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Increasing chemical space coverage by combining empirical and computational fragment screens.

Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G - ACS Chem. Biol. (2014)

Bottom Line: Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments.The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments.Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 4th St., Byers Hall, San Francisco, California 94158, United States.

ABSTRACT
Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.

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Docking ranks and inhibitory activity for 18commercial fragmentsdiscovered by docking. Fragment 60, a close analogueof fragment 54 that was used for crystallization withAmpC, is also shown. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, inparentheses.
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fig2: Docking ranks and inhibitory activity for 18commercial fragmentsdiscovered by docking. Fragment 60, a close analogueof fragment 54 that was used for crystallization withAmpC, is also shown. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, inparentheses.

Mentions: To explore the chemical space that is notcovered by the experimental library, a set of 290,225 commerciallyavailable fragments, dissimilar to the ZoBio compounds (Tc ≤0.4, using ECFP_4 fingerprints), was docked against the enzyme. Asis often true with docking and even empirical screening,32 it was impractical to follow up all hits withdetailed experiments. Therefore, an 18-compound subset of the topranking molecules was selected to assess biochemical activity. Thesecompounds were representative of the top 500 docked molecules (top0.17% of the library), with ranks from 7 to 490 out of 290,225 (Figure 2 and Supplementary Table 4). In addition to their physics-based docking scores and their dissimilarityto the ZoBio set, these fragments were selected for their chemicaldiversity, a widely used criterion,32 andfor hydrogen bonding with key active site residues (Ser64, Ala318,Asn152). Fragments that had been docked with incorrect ionizationstates or strained conformations were deprioritized, removing artifactualhits. The final 18 molecules well-represented the top 500 docked moleculesoverall: for instance, they had an average of 15.1 heavy atoms andan average net charge of −1.0, versus 15.4 and −0.9for the top 500 hits. In the AmpC activity assay (Supplementary Figure 2), 10 of them had KI values below 10 mM, with the most active having a KI of 30 μM; ligand efficiencies rangedfrom 0.19 to 0.43 (Figure 2 and Table 1). Tc values to known AmpC ligands ranged from 0.19to 0.52, with an average of 0.36, using ECFP_4 fingerprints (Table 1); this is substantially higher, indicating lessnovelty, than the 0.21 average Tanimoto coefficient observed for theNMR-derived fragment hits.


Increasing chemical space coverage by combining empirical and computational fragment screens.

Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G - ACS Chem. Biol. (2014)

Docking ranks and inhibitory activity for 18commercial fragmentsdiscovered by docking. Fragment 60, a close analogueof fragment 54 that was used for crystallization withAmpC, is also shown. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, inparentheses.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215856&req=5

fig2: Docking ranks and inhibitory activity for 18commercial fragmentsdiscovered by docking. Fragment 60, a close analogueof fragment 54 that was used for crystallization withAmpC, is also shown. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, inparentheses.
Mentions: To explore the chemical space that is notcovered by the experimental library, a set of 290,225 commerciallyavailable fragments, dissimilar to the ZoBio compounds (Tc ≤0.4, using ECFP_4 fingerprints), was docked against the enzyme. Asis often true with docking and even empirical screening,32 it was impractical to follow up all hits withdetailed experiments. Therefore, an 18-compound subset of the topranking molecules was selected to assess biochemical activity. Thesecompounds were representative of the top 500 docked molecules (top0.17% of the library), with ranks from 7 to 490 out of 290,225 (Figure 2 and Supplementary Table 4). In addition to their physics-based docking scores and their dissimilarityto the ZoBio set, these fragments were selected for their chemicaldiversity, a widely used criterion,32 andfor hydrogen bonding with key active site residues (Ser64, Ala318,Asn152). Fragments that had been docked with incorrect ionizationstates or strained conformations were deprioritized, removing artifactualhits. The final 18 molecules well-represented the top 500 docked moleculesoverall: for instance, they had an average of 15.1 heavy atoms andan average net charge of −1.0, versus 15.4 and −0.9for the top 500 hits. In the AmpC activity assay (Supplementary Figure 2), 10 of them had KI values below 10 mM, with the most active having a KI of 30 μM; ligand efficiencies rangedfrom 0.19 to 0.43 (Figure 2 and Table 1). Tc values to known AmpC ligands ranged from 0.19to 0.52, with an average of 0.36, using ECFP_4 fingerprints (Table 1); this is substantially higher, indicating lessnovelty, than the 0.21 average Tanimoto coefficient observed for theNMR-derived fragment hits.

Bottom Line: Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments.The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments.Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 4th St., Byers Hall, San Francisco, California 94158, United States.

ABSTRACT
Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.

Show MeSH
Related in: MedlinePlus