From virtual screening to real compounds

Managing the procurement process to deliver plated compounds to your door

Cresset consulting services runs computational experiments to help you understand your chemistry better. The usual result from a project is a list of compounds to make or purchase. However, we can also go further and manage your procurement process so that we deliver plated, assay-ready compounds to your lab.

Cresset optimizes the compound selection process so that you get the best possible selection of compounds delivered to the next stage in the discovery process. We work with best- in-class chemistry and shipping providers to provide you with a single point of contact so that you end up with not only the answers you want, but also the actual compounds.

This can be particularly helpful when choosing compounds to purchase after a virtual screening project.

An up-to-date 3D database of available screening compounds

Cresset’s virtual screening database contains over 10 million compounds from over 20 different vendors. It is kept continually up to date from the catalogues and is a comprehensive source of available screening compounds.

We load the compounds into the database in the form of SMILES strings or SD files. In order to make this database searchable using our virtual screening engine Blaze, each 2D compound is expanded to a set of 3D conformations. These are minimized, and up to 100 conformers are stored for each compound. Fields are added to each conformer, enabling it to be compared to the query molecule for a potential match.

Easing the logistic challenge of dealing with multiple vendors

This database gives our customers a very broad selection of chemistry, as opposed to screening compounds from only one vendor. The downside is that the final results of a virtual screen may be 500 compounds from 20 different vendors, possibly with only a handful of compounds coming from some vendors. This leads to bureaucratic and shipping overheads. Each vendor charges a fixed amount per compound, plus a flat rate shipping fee, therefore the more compounds sourced per vendor, the cheaper the final total.

Cresset can help to deal with logistic difficulties in two ways. The first is to compare the results and suggest the same or very similar compounds from alternative vendors in order to reduce the number of vendors in the final list of compounds. The second is for us to handle the procurement process for you.

Case study: from virtual screening to plated compounds

We recently worked with a customer who came to us with a known target. They had a number of published active compounds and were looking for some new chemistry for some assays they had booked with a biology CRO.

Our virtual screening work resulted in recommendations for 250 screening compounds. For additional diversity, we used Spark to do some bioisosteric replacements around the core of the known active compounds. We used these new bioisosteres for a further virtual screen and used these results to recommend a further 50 compounds.

We then did further work to optimize the selection of compounds by looking at both alternative vendors for the same compounds, and highly similar compounds from alternative vendors. Where we had found very few compounds from one vendor, we identified alternatives from larger suppliers. At the end of this process we reduced the number of vendors for the 300 compounds from about 10 to 6. Of those 300, approximately 200 were sourced from only 2 vendors.

The customer chose to completely outsource the procurement of these compounds to Cresset.

Cresset managed the process, using a dedicated chemistry provider and specialist shipping agents. The compounds were bought from the various vendors, weighted, dissolved, plated and delivered to the biology CRO to be screened. The compound procurement for this project was multi-national, including the UK, Europe, Eastern Europe and the US. The final delivery was to a California-based biology CRO.

Not only did we recommend new compounds, we delivered the final plates to the biology CRO.

Translating computational results into real compounds

Outsourcing your chemistry logistics to Cresset as part of a computational chemistry project eases logistic challenges and smooths your supply chain. We can deliver not only the answers, but also the actual compounds.

Contact us to enquire about outsourcing a computational chemistry project.