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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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Comparisonof docking-predicted (yellow) and crystallographic fragmentgeometries (green) for five NMR hits (a–e) and four dockinghits (f–i): (a) 5, (b) 13, (c) 16, (d) 20, (e) 41, (f) 44, (g) 48, (h) 50, and (i) 60 superposed on 54. Protein residues are depicted withgray carbon atoms, crystallographic water molecules as red spheres,and hydrogen bonds as red dashed lines.
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fig3: Comparisonof docking-predicted (yellow) and crystallographic fragmentgeometries (green) for five NMR hits (a–e) and four dockinghits (f–i): (a) 5, (b) 13, (c) 16, (d) 20, (e) 41, (f) 44, (g) 48, (h) 50, and (i) 60 superposed on 54. Protein residues are depicted withgray carbon atoms, crystallographic water molecules as red spheres,and hydrogen bonds as red dashed lines.

Mentions: The correspondence of the ZoBio inhibitor structures withthe predicted docking poses was spotty (Figure 3). The docking poses of fragments 13 and 16 recapitulated the interaction between the key inhibitor carboxylate,Ser64 and Ala318 (Figure 3b and c). Even herethough, several secondary interactions were missed, such as the interactionof the ketone moieties with Asn152 and Gln120, leading to root-mean-squaredeviations (rmsd) values of 3.3 and 2.5 Å for 13 and 16, respectively. For fragment 5 thedifferences were larger. This fragment was docked to place its carboxylateinto the oxyanion hole (Figure 3a), an orientationthat has been consistently observed for ligands bearing this functionalityin previous AmpC structures.33 In the crystalstructure, however, the carboxylate points out toward solvent, resultingin poor correspondence between the docked pose and the crystal structure(rmsd 5 Å). Meanwhile, the thioxopyrimidine 20 wasmodeled to dock with one aryl oxygen as anionic (calculated pKa is 7.4) and to interact with the enzyme’soxyanion hole (Figure 3d). In the crystal structure,however, the ligand appears to bind in its neutral form and adoptsa different orientation, making only one hydrogen bond with Asn152while the aryl oxygens hydrogen bond with structural water molecules(rmsd 3.5 Å). Finally, fragment 41 was observedto bind AmpC in both the TINS and SPR experiments but did not inhibitthe enzyme. Upon determination of the crystal structure, clear densityappeared at the surface of the protein, 25 Å from the catalyticsite, where the fragment interacts with Gly36, a water molecule, anda phosphate ion (Supplementary Figure 4e). Fragment 41 ranked poorly, 1196/1281, in the active-sitefocused docking screen (Figure 3e).


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)

Comparisonof docking-predicted (yellow) and crystallographic fragmentgeometries (green) for five NMR hits (a–e) and four dockinghits (f–i): (a) 5, (b) 13, (c) 16, (d) 20, (e) 41, (f) 44, (g) 48, (h) 50, and (i) 60 superposed on 54. Protein residues are depicted withgray carbon atoms, crystallographic water molecules as red spheres,and hydrogen bonds as red dashed lines.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: Comparisonof docking-predicted (yellow) and crystallographic fragmentgeometries (green) for five NMR hits (a–e) and four dockinghits (f–i): (a) 5, (b) 13, (c) 16, (d) 20, (e) 41, (f) 44, (g) 48, (h) 50, and (i) 60 superposed on 54. Protein residues are depicted withgray carbon atoms, crystallographic water molecules as red spheres,and hydrogen bonds as red dashed lines.
Mentions: The correspondence of the ZoBio inhibitor structures withthe predicted docking poses was spotty (Figure 3). The docking poses of fragments 13 and 16 recapitulated the interaction between the key inhibitor carboxylate,Ser64 and Ala318 (Figure 3b and c). Even herethough, several secondary interactions were missed, such as the interactionof the ketone moieties with Asn152 and Gln120, leading to root-mean-squaredeviations (rmsd) values of 3.3 and 2.5 Å for 13 and 16, respectively. For fragment 5 thedifferences were larger. This fragment was docked to place its carboxylateinto the oxyanion hole (Figure 3a), an orientationthat has been consistently observed for ligands bearing this functionalityin previous AmpC structures.33 In the crystalstructure, however, the carboxylate points out toward solvent, resultingin poor correspondence between the docked pose and the crystal structure(rmsd 5 Å). Meanwhile, the thioxopyrimidine 20 wasmodeled to dock with one aryl oxygen as anionic (calculated pKa is 7.4) and to interact with the enzyme’soxyanion hole (Figure 3d). In the crystal structure,however, the ligand appears to bind in its neutral form and adoptsa different orientation, making only one hydrogen bond with Asn152while the aryl oxygens hydrogen bond with structural water molecules(rmsd 3.5 Å). Finally, fragment 41 was observedto bind AmpC in both the TINS and SPR experiments but did not inhibitthe enzyme. Upon determination of the crystal structure, clear densityappeared at the surface of the protein, 25 Å from the catalyticsite, where the fragment interacts with Gly36, a water molecule, anda phosphate ion (Supplementary Figure 4e). Fragment 41 ranked poorly, 1196/1281, in the active-sitefocused docking screen (Figure 3e).

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