Katie Whalen - Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations.

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      Publication Details (including relevant citation   information):

      Whalen KL, Spies MA.

      J Chem Inf   Model. 2013 Sep 23;53(9):2349-59. doi: 10.1021/ci400244x.   Epub 2013 Sep 6.


          PMID: 24111836      [PubMed -       in process]   


        Glutamate racemase (GR) is a cofactor independent amino acid   racemase that has recently garnered increasing attention as an   antimicrobial drug target. There are numerous high resolution   crystal structures of GR, yet these are invariably bound to   either D-glutamate or very weakly bound oxygen-based salts.   Recent in silico screens have identified a number of new   competitive inhibitor scaffolds, which are not based on D-Glu,   but exploit many of the same hydrogen bond donor positions. In   silico studies on 1-H-benzimidazole-2-sulfonic acid (BISA) show   that the sulfonic acid points to the back of the GR active site,   in the most buried region, analogous to the C2-carboxylate   binding position in the GR-d-glutamate complex. Furthermore, BISA   has been shown to be the strongest nonamino acid competitive   inhibitor. Previously published computational studies have   suggested that a portion of this binding strength is derived from   complexation with a more closed active site, relative to weaker   ligands, and in which the internal water network is more isolated   from the bulk solvent. In order to validate key contacts between   the buried sulfonate moiety of BISA and moieties in the back of   the enzyme active site, as well as to probe the energetic   importance of the potentially large number of interstitial waters   contacted by the BISA scaffold, we have designed several mutants   of Asn75. GR-N75A removes a key hydrogen bond donor to the   sulfonate of BISA, but also serves to introduce an additional   interstitial water, due to the newly created space of the   mutation. GR- N75L should also show the loss of a hydrogen bond   donor to the sulfonate of BISA, but does not (a priori) seem to   permit an additional interstitial water contact. In order to   investigate the dynamics, structure, and energies of this   water-mediated complexation, we have employed the extended linear   response (ELR) approach for the calculation of binding free   energies to GR, using the YASARA2 knowledge based force field on   a set of ten GR complexes, and yielding an R-squared value of   0.85 and a RMSE of 2.0 kJ/mol. Surprisingly, the inhibitor set   produces a uniformly large interstitial water contribution to the   electrostatic interaction energy (<V(el)>), ranging from 30   to >50%, except for the natural substrate (D-glutamate), which   has only a 7% contribution of <V(el)> from water. The   broader implications for predicting and exploiting significant   interstitial water contacts in ligand-enzyme complexation are   discussed.

      Address (URL): http://www.ncbi.nlm.nih.gov/pubmed/24111836