientific article published on 22 February 2019

Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation.

scientific article published on 10 October 2017

Impact of Target Warhead and Linkage Vector on Inducing Protein Degradation: Comparison of Bromodomain and Extra-Terminal (BET) Degraders Derived from Triazolodiazepine (JQ1) and Tetrahydroquinoline (I-BET726) BET Inhibitor Scaffolds

scientific article published on 08 June 2017

Inhibition ofMycobacterium tuberculosisPantothenate Synthetase by Analogues of the Reaction Intermediate

scientific article

Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery

scientific article

Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach

scientific article

Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions?

scientific article

Iterative design and optimization of initially inactive Proteolysis Targeting Chimeras (PROTACs) identify VZ185 as a potent, fast and selective von Hippel-Lindau (VHL)-based dual degrader probe of BRD9 and BRD7

scientific article published on 28 December 2018

Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme Ube2T and Induces Structural Rearrangements

scientific article published on 21 September 2017

Multimeric Complexes among Ankyrin-Repeat and SOCS-box Protein 9 (ASB9), ElonginBC, and Cullin 5: Insights into the Structure and Assembly of ECS-type Cullin-RING E3 Ubiquitin Ligases

scientific article

NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes

scientific article

New Synthetic Routes to Triazolo-benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective Bromo and Extra-Terminal (BET) Bromodomain Inhibition.

scientific article published on 14 September 2015

Nucleophile Selectivity of Chorismate-Utilizing Enzymes

scholarly article by Olivier Kerbarh published in April 2007

Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition.

scientific article

Optimization of the Interligand Overhauser Effect for Fragment Linking: Application to Inhibitor Discovery against Mycobacterium tuberculosis Pantothenate Synthetase

scientific article

Potent and selective chemical probe of hypoxic signalling downstream of HIF-α hydroxylation via VHL inhibition

scientific article (publication date: 4 November 2016)

Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods

scientific article

Publisher Correction: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

scientific article published on 01 August 2019

RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response

scientific article published on 29 January 2019

Rapid and Reversible Knockdown of Endogenously Tagged Endosomal Proteins via an Optimized HaloPROTAC Degrader

scientific article published on 22 April 2019

Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies.

scientific article published on 25 January 2017

SPR-Measured Dissociation Kinetics of PROTAC Ternary Complexes Influence Target Degradation Rate

scientific article published on 22 February 2019

Salicylate biosynthesis: overexpression, purification, and characterization of Irp9, a bifunctional salicylate synthase from Yersinia enterocolitica

scientific article published on August 2005

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

scientific article published on 19 May 2016

Spy vs. spy: selecting the best reporter for F NMR competition experiments

article

Stereoselective synthesis of allele-specific BET inhibitors

scientific article published on 05 August 2020

Structural basis of PROTAC cooperative recognition for selective protein degradation

scientific article

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase.

scientific article published on 10 June 2019

Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

scientific article

Structure-Based Design of a Macrocyclic PROTAC

scientific article published on 12 December 2019

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities

scientific article (publication date: 23 October 2014)

Structure-Guided Design of Peptides as Tools to Probe the Protein-Protein Interaction between Cullin-2 and Elongin BC Substrate Adaptor in Cullin RING E3 Ubiquitin Ligases

scientific article

Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase

scholarly article by Xavier Lucas et al published 23 August 2018 in Journal of Medicinal Chemistry

Target validation: Switching domains

scientific article

Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni

scientific article published on 9 February 2017

Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.

scientific article published on 12 March 2018

Targeting Low-Druggability Bromodomains: Fragment Based Screening and Inhibitor Design against the BAZ2B Bromodomain

scientific article

Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1α Interaction

scientific article

The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound

scientific article published in June 2005

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands.

scientific article published on 23 March 2018

Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity

scientific article published on 21 October 2021

pH-tuneable binding of 2′-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study

scientific article

List of works by Alessio Ciulli

3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation

A Fragment-Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry

Allosteric Targeting of the Fanconi Anemia Ubiquitin-Conjugating Enzyme Ube2T by Fragment Screening.

Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase

Application of fragment screening and merging to the discovery of inhibitors of the Mycobacterium tuberculosis cytochrome P450 CYP121

BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

Biophysical tools to monitor enzyme-ligand interactions of enzymes involved in vitamin biosynthesis.

Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery

Chemical genetics approaches for selective intervention in epigenetics

Correction to "3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation"

Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate bound: substrate recognition, conformational change, and cooperativity

Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions

Design and Characterization of SGK3-PROTAC1, an Isoform Specific SGK3 Kinase PROTAC Degrader

Development of BromoTag: A “Bump-and-Hole”–PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins

Development of NanoLuc-targeting protein degraders and a universal reporter system to benchmark tag-targeted degradation platforms

Dissecting Fragment-Based Lead Discovery at the von Hippel-Lindau Protein:Hypoxia Inducible Factor 1α Protein-Protein Interface

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones

Gram-Scale Laboratory Synthesis of TC AC 28, a High-Affinity BET Bromodomain Ligand

Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-

Highly Selective PTK2 Proteolysis Targeting Chimeras to Probe Focal Adhesion Kinase Scaffolding Functions

Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation.

Impact of Target Warhead and Linkage Vector on Inducing Protein Degradation: Comparison of Bromodomain and Extra-Terminal (BET) Degraders Derived from Triazolodiazepine (JQ1) and Tetrahydroquinoline (I-BET726) BET Inhibitor Scaffolds

Inhibition ofMycobacterium tuberculosisPantothenate Synthetase by Analogues of the Reaction Intermediate

Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery

Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach

Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions?

Iterative design and optimization of initially inactive Proteolysis Targeting Chimeras (PROTACs) identify VZ185 as a potent, fast and selective von Hippel-Lindau (VHL)-based dual degrader probe of BRD9 and BRD7

Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme Ube2T and Induces Structural Rearrangements

Multimeric Complexes among Ankyrin-Repeat and SOCS-box Protein 9 (ASB9), ElonginBC, and Cullin 5: Insights into the Structure and Assembly of ECS-type Cullin-RING E3 Ubiquitin Ligases

NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes

New Synthetic Routes to Triazolo-benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective Bromo and Extra-Terminal (BET) Bromodomain Inhibition.

Nucleophile Selectivity of Chorismate-Utilizing Enzymes

Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition.

Optimization of the Interligand Overhauser Effect for Fragment Linking: Application to Inhibitor Discovery against Mycobacterium tuberculosis Pantothenate Synthetase

Potent and selective chemical probe of hypoxic signalling downstream of HIF-α hydroxylation via VHL inhibition

Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods

Publisher Correction: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response

Rapid and Reversible Knockdown of Endogenously Tagged Endosomal Proteins via an Optimized HaloPROTAC Degrader

Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies.

SPR-Measured Dissociation Kinetics of PROTAC Ternary Complexes Influence Target Degradation Rate

Salicylate biosynthesis: overexpression, purification, and characterization of Irp9, a bifunctional salicylate synthase from Yersinia enterocolitica

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

Spy vs. spy: selecting the best reporter for F NMR competition experiments

Stereoselective synthesis of allele-specific BET inhibitors

Structural basis of PROTAC cooperative recognition for selective protein degradation

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase.

Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

Structure-Based Design of a Macrocyclic PROTAC

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities

Structure-Guided Design of Peptides as Tools to Probe the Protein-Protein Interaction between Cullin-2 and Elongin BC Substrate Adaptor in Cullin RING E3 Ubiquitin Ligases

Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase

Target validation: Switching domains

Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni

Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.

Targeting Low-Druggability Bromodomains: Fragment Based Screening and Inhibitor Design against the BAZ2B Bromodomain

Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1α Interaction

The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands.

Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity

pH-tuneable binding of 2′-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study