In practice, this idea has had two limitations that have prevented wide-scale adoption: the virtual libraries have rarely been carefully curated for true synthetic accessibility 8, and there were well-founded concerns that computational methods, such as molecular docking, were not accurate enough to prioritize true hits within this large space 9. Naturally, very few of these compounds can ever be actually synthesized because of time, cost and storage limitations, but one can imagine a computational method to prioritize those that should be pursued. Large numbers of molecules-certainly into the tens of billions, and likely many more-may be enumerated in a virtual library. However, as DNA-encoded libraries are restricted to reactions on DNA, reaction chemistries are limited to aqueous solutions, thereby limiting the type of chemical reactions and subsequent chemical libraries available with this technology 6.Ĭomputational approaches using virtual libraries are an attractive way to explore a much larger chemical space 7. DNA-encoded libraries 5, where molecules are synthesized on DNA that encodes their chemistry, begin to address this problem by offering investigators libraries of 10 8 molecules, sometimes more, in a single, highly compact format and multiple such libraries can be used in a single campaign. While the libraries physically screened in HTS were an enormous expansion on those used by classical, pre-molecular pharmacology 3, they nevertheless represent only a tiny fraction of possible ‘drug-like’ molecules 4. High-throughput screening (HTS) of libraries of 500,000 to 3 million molecules has been used since the 1990s 1, and multiple drugs have had their origins in this technique 2. Screening chemical libraries using biophysical assays has long been the dominant approach to discover new chemotypes for chemical biology and drug discovery.
#Pymol tutorial carlsson lab software#
Docking software described in the outlined protocol (DOCK3.7) is made freely available for academic research to explore new hits for a range of targets. These guidelines should be useful regardless of the docking software used. Additional controls are suggested to ensure specific activity for experimentally validated hit compounds. Here we outline best practices and control docking calculations that help evaluate docking parameters for a given target prior to undertaking a large-scale prospective screen, with exemplification in one particular target, the melatonin receptor, where following this procedure led to direct docking hits with activities in the subnanomolar range. Accordingly, it is important to establish controls, as are common in other fields, to enhance the likelihood of success in spite of these challenges. To accomplish this goal at speed, approximations are used that result in undersampling of possible configurations and inaccurate predictions of absolute binding energies. This allows the rapid and cost-effective exploration and categorization of vast chemical space into a subset enriched with potential hits for a given target. As computer efficiency has improved and compound libraries have grown, the ability to screen hundreds of millions, and even billions, of compounds has become feasible for modest-sized computer clusters. Structure-based docking screens of large compound libraries have become common in early drug and probe discovery.
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