DRUG DISCOVERY


and build’ fashion, whereby the rigid core is used as a chassis upon which further functionality is placed (Fig 3).


Relatively simple chemistries are often used, such as amide, ester and ether bond formation, allowing rapid exploration of structure-activity relationships. Where larger molecules are involved there is clearly an additional effect on the overall gross shape of the molecule, for example inducing kinks or bends in what might otherwise be a linear molecule. In other examples, the Enzacores are used as peripheral building blocks, where amines, alcohols and acids are sited towards the outer edges of the molecule to participate in events such as hydrogen bonding, rather than having a central structural role. In other instances they may be utilised for both binding and structure.


The examples shown illustrate Enzacore structures in action, leading to very potent biological activities reported in the patent literature. This type of molecule now features as an integral part of the discovery and development process. The molecules represent a relatively new type of building block for medicinal chemistry, requiring expertise in chiral technology, and especially biocatalysis, for their synthesis. This draws upon the long history of application of enzymes for the large-scale synthesis of pharmaceutical intermediates in clinical development.


New biological activity


Returning to the basic task of finding a new valuable biological activity, Enzacores have been formatted so that they are ready to use, and can be manipulated into advanced fragments for screening purposes in just one or two steps. It is worth explaining the processes that guide what structures are best to make, and that present the greatest chance of identifying new activity. Here the power of Prosarix’s computational chemistry platform is exploited, where it is used to design and create a large database of millions of compounds containing Enzacore structures.


Cl OH N O


BristolMyers Squibb CCR1 IC50 0.7nM


HN O


H N


OH Cl


F.HoffmannLa Roche Factor Xa Ki =6nM


Fig 3. Recent examples of highly potent compounds with an Enzacore-like chassis for aiding in ‘plug and build’ drug discovery.


S NO O O NH


These have been derivatised with common building blocks within the computer to create virtual structures that, if required, can be


synthesised with a good degree of confidence. To determine the most useful


structures to make, Prosarix’s newly developed AutoStereTM software was applied, whereby millions of


H2N


HO2C HO2C


HO NH2 CO2H CO2H


EnzacoresTM (underivatised)


NH HO NH2 Fig 2. Selected examples from Enzacore panels.


Enzacore structures were cross-checked to bioactive conformations of known drugs, metabolites and natural products. All of these structures were already known to bind strongly to important biological drug targets. From this analysis, we have identified the first sets of Enzacore structures to make, and what the best modifications are, to create novel advanced fragments that have the highest chance of finding biological activity. Before embarking on any synthesis, evaluation of the possible synthetic approaches is undertaken, and Enzagen’s knowledge of biocatalysis is utilised to design the optimum (and scaleable) route. Once prepared, the derivatised Enzacores (typically 50-100 derivatives covering two to four stereochemical shapes for any given Enzacore) can then be used in multiple approaches, from specialised fragment-based drug discovery methods that use NMR and X- ray crystallography, to standard screening assays against an isolated protein target, to high-information-content whole cell bioassays. Enzacores conform to the prevailing conventions such as Lipinski’s Rule of 5, and contain a careful balance of properties such as reasonable water solubility, but include


O NH F


suitably designed appending groups to assist binding properties. To date, the cores have been used to generate a number of potent compounds in a wide variety of biological assays such as histone deacetylase, anti- angiogenesis and kinases, thereby validating the design approaches discussed in this article.


Pharma and biotech companies are finding biological activity in a variety of in vitro assays using the Enzacores platform. Furthermore, with this initial result they then have the opportunity to further turn their biological readout into the beginnings of a new and valuable drug where they own and have control of all the IP. The easy-to-use format and the ability to further ‘tune’ the core is adding real value to their drug discovery programmes.


The potency of a hit molecule will undoubtedly have to be improved, and this can be done with standard chemical methods employed in SAR studies. Having multiple ‘handles’, the Enzacore-derived molecule can be built and extended in more than one way, and potency, selectivity and overall physical properties can be quickly explored using these. This contrasts with the large hit-finding libraries of old. These tended towards flatter ‘fully decorated’ molecules with more limited scope for further improvement. Furthermore, hand-in-hand with the use of Enzacores, and their ability to be imaginatively built out, the creation of robust intellectual property to protect the new structures is assured. A further aspect of the Enzacore panel is easy access to the various possible stereochemical shapes for the medicinal chemist. The availability of these different isomers allows a rapid study of their biological effects, and such peripheral studies can identify whether different isomers have


November/December 2011 sp2 33 H2N


NH2 CO2H


OH H2N CO2H H2N


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