Bis-imidazoles as molecular probes for peripheral sites of the zinc endopeptidase of botulinum neurotoxin serotype A

Merino, Isidro; Thompson, Jason D.; Millard, Charles B.; Schmidt, James J.; Pang, Yuan Ping

doi:10.1016/j.bmc.2006.01.015

Cited by 19 publications

(9 citation statements)

References 36 publications

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“…To avoid the conflict, optimization should be directed towards improving inhibitor affinity with a small increase in molecular weight. This strategy is necessary in early stages of optimization of a micromolar lead because a bivalence or fragment-based approach will be used in later stages of the optimization to take advantage of peripheral sites or exosites on the endopeptidase to achieve high affinity [12], [13], [17], [40], [41]. The bivalence or fragment-based approach will be inapplicable to the optimization if the molecular weight of a lead is already too high.…”

Section: Discussionmentioning

confidence: 99%

Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A

et al. 2007

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Optimization of a serotype-selective, small-molecule inhibitor of botulinum neurotoxin serotype A (BoNTA) endopeptidase is a formidable challenge because the enzyme-substrate interface is unusually large and the endopeptidase itself is a large, zinc-binding protein with a complex fold that is difficult to simulate computationally. We conducted multiple molecular dynamics simulations of the endopeptidase in complex with a previously described inhibitor (K i app of 7±2.4 µM) using the cationic dummy atom approach. Based on our computational results, we hypothesized that introducing a hydroxyl group to the inhibitor could improve its potency. Synthesis and testing of the hydroxyl-containing analog as a BoNTA endopeptidase inhibitor showed a twofold improvement in inhibitory potency (K i app of 3.8±0.8 µM) with a relatively small increase in molecular weight (16 Da). The results offer an improved template for further optimization of BoNTA endopeptidase inhibitors and demonstrate the effectiveness of the cationic dummy atom approach in the design and optimization of zinc protease inhibitors.

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Section: Discussionmentioning

confidence: 99%

Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A

et al. 2007

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“…Intoxication occurs within hours and antibodies must administered within this period [12]. A number of small molecule inhibitors of BoNT/A have been developed in the past, and have primarily targeted the zinc in the LC active site [13–16]. Most of these active-site inhibitors (e.g.…”

Section: Introductionmentioning

confidence: 99%

Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening

Legler

Southall

et al. 2014

J Comput Aided Mol Des

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Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hot-spots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.

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“…This is evidenced by the fact that only a handful of small molecules with IC 50 and/or K i values < 15 mm are described in the literature. [28,29,[32][33][34][35][36][37][38] Among these, only one compound, Zn coordinating o,p-(dichloro)-cinnamic hydroxamate (o,p-DCH), is reported to possess an inhibition constant lower than 0.5 mm (IC 50 = 0.41 mm); however, when examined in our HPLC-based assay, o,p-DCH was found to be significantly less potent, with an IC 50 value of > 29 mm, [28] and in a subsequent publication [37] it was shown to be toxic to neurons and demonstrated poor in vivo protection.…”

Section: Resultsmentioning

confidence: 98%

Three‐Dimensional Database Mining Identifies a Unique Chemotype that Unites Structurally Diverse Botulinum Neurotoxin Serotype A Inhibitors in a Three‐Zone Pharmacophore

et al. 2008

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A search query consisting of two aromatic centers and two cationic centers was defined based on previously identified small molecule inhibitors of the botulinum neurotoxin serotype A light chain (BoNT/A LC) and used to mine the National Cancer Institute Open Repository. Ten small molecule hits were identified, and upon testing, three demonstrated inhibitory activity. Of these, one was structurally unique, possessing a rigid diazachrysene scaffold. The steric limitations of the diazachrysene imposed a separation between the overlaps of previously identified inhibitors, revealing an extended binding mode. As a result, the pharmacophore for BoNT/A LC inhibition has been modified to encompass three zones. To demonstrate the utility of this model, a novel three-zone inhibitor was mined and its activity was confirmed.

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Bis-imidazoles as molecular probes for peripheral sites of the zinc endopeptidase of botulinum neurotoxin serotype A

Cited by 19 publications

References 36 publications

Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A

Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A

Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening

Three‐Dimensional Database Mining Identifies a Unique Chemotype that Unites Structurally Diverse Botulinum Neurotoxin Serotype A Inhibitors in a Three‐Zone Pharmacophore

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