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Sep 1, 2009 (Vol. 29, No. 15)

Demystifying Medicinal Chemistry Efforts

Bioisostere Tools Aim to Make Optimized and Innovative Chemistry More Accessible

  • Field-Based Approaches to Finding Bioisosteres

    Click Image To Enlarge +
    Figure 2. The results of a FieldStere experiment to find bioisosteres for the lactone portion of rofecoxib (red)

    Modern computing has facilitated the development of a more accurate and biologically intuitive view of active molecules than the 2-D structures used by medicinal chemists. Field-based methods work by representing the chemical structure, not as a 2-D skeleton, but as a series of surface properties (molecular electrostatic potentials) that correspond to what the protein target actually interacts with when binding to a compound in its bioactive conformation.

    Field-based tools mimic empirical observations of protein-drug interactions closely, and allow direct comparisons of the biologically important activities and properties of molecules completely independent of their 2-D structure.

    Biologists can now use field-based tools to identify bioisosteres. Systems such as Cresset BioMolecular Discovery’s FieldStere are powerful enough to scan a wide range of chemical space and provide biologically intuitive results. Such tools can quickly generate a range of potential lead molecules directly from a set of initial hits with or without an x-ray structure of the target, where the lead molecule is free from known IP, ADME, or toxicity issues.

    Using FieldStere is simple—enter an active hit structure, remove the portion of the molecule to be changed, specify any constraints on the type of chemistry required at the attachment points, and chose the fragment database to be searched. The results are automatically scored for similarity to the original compound and ranked in bioisosteric similarity order.

    In scoring bioisosteres it is essential to remember that molecular fields are a property of the whole molecule and not of the isolated replacement fragment.  Replacement fragments cannot be accurately assessed in isolation from the whole molecule as their properties can have a significant effect on the rest of the molecule. Scoring the whole molecule has an additional benefit in that the user is presented with a list of potentially active molecules with their full molecular properties such as rule-of-five violations and calculated LogP, which allows them to directly select molecules for synthesis more easily.

    The originality and synthesizability of compounds produced using field  technology is demonstrated in Figures 2 and 3. Using rofecoxib as a starting point, bioisosteres were sought that did not contain its lactone moiety. The chemistry space that was searched was limited by specifying that the replacement must contain an aromatic carbon attached to the remaining phenyl group. The results contain a range of bioisosteres from the reassuringly obvious such as Valdecoxib and Parecoxib to more interesting actives such as an analog of Etoricoxib. However, the results also contain nonobvious (and therefore potentially more innovative) bioisosteres such as the 12nM thiazolotriazole compound.

    Accurate bioisostere identification tools such as FieldStere can shorten development time and increase the novelty of the lead series. It allows biologists working in companies without a large dedicated medicinal chemistry team to quickly gain insight into the diversity of the available active chemical space and provide much better chemistry starting points to their outsourcing partners. This in turn can reduce the number of wasted syntheses and increase the range of chemical and IP space explored.

  • Click Image To Enlarge +
    Figure 3. FieldStere screenshot showing the COX-2 results


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