Most libraries for fragment-based drug discovery are restricted to 1 0

Most libraries for fragment-based drug discovery are restricted to 1 0 0 compounds but over 500 0 fragments are commercially available and potentially accessible by virtual testing. than those found out by NMR the docking-derived fragments packed chemotype holes from your empirical library. Crystal constructions of nine of the fragments in complex with AmpC β-lactamase revealed fresh binding sites and explained the relatively high affinity of the docking-derived fragments. The living of chemotype holes is EPZ-5676 likely a general feature of fragment libraries as calculation suggests that to represent the fragment substructures of actually known biogenic molecules would demand a library of minimally over 32 0 fragments. Combining computational and empirical fragment screens enables the finding of unpredicted chemotypes here from the NMR display EPZ-5676 while taking chemotypes missing from your empirical library and tailored to the prospective with little extra cost in resources. Fragment-based screening and optimization are now widely used in drug finding 1 fortified from the registration of the 1st drug originating from a fragment-based display.2 In such screens low-molecular weight compounds (150-300 Da)3 are sought as early hits which are then optimized for affinity permeability and related pharmacological properties. The low molecular excess weight of fragment molecules imposes practical difficulties as it typically limits their affinities to the mid-micromolar to low-millimolar range. However judged by their ligand effectiveness (LE) ΔGb/weighty atom count (HAC) fragments have advantages over additional actives from early finding and can often become optimized for affinity without sacrificing their beneficial physical properties.4 5 Also the combinatorial collapse of diversity at small molecular sizes allows fragment libraries to protect chemical space many orders of magnitude better than larger libraries such as those used in high-throughput screens (HTS).6 7 The collapse of chemical diversity in the fragment level combined with the need to use low-throughput biophysical assays to detect low-affinity binding 8 9 has led to small fragment libraries (1 0 0 compounds).10 11 Several of these have been optimized for diversity10 and may recapitulate the chemotypes present in drug-like actives for a number of targets 12 13 leading to active molecules in multiple screens.14?17 Still this is not the same as saying that fragment libraries cover most of biorelevant chemical space. As you will find over 700 0 fragments that are commercially available fragment screens may miss interesting and readily accessible chemotypes. In basic principle compounds unrepresented in any particular empirical screening library may be utilized computationally. Molecular docking can sample all available compounds and prioritize those that sterically and energetically match target sites.18 Issues about reliability however have limited the use of docking in fragment discovery: fragments can adopt multiple orientations in the binding site 19 and rating functions optimized for larger drug-like molecules may be inappropriate for fragments.20 In several fragment screens docking offers EPZ-5676 uncovered potent hits 21 and expected docked structures have been confirmed by subsequent crystallography.22 Still few studies possess compared docking and empirical fragment screens directly and prospectively.23 We thus thought it interesting to compare an empirical display of a fragment library having a docking display of the Hapln4 same library run in parallel against the same target. We screened an experimental fragment library of 1 1 281 molecules using target-immobilized NMR screening (TINS) to detect binding.24 We wondered whether the docking display would prioritize the same active molecules found empirically and whether the fragment library would illuminate chemotypes unknown for the prospective. More germane to this EPZ-5676 study we pondered if notwithstanding its diversity the 1 281 experimental fragment library would miss chemotypes that might be prioritized by docking a much larger library of commercially available fragments. To investigate these questions at atomic resolution we targeted the model enzyme and drug target AmpC β-lactamase. AmpC has been extensively analyzed for mechanism and biophysics25?27 and has served like a model system for different drug discovery methods including HTS 28 structure-based testing 29 and covalent inhibition.30 The enzyme which lends itself to facile EPZ-5676 crystallography and enzymology is the most widespread resistance determinant to β-lactam antibiotics such.