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A team from the Institute for Molecular Recognition and Technological Development (IDM) at the Universitat Politècnica de València (UPV) and the University of Oxford have developed new software that, among many other applications, facilitates the design of molecular boxes for drug encapsulation. Called CageCavityCalc -C3-, this software explicitly allows for the automated calculation and visualisation of the cavity size of molecular boxes used in biological applications and which are used, for example, for the administration of anticancer drugs.

‘The CageCavityCalc software uses a novel algorithm that allows the calculation of the cavity size of molecular boxes and properties such as hydrophobicity and electrostatic potential, which provides key information to optimise the design of the molecular box that houses the drugs for their subsequent release into the organism in the most efficient way possible,' explains Vicente Martí Centelles.

Molecular boxes are also used in other applications such as sensors and molecular recognition, catalysis, etc. The fundamental key to their optimal functioning lies in their internal cavity so that they can encapsulate host molecules and modulate their properties. 'However, nowadays, designing boxes with specific properties is challenging, and software development to help predict the properties is essential. And our work responds to this challenge,' says Vicente Martí Centelles.

According to the IDM researcher, to date, the calculation of molecular properties and cavities requires the use of ‘command-line’ based software and parameter adjustments by the user. CageCavityCalc, on the other hand, has a graphical interface that allows non-specialists to use the tool without the need for computer programming skills. In addition, the cavity calculation is fully automated, which avoids the need for parameter adjustments to perform the calculation.

'The main advantage of the CageCavityCalc software is its efficiency, simplicity of use, and the fact that it is free and open source. It streamlines cavity calculations, thus facilitating the development of new functional molecular boxes with the right properties for their different applications. In short, it greatly simplifies the design of these boxes while optimising their operation,’ concludes Vicente Martí Centelles.

Reference

Vicente Martí-Centelles, Tomasz K. Piskorz, Fernanda Duarte. CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages. J. Chem. Inf. Model. 2024, 64, 14, 5604–5616. https://doi.org/10.1021/acs.jcim.4c00355