Computational improvement of small-molecule inhibitors of Bacillus anthracis protective antigen activation through isostere-based substitutions

Abstract

There has recently been interest in the development of small-molecule inhibitors of the oligomerization of Bacillus anthracis protective antigen for therapeutic use. Some of the proposed lead compounds have, however, unfavorable solubility in aqueous medium, which prevents their clinical use. In this computational work, we have designed several hundreds of derivatives with progressively higher hydro-solubility and tested their ability to dock the relevant binding cavity. The highest-ranking docking hits were then subjected to 125 ns-long simulations to ascertain the stability of the binding modes. Several of the potential candidates performed quite disappointingly, but two molecules showed very stable binding modes throughout the complete simulations. Besides the identification of these two promising leads, these molecular dynamics simulations allowed the discovery of several insights that shall prove useful in the further improvement of these candidates toward higher potency and stability.

Communicated by Ramaswamy H. Sarma

Keywords:

• Anthrax
• lead compounds
• molecular dynamics
• docking

Disclosure statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Additional information

Funding

This work was performed using computational resources acquired under project PTDC/QUI-QUI/111288/2009 and funded by FEDER through Programa Operacional Factores de Competitividade – COMPETE and by Portuguese Funds through FCT – Fundação para a Ciência e a Tecnologia.