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Covalent docking of large libraries for the discovery of chemical probes.

London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J - Nat. Chem. Biol. (2014)

Bottom Line: Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns.Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules.Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.

ABSTRACT
Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).

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Reversible covalent JAK3 inhibitors discovered via dockinga. First- and second-generation virtual libraries of cyanoacrylamide fragments were screened by DOCKovalent vs. JAK3. Compounds 28–42 were selected and synthesized as described in the Supplementary Information. b. JAK3 inhibition at 1 μM and 5 μM. c. Cyanoacrylamides 31 and 33 are selective for JAK3 over JAK1, JAK2, and TYK2. JAK3 IC50 = 49 nM and 93 nM, respectively. Data represent mean values of two independent experiments ± s.d.
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Figure 4: Reversible covalent JAK3 inhibitors discovered via dockinga. First- and second-generation virtual libraries of cyanoacrylamide fragments were screened by DOCKovalent vs. JAK3. Compounds 28–42 were selected and synthesized as described in the Supplementary Information. b. JAK3 inhibition at 1 μM and 5 μM. c. Cyanoacrylamides 31 and 33 are selective for JAK3 over JAK1, JAK2, and TYK2. JAK3 IC50 = 49 nM and 93 nM, respectively. Data represent mean values of two independent experiments ± s.d.

Mentions: We purchased eight arylbromides and three boronic acids common among the top 0.2% of the docked library (Supplementary Table 9). From these building blocks, we synthesized 15 inhibitors (Compounds 28–42; Fig. 4a). Compound 42 was prepared from a commercially available aldehyde. Each compound was initially tested against JAK3 at two concentrations. Nine of the 15 compounds inhibited the kinase by > 50% at 5 μM, and five maintained > 50% inhibition at 1 μM (Fig. 4b).


Covalent docking of large libraries for the discovery of chemical probes.

London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J - Nat. Chem. Biol. (2014)

Reversible covalent JAK3 inhibitors discovered via dockinga. First- and second-generation virtual libraries of cyanoacrylamide fragments were screened by DOCKovalent vs. JAK3. Compounds 28–42 were selected and synthesized as described in the Supplementary Information. b. JAK3 inhibition at 1 μM and 5 μM. c. Cyanoacrylamides 31 and 33 are selective for JAK3 over JAK1, JAK2, and TYK2. JAK3 IC50 = 49 nM and 93 nM, respectively. Data represent mean values of two independent experiments ± s.d.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232467&req=5

Figure 4: Reversible covalent JAK3 inhibitors discovered via dockinga. First- and second-generation virtual libraries of cyanoacrylamide fragments were screened by DOCKovalent vs. JAK3. Compounds 28–42 were selected and synthesized as described in the Supplementary Information. b. JAK3 inhibition at 1 μM and 5 μM. c. Cyanoacrylamides 31 and 33 are selective for JAK3 over JAK1, JAK2, and TYK2. JAK3 IC50 = 49 nM and 93 nM, respectively. Data represent mean values of two independent experiments ± s.d.
Mentions: We purchased eight arylbromides and three boronic acids common among the top 0.2% of the docked library (Supplementary Table 9). From these building blocks, we synthesized 15 inhibitors (Compounds 28–42; Fig. 4a). Compound 42 was prepared from a commercially available aldehyde. Each compound was initially tested against JAK3 at two concentrations. Nine of the 15 compounds inhibited the kinase by > 50% at 5 μM, and five maintained > 50% inhibition at 1 μM (Fig. 4b).

Bottom Line: Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns.Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules.Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.

ABSTRACT
Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).

Show MeSH
Related in: MedlinePlus