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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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SPR status, docking rank,and inhibitory activity for 34 hits discoveredby NMR. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, in parentheses.*Competitive for binding in the presence of benzo[b]thiophene-2-boronic acid (Supplementary Figure1) in a secondary TINS assay. **New rank for fragment 32 docked as a diacid (Supplementary Table3).
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fig1: SPR status, docking rank,and inhibitory activity for 34 hits discoveredby NMR. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, in parentheses.*Competitive for binding in the presence of benzo[b]thiophene-2-boronic acid (Supplementary Figure1) in a secondary TINS assay. **New rank for fragment 32 docked as a diacid (Supplementary Table3).

Mentions: As with most enzymes,inhibitor bindingaffinities for AmpC are equivalent to competitive KI values, by linkage equilibrium. Pragmatically, inhibitionis also the relevant functional read-out for the enzyme. Therefore,34 of the 35 NMR hits tested by SPR were investigated for AmpC inhibition(one was no longer available) (Supplementary Figure2). Of these, nine fragments had KI values below 10 mM, with the most potent having a KI of 0.2 mM (Figure 1 and Table 1). Seven of these fragments (1, 7, 9, 13, 16, 20, and 32) had well-defined SPR binding curves,with the two less potent ones (5 and 17)having weak SPR signals (Figure 1 and Supplementary Table 2). Ligand efficiencies rangedfrom 0.14 to 0.31 (Figure 1 and Table 1). Compared with known AmpC inhibitors, the highestpairwise Tanimoto coefficients (Tc) (EFCP_4 fingerprints) ranged from0.16 to 0.28 (average 0.21), indicating high topological novelty forthe NMR-derived fragments (Table 1). For theother 25 compounds, no measurable inhibition was detected up to aconcentration of 10 mM or to the solubility limit of the compound.For one of these 25, binding to the protein was nevertheless observedby X-ray crystallography at the surface, about 25 Å away fromthe active site (fragment 41, below).


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)

SPR status, docking rank,and inhibitory activity for 34 hits discoveredby NMR. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, in parentheses.*Competitive for binding in the presence of benzo[b]thiophene-2-boronic acid (Supplementary Figure1) in a secondary TINS assay. **New rank for fragment 32 docked as a diacid (Supplementary Table3).
© Copyright Policy
Related In: Results  -  Collection

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

fig1: SPR status, docking rank,and inhibitory activity for 34 hits discoveredby NMR. Inhibitors are in blue. The KI is indicated, followed by the ligand efficiency, in parentheses.*Competitive for binding in the presence of benzo[b]thiophene-2-boronic acid (Supplementary Figure1) in a secondary TINS assay. **New rank for fragment 32 docked as a diacid (Supplementary Table3).
Mentions: As with most enzymes,inhibitor bindingaffinities for AmpC are equivalent to competitive KI values, by linkage equilibrium. Pragmatically, inhibitionis also the relevant functional read-out for the enzyme. Therefore,34 of the 35 NMR hits tested by SPR were investigated for AmpC inhibition(one was no longer available) (Supplementary Figure2). Of these, nine fragments had KI values below 10 mM, with the most potent having a KI of 0.2 mM (Figure 1 and Table 1). Seven of these fragments (1, 7, 9, 13, 16, 20, and 32) had well-defined SPR binding curves,with the two less potent ones (5 and 17)having weak SPR signals (Figure 1 and Supplementary Table 2). Ligand efficiencies rangedfrom 0.14 to 0.31 (Figure 1 and Table 1). Compared with known AmpC inhibitors, the highestpairwise Tanimoto coefficients (Tc) (EFCP_4 fingerprints) ranged from0.16 to 0.28 (average 0.21), indicating high topological novelty forthe NMR-derived fragments (Table 1). For theother 25 compounds, no measurable inhibition was detected up to aconcentration of 10 mM or to the solubility limit of the compound.For one of these 25, binding to the protein was nevertheless observedby X-ray crystallography at the surface, about 25 Å away fromthe active site (fragment 41, below).

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