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9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain.

Picaud S, Strocchia M, Terracciano S, Lauro G, Mendez J, Daniels DL, Riccio R, Bifulco G, Bruno I, Filippakopoulos P - J. Med. Chem. (2015)

Bottom Line: The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4.Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket.The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.

View Article: PubMed Central - PubMed

Affiliation: †Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.

ABSTRACT
The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.

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Purine fragments bindto human bromodomains. (A) Structure of olomoucine,a potent cyclin-dependent kinase inhibitor and numbering of the 2-amine-9H-purine core scaffold. (B) Purine fragments tested as bromodomainligands. (C) Docking pose of 1 (yellow stick representation)onto the bromodomain of BRD4(1) positions the bulky halogen groupon the top of the binding pocket. The protein is shown as a whiteribbon (starting model, PDB code 4MEN) or in magenta (docked model) with characteristicresidues shown as sticks in the same color scheme. (D) Alternativebinding of compound 1 into the bromodomain of BRD4(1)with the 6-chloro substituent adopting an acetyllysine mimetic pose.The compound and protein are colored as in (C). PDB code 4MEN was used as thestarting model for docking. (E) Docking of compound 2a positions the 2-amine-9H-purine ring system ofthe ligand within the Kac cavity, sterically packing between V87 andI146, suggesting that this scaffold topology can be further utilizedto target bromodomains. The same color scheme as in (C) and (D) isused with the ligand shown as orange sticks. PDB code 4MEN was used as thestarting model for docking. (F) Fragments were tested in a thermalshift assay against bromodomains of the BET subfamily as well as representativemembers from other families. Thermal shifts are color-coded as indicatedin the inset. 9H-Purines showed weak binding acrossthe panel.
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fig1: Purine fragments bindto human bromodomains. (A) Structure of olomoucine,a potent cyclin-dependent kinase inhibitor and numbering of the 2-amine-9H-purine core scaffold. (B) Purine fragments tested as bromodomainligands. (C) Docking pose of 1 (yellow stick representation)onto the bromodomain of BRD4(1) positions the bulky halogen groupon the top of the binding pocket. The protein is shown as a whiteribbon (starting model, PDB code 4MEN) or in magenta (docked model) with characteristicresidues shown as sticks in the same color scheme. (D) Alternativebinding of compound 1 into the bromodomain of BRD4(1)with the 6-chloro substituent adopting an acetyllysine mimetic pose.The compound and protein are colored as in (C). PDB code 4MEN was used as thestarting model for docking. (E) Docking of compound 2a positions the 2-amine-9H-purine ring system ofthe ligand within the Kac cavity, sterically packing between V87 andI146, suggesting that this scaffold topology can be further utilizedto target bromodomains. The same color scheme as in (C) and (D) isused with the ligand shown as orange sticks. PDB code 4MEN was used as thestarting model for docking. (F) Fragments were tested in a thermalshift assay against bromodomains of the BET subfamily as well as representativemembers from other families. Thermal shifts are color-coded as indicatedin the inset. 9H-Purines showed weak binding acrossthe panel.

Mentions: In light of the successfulfragment-based programs and the reliabilityfor discovering BRDs inhibitors, we started to investigate the purinescaffold as a putative Kac mimetic. Purine is a privileged chemicaltemplate, as it is one of the most abundant N-based heterocycles innature,45 and a number of purine-baseddrugs are currently approved and used for the treatment of cancer(6-mercaptopurine, 6-thioguanine), viral infections such as AIDS andherpes (carbovir, abacavir, acyclovir, ganciclovir), hairy cell leukemia(cladribine), and organ rejection (azathioprine).46 Moreover, purine based compounds have emerged as reliablechemical–biology tools, since they can interact with a varietyof biological targets involved in a number of diseases. Some suchexamples include their activity as microtubule (myoseverin), 90-heatshock protein (PU3), sulfotransferase (NG38), adenosine receptor (KW-6002),and cyclin-dependent kinase (olomoucine, Figure 1A; roscovitine) inhibitors.47,48


9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain.

Picaud S, Strocchia M, Terracciano S, Lauro G, Mendez J, Daniels DL, Riccio R, Bifulco G, Bruno I, Filippakopoulos P - J. Med. Chem. (2015)

Purine fragments bindto human bromodomains. (A) Structure of olomoucine,a potent cyclin-dependent kinase inhibitor and numbering of the 2-amine-9H-purine core scaffold. (B) Purine fragments tested as bromodomainligands. (C) Docking pose of 1 (yellow stick representation)onto the bromodomain of BRD4(1) positions the bulky halogen groupon the top of the binding pocket. The protein is shown as a whiteribbon (starting model, PDB code 4MEN) or in magenta (docked model) with characteristicresidues shown as sticks in the same color scheme. (D) Alternativebinding of compound 1 into the bromodomain of BRD4(1)with the 6-chloro substituent adopting an acetyllysine mimetic pose.The compound and protein are colored as in (C). PDB code 4MEN was used as thestarting model for docking. (E) Docking of compound 2a positions the 2-amine-9H-purine ring system ofthe ligand within the Kac cavity, sterically packing between V87 andI146, suggesting that this scaffold topology can be further utilizedto target bromodomains. The same color scheme as in (C) and (D) isused with the ligand shown as orange sticks. PDB code 4MEN was used as thestarting model for docking. (F) Fragments were tested in a thermalshift assay against bromodomains of the BET subfamily as well as representativemembers from other families. Thermal shifts are color-coded as indicatedin the inset. 9H-Purines showed weak binding acrossthe panel.
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fig1: Purine fragments bindto human bromodomains. (A) Structure of olomoucine,a potent cyclin-dependent kinase inhibitor and numbering of the 2-amine-9H-purine core scaffold. (B) Purine fragments tested as bromodomainligands. (C) Docking pose of 1 (yellow stick representation)onto the bromodomain of BRD4(1) positions the bulky halogen groupon the top of the binding pocket. The protein is shown as a whiteribbon (starting model, PDB code 4MEN) or in magenta (docked model) with characteristicresidues shown as sticks in the same color scheme. (D) Alternativebinding of compound 1 into the bromodomain of BRD4(1)with the 6-chloro substituent adopting an acetyllysine mimetic pose.The compound and protein are colored as in (C). PDB code 4MEN was used as thestarting model for docking. (E) Docking of compound 2a positions the 2-amine-9H-purine ring system ofthe ligand within the Kac cavity, sterically packing between V87 andI146, suggesting that this scaffold topology can be further utilizedto target bromodomains. The same color scheme as in (C) and (D) isused with the ligand shown as orange sticks. PDB code 4MEN was used as thestarting model for docking. (F) Fragments were tested in a thermalshift assay against bromodomains of the BET subfamily as well as representativemembers from other families. Thermal shifts are color-coded as indicatedin the inset. 9H-Purines showed weak binding acrossthe panel.
Mentions: In light of the successfulfragment-based programs and the reliabilityfor discovering BRDs inhibitors, we started to investigate the purinescaffold as a putative Kac mimetic. Purine is a privileged chemicaltemplate, as it is one of the most abundant N-based heterocycles innature,45 and a number of purine-baseddrugs are currently approved and used for the treatment of cancer(6-mercaptopurine, 6-thioguanine), viral infections such as AIDS andherpes (carbovir, abacavir, acyclovir, ganciclovir), hairy cell leukemia(cladribine), and organ rejection (azathioprine).46 Moreover, purine based compounds have emerged as reliablechemical–biology tools, since they can interact with a varietyof biological targets involved in a number of diseases. Some suchexamples include their activity as microtubule (myoseverin), 90-heatshock protein (PU3), sulfotransferase (NG38), adenosine receptor (KW-6002),and cyclin-dependent kinase (olomoucine, Figure 1A; roscovitine) inhibitors.47,48

Bottom Line: The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4.Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket.The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.

View Article: PubMed Central - PubMed

Affiliation: †Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.

ABSTRACT
The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.

Show MeSH