Protecting our warfighters? Yes, there is an app for that. To provide our troops with enhanced countermeasure protections, it is imperative that defense agencies develop cost-effective products that allow for faster lab-to-battlefield application. One effort underway, funded by the Defense Threat Reduction Agency’s Chemical and Biological Technologies Department, is developing an app that enables researchers to expedite countermeasure studies.
Natural proteins used for research are expensive, fragile and inefficient. As such, researchers are increasingly turning to biomimetics — human made substances that imitate natural ones. However, until now, there has not been a quick or easy way to design biomimetics for a specific function.
An effort by Temple University’s Christian Schafmeister, Ph.D., has resulted in a modeling app that changes that. Computer-Aided Nanostructure Design and Optimization (CANDO) provides scientists the capability to rationally design biomimetics, similar to how microcircuits, software and machines are designed. The app performs conformational analysis on molecules constructed from non-natural building blocks, searches molecules for substructures, automatically assigns atom types, identifies rings, carries out conformational searching and automatically determines stereochemistry.
CANDO continually builds conformational databases of these building blocks to further enable the creation of improved biomimetics. Using the web browser-based Jupyter notebook interface, CANDO allows chemists to write software that assembles chemical structures into new molecules. In addition, the app allows researchers to construct 3-D coordinates of the resulting molecules, sketches molecules, build 3-D structures, visualize them within the browser and prepare them for sophisticated simulations. CANDO implements a programming environment where chemistry apps can be written and deployed through an internet-based package manager for open use.
Schafmeister used CANDO to create a stable metallo-enzyme that mimics proteins to accelerate organophosphonate rearrangements. These biomimetics are composed of a central scaffold that can be modified with various functional groups in order to create the perfect pocket where catalytic activity can happen. Called “spiroligomers,” these biomimetics have extraordinary utility because they form well-defined, predictable molecular shapes that can be readily modified and customized. These can be assembled to build controllable, tunable enzymes.
Adversaries continue to use and synthesize new threats. Mother Nature has had little time to evolve proteins to thwart known threat agents and no time to defeat synthesized ones. Advances in computational biomimetic design present a unique opportunity to pursue rational design and synthesis of small molecules that can effectively respond to current threats and be rapidly engineered to address emerging ones for the next generation of countermeasures to safeguard our warfighters.
POC: Catherine Keaty, Ph.D.; catherine.l.keaty.civ@mail.mil