Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design

Yuan-Ping Pang, Anuradha Vummenthala, Rajesh K. Mishra, Jewn Giew Park, Shaohua Wang, Jon Davis, Charles B. Millard, James J. Schmidt

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

Botulinum neurotoxin serotype A (BoNTA) causes a life-threatening neuroparalytic disease known as botulism. Current treatment for post exposure of BoNTA uses antibodies that are effective in neutralizing the extracellular toxin to prevent further intoxication but generally cannot rescue already intoxicated neurons. Effective small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are desirable because such inhibitors potentially can neutralize the intracellular BoNTA and offer complementary treatment for botulism. Previously we reported a serotype-selective, small-molecule BoNTAe inhibitor with a Ki app value of 3.8±0.8 μM. This inhibitor was developed by lead identification using virtual screening followed by computer-aided optimization of a lead with an IC50 value of 100 μM. However, it was difficult to further improve the lead from micromolar to even high nanomolar potency due to the unusually large enzyme-substrate interface of BoNTAe. The enzyme-substrate interface area of 4,840 Å2 for BoNTAe is about four times larger than the typical protein-protein interface area of 750-1,500 Å2. Inhibitors must carry several functional groups to block the unusually large interface of BoNTAe, and syntheses of such inhibitors are therefore time-consuming and expensive. Herein we report the development of a serotype-selective, small-molecule, and competitive inhibitor of BoNTAe with a Ki value of 760±170 nM using synthesis-based computer-aided molecular design (SBCAMD). This new approach accounts the practicality and efficiency of inhibitor synthesis in addition to binding affinity and selectivity. We also report a three-dimensional model of BoNTAe in complex with the new inhibitor and the dynamics of the complex predicted by multiple molecular dynamics simulations, and discuss further structural optimization to achieve better in vivo efficacy in neutralizing BoNTA than those of our early micromolar leads. This work provides new insight into structural modification of known small-molecule BoNTAe inhibitors. It also demonstrates that SBCAMD is capable of improving potency of an inhibitor lead by nearly one order of magnitude, even for BoNTAe as one of the most challenging protein targets. The results are insightful for developing effective small-molecule inhibitors of protein targets with large active sites.

Original languageEnglish (US)
Article numbere7730
JournalPLoS One
Volume4
Issue number11
DOIs
StatePublished - Nov 10 2009

Fingerprint

botulinum toxin
Computer-Aided Design
Endopeptidases
Neurotoxins
serotypes
proteinases
Protease Inhibitors
Molecules
synthesis
meprin A
Botulism
Proteins
botulism
enzyme substrates
Structural optimization
neutralization
Substrates
Enzymes
Functional groups
Neurons

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design. / Pang, Yuan-Ping; Vummenthala, Anuradha; Mishra, Rajesh K.; Park, Jewn Giew; Wang, Shaohua; Davis, Jon; Millard, Charles B.; Schmidt, James J.

In: PLoS One, Vol. 4, No. 11, e7730, 10.11.2009.

Research output: Contribution to journalArticle

Pang, Yuan-Ping ; Vummenthala, Anuradha ; Mishra, Rajesh K. ; Park, Jewn Giew ; Wang, Shaohua ; Davis, Jon ; Millard, Charles B. ; Schmidt, James J. / Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design. In: PLoS One. 2009 ; Vol. 4, No. 11.
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