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Getting predictive with bioisosteres
CAMBRIDGE & SHEFFIELD, U.K.— Early December saw Optibrium and Digital Chemistry, providers of software and database solutions for drug discovery, agree to collaborate on the integration of Digital Chemistry's BIOSTER database of precedented bioisostere replacements with Optibrium's StarDrop software suite. The combination is expected to allow drug discovery teams to "quickly identify novel, high-quality compounds based on the BIOSTER molecular transformations and prioritize these within StarDrop's intuitive environment that guides the design and selection of compounds with an optimal balance of properties," according to the companies.
Noting that StarDrop customers already use the software in a user-friendly and intuitive way, Optibrium CEO Matthew Segall goes on to explain that part of that software platform is a module called Nova, "and it takes things to the next step—from taking a lot of potential compounds and helping to quickly finding the best of them to actually generating new ideas," he tells ddn. "We launched that almost two years ago, and it's been very successful. What it does is take a compound and generate new, related structures and then prioritizes them against your project's objectives."
As part of the collaboration with Optibrium, the BIOSTER database will be converted into transformations that can be applied in StarDrop's Nova module, which automatically generates new, chemically relevant compound structures to stimulate the search for high-quality chemistry related to initial hit or lead compounds.
"What became clear to us is that Digital Chemistry's BIOSTER database was a unique repository of what chemists have done in the past in terms of successful chemistry replacements," Segall continues. "When you take a compound and look at well over 20,000 replacements that have been made in practice, you can find out which apply to your situation and decide which are most interesting to pursue within StarDrop's functionality. Putting our platform together with Digital Chemistry's database makes it possible to do great chemistry and improve overall characteristics of a compound."
The combination is also very effective for lead hopping, he points out.
"If you have problems or challenges with a compound, you can move to a new chemical space to see if you can maintain the biological activity you want while overcoming the hurdles of your previous line of exploration, or follow up with a backup series that might be as good as—or better than—your lead series," Segall says. "This is also useful for patent protection and patent busting, which are sort of flip sides of the same coin. You can explore alternative chemistry to see what may lie outside of the scope of your own patents so that you can see where competitors might find inroads to cut into your potential market share as well as see if there are areas that you could file new patents and secure addition intellectual property protection."
BIOSTER is no newcomer to the scene; the database has been around for some two decades. But as Julian Hayward, managing director of Digital Chemistry, notes, this collaboration provides a very convenient way of getting salient information from that database into the hands of chemists to predict novel compounds.
"This is the first time, to the best of our knowledge, that the data from BIOSTER has been provided in a predictive environment, and that is a huge leap," Hayward notes. "BIOSTER is a database that's been manually curated for more than 20 years, and it's exciting to realize a long-held ambition to allow the data to be used in a predictive way, dramatically improving the usefulness of the data and fulfilling a significant requirement for a large number of users. It's also worthwhile noting that this is a constantly evolving product, kept current with annual updates compiled by the database creator and leading expert in the field, Dr. István Ujváry."
The two companies were actually introduced by a third party familiar with both organizations, who wanted Digital Chemistry to do a project using StarDrop, Segall explains, and he recalls that after originally focusing on doing the specific project, the two companies quickly learned that there was a lot of potential to work together beyond that.
"Digital Chemistry has developed excellent databases and methods for cheminformatics, and we specialize in putting cheminformatics on the desktop of drug discovery scientists in an intuitive way. It occurred to us that there was a lot of synergy if we were to collaborate more completely," Segall says. The idea of collaborating on a product that combined their respective offerings became an official topic of discussion about a year ago, and the companies spent the early part of 2012 doing market research. "We talked to customers on an individual basis and made sure there was resonance in the greater market," Segall notes. "We got great feedback."
"Since its conception two decades ago, BIOSTER has strived to analyze and catalogue historically documented fragment replacement strategies to assist medicinal and pesticide chemists in their quest for new bioactive molecules," said Ujváry, managing director of iKem BT in Budapest, Hungary, and the developer of BIOSTER, in the news release about the collaboration. "The sophisticated Nova module of Optibrium's StarDrop software suite offers an exciting new tool for navigation through the chemical space of sets of bioisosteric and other transformations of this unique database. I am certain that the collaboration between Optibrium and Digital Chemistry will result in a versatile and popular new product."