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Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors.

Kavanagh ME, Coyne AG, McLean KJ, James GG, Levy CW, Marino LB, de Carvalho LP, Chan DS, Hudson SA, Surade S, Leys D, Munro AW, Abell C - J. Med. Chem. (2016)

Bottom Line: Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM).Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands.Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.

ABSTRACT
The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.

No MeSH data available.


Related in: MedlinePlus

Proposedoptimization strategies for Ar1, Ar2, and Ar3 of leadCYP121 inhibitor 2. (a) Overlaid X-ray crystal structuresof biaryl fragment 5 (yellow) (PDB 4KTF) and benzamide fragment 7 (green) (PDB 5EDT) bound to CYP121. The associated omit Fo–Fc electron densitymap of fragment 7 contoured to 3σ can be foundin Supporting Information Figure S5. (b)Overlaid X-ray crystal structures of CYP121 in complex with retrofragment 5 (yellow) and with heme binding fragments 8 (copper)(PDB 4G44) and 9 (cyan) (PDB 4G45),27 indicating the proposed meta-attachment point for substituents and distance (6.5Å) to the heme coordinating position (yellow dashed line). (c)Docking of Ar3 analogues of lead 2, elaborating fromthe 5-aminopyrazole group of retrofragment 5 (gray) withcarbonyl (orange) or methylene (green) linkages to enhance bindinginteractions with the distal active site pocket (Asn74, Thr65, graysticks) of CYP121. Figures prepared using PyMOL v1.7.4 (Schrödinger,LLC).
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fig4: Proposedoptimization strategies for Ar1, Ar2, and Ar3 of leadCYP121 inhibitor 2. (a) Overlaid X-ray crystal structuresof biaryl fragment 5 (yellow) (PDB 4KTF) and benzamide fragment 7 (green) (PDB 5EDT) bound to CYP121. The associated omit Fo–Fc electron densitymap of fragment 7 contoured to 3σ can be foundin Supporting Information Figure S5. (b)Overlaid X-ray crystal structures of CYP121 in complex with retrofragment 5 (yellow) and with heme binding fragments 8 (copper)(PDB 4G44) and 9 (cyan) (PDB 4G45),27 indicating the proposed meta-attachment point for substituents and distance (6.5Å) to the heme coordinating position (yellow dashed line). (c)Docking of Ar3 analogues of lead 2, elaborating fromthe 5-aminopyrazole group of retrofragment 5 (gray) withcarbonyl (orange) or methylene (green) linkages to enhance bindinginteractions with the distal active site pocket (Asn74, Thr65, graysticks) of CYP121. Figures prepared using PyMOL v1.7.4 (Schrödinger,LLC).

Mentions: Our approach to developingpotent CYP121 inhibitors focused on three independent series of analogues,each optimizing the interactions of the Ar1, Ar2, and Ar3 rings oflead compound 2, respectively (Figure 4a–c). Analogues were designed as derivatives of eitherthe biaryl scaffold 5, which had been identified as themost LE retrofragment that also retained the original binding modeof 2, or the monoaryl 4 scaffold, whichhad been identified to participate in a conserved hydrogen-bondingnetwork and bound to CYP121 in close proximity to the heme cofactor.


Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors.

Kavanagh ME, Coyne AG, McLean KJ, James GG, Levy CW, Marino LB, de Carvalho LP, Chan DS, Hudson SA, Surade S, Leys D, Munro AW, Abell C - J. Med. Chem. (2016)

Proposedoptimization strategies for Ar1, Ar2, and Ar3 of leadCYP121 inhibitor 2. (a) Overlaid X-ray crystal structuresof biaryl fragment 5 (yellow) (PDB 4KTF) and benzamide fragment 7 (green) (PDB 5EDT) bound to CYP121. The associated omit Fo–Fc electron densitymap of fragment 7 contoured to 3σ can be foundin Supporting Information Figure S5. (b)Overlaid X-ray crystal structures of CYP121 in complex with retrofragment 5 (yellow) and with heme binding fragments 8 (copper)(PDB 4G44) and 9 (cyan) (PDB 4G45),27 indicating the proposed meta-attachment point for substituents and distance (6.5Å) to the heme coordinating position (yellow dashed line). (c)Docking of Ar3 analogues of lead 2, elaborating fromthe 5-aminopyrazole group of retrofragment 5 (gray) withcarbonyl (orange) or methylene (green) linkages to enhance bindinginteractions with the distal active site pocket (Asn74, Thr65, graysticks) of CYP121. Figures prepared using PyMOL v1.7.4 (Schrödinger,LLC).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835159&req=5

fig4: Proposedoptimization strategies for Ar1, Ar2, and Ar3 of leadCYP121 inhibitor 2. (a) Overlaid X-ray crystal structuresof biaryl fragment 5 (yellow) (PDB 4KTF) and benzamide fragment 7 (green) (PDB 5EDT) bound to CYP121. The associated omit Fo–Fc electron densitymap of fragment 7 contoured to 3σ can be foundin Supporting Information Figure S5. (b)Overlaid X-ray crystal structures of CYP121 in complex with retrofragment 5 (yellow) and with heme binding fragments 8 (copper)(PDB 4G44) and 9 (cyan) (PDB 4G45),27 indicating the proposed meta-attachment point for substituents and distance (6.5Å) to the heme coordinating position (yellow dashed line). (c)Docking of Ar3 analogues of lead 2, elaborating fromthe 5-aminopyrazole group of retrofragment 5 (gray) withcarbonyl (orange) or methylene (green) linkages to enhance bindinginteractions with the distal active site pocket (Asn74, Thr65, graysticks) of CYP121. Figures prepared using PyMOL v1.7.4 (Schrödinger,LLC).
Mentions: Our approach to developingpotent CYP121 inhibitors focused on three independent series of analogues,each optimizing the interactions of the Ar1, Ar2, and Ar3 rings oflead compound 2, respectively (Figure 4a–c). Analogues were designed as derivatives of eitherthe biaryl scaffold 5, which had been identified as themost LE retrofragment that also retained the original binding modeof 2, or the monoaryl 4 scaffold, whichhad been identified to participate in a conserved hydrogen-bondingnetwork and bound to CYP121 in close proximity to the heme cofactor.

Bottom Line: Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM).Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands.Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.

ABSTRACT
The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.

No MeSH data available.


Related in: MedlinePlus