Limits...
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

Deconstruction of lead compound 2 into retrosyntheticfragments 3–6 was used to assessthe binding affinity, ligand efficiency (LE), and group efficiency(GE) contribution of the individual components. The three aromaticrings decorating the aminopyrazole core of lead compound 2 have been labeled Ar1, Ar2, and Ar3 as illustrated, which refersto the orientation the rings occupy in the X-ray crystal structureof 2 in complex with CYP121 (Figure 1). Retrofragments 3 and 4 represent Ar1 and Ar2, respectively. The lower panel tabulatesthe binding affinity (KD) and LE and GEproperties of compounds from the sequential reconstruction of lead 2 from component monoaryl (3 and 4) and biaryl (5 and 6) retrofragments. KD values were determined using ITC. LE was calculatedfrom the Gibbs free energy of binding divided by the number of heavyatoms (ΔG/HA).29,30 GE contributionsof the three aromatic rings Ar1, Ar2, and Ar3 were calculated fromthe change in Gibbs free energy per added heavy atom (−ΔΔG/ΔHA) as the retrofragments wereprogressively recombined to form lead compound 2.31KD previously reported.28
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4835159&req=5

fig3: Deconstruction of lead compound 2 into retrosyntheticfragments 3–6 was used to assessthe binding affinity, ligand efficiency (LE), and group efficiency(GE) contribution of the individual components. The three aromaticrings decorating the aminopyrazole core of lead compound 2 have been labeled Ar1, Ar2, and Ar3 as illustrated, which refersto the orientation the rings occupy in the X-ray crystal structureof 2 in complex with CYP121 (Figure 1). Retrofragments 3 and 4 represent Ar1 and Ar2, respectively. The lower panel tabulatesthe binding affinity (KD) and LE and GEproperties of compounds from the sequential reconstruction of lead 2 from component monoaryl (3 and 4) and biaryl (5 and 6) retrofragments. KD values were determined using ITC. LE was calculatedfrom the Gibbs free energy of binding divided by the number of heavyatoms (ΔG/HA).29,30 GE contributionsof the three aromatic rings Ar1, Ar2, and Ar3 were calculated fromthe change in Gibbs free energy per added heavy atom (−ΔΔG/ΔHA) as the retrofragments wereprogressively recombined to form lead compound 2.31KD previously reported.28

Mentions: Despite a 100-fold improvement in binding affinity betweenfragment 1 and lead 2, the low ligand efficiency(LE)29,30 of 2 (LE = 0.23) led us toundertake a deconstruction–reconstructionapproach to identify more efficient scaffolds for subsequent optimization.Retrofragmentation of 2 to its component “fragments”was used to assess the binding contribution, or group efficiency (GE),31 of the three aromatic rings that decorate theamino-pyrazole core, hereafter referred to as Ar1, Ar2, and Ar3, asdefined in Figure 3.


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)

Deconstruction of lead compound 2 into retrosyntheticfragments 3–6 was used to assessthe binding affinity, ligand efficiency (LE), and group efficiency(GE) contribution of the individual components. The three aromaticrings decorating the aminopyrazole core of lead compound 2 have been labeled Ar1, Ar2, and Ar3 as illustrated, which refersto the orientation the rings occupy in the X-ray crystal structureof 2 in complex with CYP121 (Figure 1). Retrofragments 3 and 4 represent Ar1 and Ar2, respectively. The lower panel tabulatesthe binding affinity (KD) and LE and GEproperties of compounds from the sequential reconstruction of lead 2 from component monoaryl (3 and 4) and biaryl (5 and 6) retrofragments. KD values were determined using ITC. LE was calculatedfrom the Gibbs free energy of binding divided by the number of heavyatoms (ΔG/HA).29,30 GE contributionsof the three aromatic rings Ar1, Ar2, and Ar3 were calculated fromthe change in Gibbs free energy per added heavy atom (−ΔΔG/ΔHA) as the retrofragments wereprogressively recombined to form lead compound 2.31KD previously reported.28
© Copyright Policy
Related In: Results  -  Collection

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

fig3: Deconstruction of lead compound 2 into retrosyntheticfragments 3–6 was used to assessthe binding affinity, ligand efficiency (LE), and group efficiency(GE) contribution of the individual components. The three aromaticrings decorating the aminopyrazole core of lead compound 2 have been labeled Ar1, Ar2, and Ar3 as illustrated, which refersto the orientation the rings occupy in the X-ray crystal structureof 2 in complex with CYP121 (Figure 1). Retrofragments 3 and 4 represent Ar1 and Ar2, respectively. The lower panel tabulatesthe binding affinity (KD) and LE and GEproperties of compounds from the sequential reconstruction of lead 2 from component monoaryl (3 and 4) and biaryl (5 and 6) retrofragments. KD values were determined using ITC. LE was calculatedfrom the Gibbs free energy of binding divided by the number of heavyatoms (ΔG/HA).29,30 GE contributionsof the three aromatic rings Ar1, Ar2, and Ar3 were calculated fromthe change in Gibbs free energy per added heavy atom (−ΔΔG/ΔHA) as the retrofragments wereprogressively recombined to form lead compound 2.31KD previously reported.28
Mentions: Despite a 100-fold improvement in binding affinity betweenfragment 1 and lead 2, the low ligand efficiency(LE)29,30 of 2 (LE = 0.23) led us toundertake a deconstruction–reconstructionapproach to identify more efficient scaffolds for subsequent optimization.Retrofragmentation of 2 to its component “fragments”was used to assess the binding contribution, or group efficiency (GE),31 of the three aromatic rings that decorate theamino-pyrazole core, hereafter referred to as Ar1, Ar2, and Ar3, asdefined in Figure 3.

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