Maintained and developed in the Group of Vincent Zoete and Olivier Michielin (University of Lausanne), the SIB Resource SwissDrugDesign is a platform of tools dedicated to computer-aided drug design. On 16 December 2018, the count of total jobs run on the platform passed the symbolic one-million mark, highlighting a remarkable acceleration of usage over the past years. We asked our Group Leaders Vincent Zoete and Olivier Michielin to tell us more about the milestone that has been reached and about the tools themselves.

About computer-aided drug design (CADD)

Drug design is the process by which medicinal chemists attempt to discover new medication. The latter is usually a small organic molecule that activates or inhibits the function of a biomolecule of therapeutic interest, such as a protein. Any drug discovery endeavor is therefore much akin to finding the right key for a specific lock, with millions of organic molecules – or potential keys – known to date, and a nearly infinite number of possibilities. In silico techniques known as ‘computer-aided drug design’ allow scientists to save precious time and resources by helping the identification and optimization of the best candidates for a specific target, before heading to the experimental lab to synthesize and test their properties.

Why was SwissDrugDesign created in the first place?

They are hundreds of tools available to scientists to conduct CADD. With SwissDrugDesign, launched in 2010, we intended to provide users with a complete, interoperable, web-based pipeline. Today, SwissDrugDesign includes tools for molecular docking (i.e. finding the best fit between the potential drug and the targeted biomolecule), target prediction or the discovery of active compounds, all the way to pharmacokinetics and druglikeness. The latter allows predicting if a molecule has the suited properties to become an actual drug, based on its expected fate in the organism once administered.

What does a million jobs run mean?

Each job corresponds to the submission of at least one molecule on our tools by a user in order to perform a calculation. The figure of 1,000,000 was achieved thanks to an acceleration in the use of the tools, reaching more than 400,000 jobs in 2018, as compared to 280,000 in 2017 and 115’000 in 2016. All in all, our users return more and more frequently, showing that they seem not only to have perfectly adopted our tools but also to be satisfied with them.

How do you explain such remarkable increase in the use of the tools over the past couple of years?

One reason is that the historical tools, SwissDock and SwissParam – which have steadily increased their user base since 2010 – have been complemented in recent years by other tools, such as SwissADME, SwissTargetPrediction or SwissSimilarity, which have reached an even wider audience, as they target needs that only few other available resources can offer.
Another reason is that despite the large variety of CADD methods available online, the tools grouped under the SwissDrugDesign umbrella beneficiate from several advantages: (1) they are free of charge for academic research - a clear ‘plus’ in a field where tools can become quite expensive; (2) despite the innovative and professional-scale technologies behind the scene, we pay attention to create easy-to-use web interfaces, making our tools suitable even to non-specialists such as teachers or undergraduate students; (3) being both on the developer and user side of the tools – which we use as part of our own drug discovery projects and collaborations – we created pipelines of complementary approaches, covering a large repertoire of activities, with interoperable interfaces; (4) finally, some of the approaches are unique to SwissDrugDesign.
Finally, we benefit from SIB’s long-standing support, which allows us to maintain the tools in the long term. This is extremely reassuring for scientists, who need to insure the reproducibility of their results and keep access to the tools for the duration of their project.

What is 2019 holding for CADD experts?

New tools such as Swiss-PO are currently being developed in our group and will strengthen the SwissDrugDesign portfolio, as well as extending it to precision medicine. Swiss-PO will help predicting the impact of mutations encountered in the genome of cancer cells, when they are not already known. It will support the oncologists in the choice of the most appropriate treatment for each patient.
We will keep honing and updating the existing tools to maintain them at the edge of the domain: we are for instance collaborating with SIB’s UX team (User eXperience) to provide our users with improved web interfaces.