Application of Combinatorial Chemistry Science on Modern ... of Combinatorial Chemistry Science on Modern Drug Discovery J. Phillip Kennedy, Lyndsey Williams, Thomas M. Bridges, R

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  • Application of Combinatorial Chemistry Science on Modern DrugDiscovery

    J. Phillip Kennedy, Lyndsey Williams, Thomas M. Bridges, R. Nathan Daniels,David Weaver, and Craig W. Lindsley*

    Departments of Pharmacology and Chemistry, Vanderbilt Program in Drug DiscoVery, VanderbiltInstitute of Chemical Biology, Vanderbilt UniVersity Medical Center, Vanderbilt UniVersity,

    NashVille, Tennessee, USA 37232

    ReceiVed NoVember 19, 2007

    Drug discovery is a competitive discipline that requiresconstant innovation and refinement as a combination ofmarket, patient, and regulatory concerns require that com-panys balance their novel, clinically unvalidated moleculartargets with validated targets (KO, ASO, siRNA) becausethe attrition rate for novel targets is substantial. The dramaticconsolidations across the pharmaceutical industry in recentyears clearly point to the complexities of modern drugdiscovery. With the high attrition rates (many Phase II andIII efficacy failures) and limited human resources, drugdiscovery efforts must focus on a large and diverse collectionof molecular targets, and judiciously employ enablingtechnologies and new paradigms to simultaneously developmultiple early stage programs to balance risk. Importantly,the goal at the outset of a nascent program is to rapidlyprovide target validation in vivo with a novel small moleculeor deliver a quick kill for the program so that resourcescan be reassigned. Coupled with these concerns is the needto establish intellectual property to support broad genericpatent claims early in the development process becausechemical space is shrinking at an alarming rate and corporatescreening collections are becoming ubiquitous.1 Combina-torial chemistry emerged as a white knight with thepotential to address all of these major issues facing thepharmaceutical industry.15

    The 1990s witnessed a surge in combinatorial chemistrythat infiltrated both academic and industrial laboratories. Inthe pharmaceutical industry, combinatorial chemistry, in theform of classical solid-phase organic synthesis and largecompound libraries, promised to rapidly deliver new clinicalcandidates and drugs for companys struggling pipelines. Bythe early 2000s, it was clear to many companies that, afterhuge investments, combinatorial chemistry failed to deliveron its promises and most industrial combinatorial chemistrylaboratories were disbanded.1 Why? Drug discovery is notasimplenumbersgame.Synthesizinga libraryof1000-10 000molecules does not increase the odds of discovering apreclinical candidate. There are far too many caveats. Thefirst of these caveats is library design. If the scaffold on whicha 10 000-member library was prepared does not orientappended monomers in a biologically relevant way for a

    particular target, then the library will not afford activecompounds. Second, to generate a 10 000 member librarybased on a single template requires a large number ofmonomers, and depending on the functional groups em-ployed, the diversity in monomers may be slight, if any,providing a library of little diversity. As a result, all thecompounds are topologically similar, and the SAR willappear flat or, if poorly designed for a particular biologicaltarget, inactive. Indeed, Sauer and Schwartz developed acomputational tool that demonstrated that single-scaffoldlibraries, regardless of their size, are restricted to a limitednumber of molecular shapes, as opposed to smaller librariesdesigned around multiple scaffolds.6 Because molecularshape is intrinsically linked to biological activity, the greaterthe structural diversity in a library, the better the odds ofidentifying ligands for a broad range of biological targets.6

    Beyond structural diversity, the time required to design,synthesize, purify, and characterize a 1000-10 000-memberlibrary exponentially exceeded the time frame in which lead-optimization efforts operate; therefore, the project team hadusually moved into new chemical space before the librarywas finally ready to be evaluated, rendering it irrelevantbefore screening occurred. Compound characterization withlarge libraries was always suspect because it typically reliedsolely on mass spectroscopy, suggesting the desired masswas in the well with little quantiation which resulted inmany false hits and complex deconvulution exercises toidentify the active component in a well. Finally, solid-phase chemistry and large-library synthesis required ex-perts and was not embraced widely by classical medicinalchemists. It was felt that solid-phase synthesis was onlyuseful for large-library synthesis because a one-step func-tionalization required a minimum of three synthetic steps(Figure 1): a loading step, a monomer incorporation step,and a cleavage step (light, acid, base, or fluoride). Moreover,each library member had an artificial handle at the cleavagesite (unless a traceless linker was employed) usually anamine, acid, or hydroxyl moiety. Further contributing to thepoor acceptance of combinatorial chemistry by medicinalchemists was the lack of direct translation of solutionchemistry to the solid phase and the need to optimize theloading, diversity, and cleavage steps.1

    * To whom correspondence should be addressed. E-mail:

    J. Comb. Chem. XXXX, xxx, 000000 A

    10.1021/cc700187t CCC: $37.00 XXXX American Chemical SocietyPublished on Web 01/26/2008

  • While solid-phase chemistry has lost favor in smallmolecule drug discovery, it remains the preferred methodfor peptide synthesis, especially for peptide active pharma-ceutical ingredients (APIs) and peptide-containing polymers.7,8

    As of 2007, solid-phase peptide synthesis is the method ofchoice for all phases of development for peptide pharma-ceutical candidates, from discovery to commercial produc-tion.7 Peptide APIs represent a significant class of pharma-ceutical products with yearly sales in excess of $12 billion/year with a growth rate of 4%, and the majority of these(>50%) are prepared via solid-phase peptide synthesis.7 Onesuch peptide, Leuprolide, has achieved blockbuster statuswith worldwide sales in excess of $ 2 billion/year. Withoutquestion, solid-phase synthesis maintains a pivotal role inmodern drug discovery and development.8

    Historically, the scope, mission, and technology platformsof lead-optimization groups varied considerably across thedrug discovery industry leading to highly variable successrates.25 Some organizations had clearly defined hand-offscriteria that fragmented lead optimization into a hit-to-leadphase and a chemical lead-optimization phase. Hit-to-leadfocused on optimizing screening hits, usually by librarysynthesis (solution or solid phase), for target potency withminimal concern for selectivity, ancillary pharmacology, andpharmacokinetics (PK). Hits meeting certain potency criteriaand displaying robust structureactivity-relationships (SAR)would then be handed-off to a second group for the lead-optimization phase, wherein more classical medicinal chem-istry (single compound synthesis and intense DMPK profil-ing) would occur.25

    After several years of combinatorial chemistry back-lash,the science behind combinatorial chemistry is now at theforefront of modern drug discovery. As a result, leadoptimization in drug discovery has changed significantly inthe past five years, and no longer needs to be fragmentedinto separate hit-to-lead and lead-optimization phases; how-ever, centralized groups with expertise in parallel and librarysynthesis do add value.25 Major advances have been madein high-throughput screening (HTS) technologies, which haveenabled detection of novel modes of target modulation. Oncedominated by radioligand binding assays and limited todetection of classical agonists and antagonists by HTS,kinetic imaging plate readers, such as FDSS and FLIPR,allow for the identification of allosteric ligands which providepositive and negative modulation of both known and novel

    targets, offering new chemotypes and improved selectivityand safety profiles.9,10 Chemical lead optimization, fromevaluation of screening hits to preclinical candidate identi-fication, is now a seamless process drawing upon newtechnologies for accelerated synthesis, purification, andscreening. Directed, iterative compound libraries are nowemployed throughout the lead-optimization continuum withsingle compound synthesis restricted to an as needed basisfor complex, multistep chemistry. With the incorporation ofDMPK (drug metabolism and pharmacokinetics) inputs atthe initiation of a lead-optimization program, molecules arenot solely optimized for target potency and selectivity, butalso with respect to reducing protein binding, improvingpharmacokinetics, and diminishing CYP inhibition.114 More-over, closed loop work-flows are in place so that chemicalsynthesis and primary screening data operate on a one weekturn around for hundreds of compounds/week, with DMPKdata cycling every other week to improve compound designand provide expedited timelines for the development of proofof concept compounds to rapidly provide go/no go decisionpoints for novel molecular targets and deliver preclinicalcandidates with limited human resources. To avoid thenegative stigma surrounding combinatorial chemistry in bothindustrial and academic laboratories, this new paradigm forlead optimization is coined technology-enabled synthesisor TES; however, a more accurate moniker would betechnology-enhanced medicinal chemistry.1524

    Advances in High-Throughput Screening Technologies

    The science of combinatorial chemistry has also impactedand influenced high-throughput screening by advocating aphilosophy that values the ability to automate complexbiological assays, allow screening of difficult-to-screentargets and to detect novel mechanisms of target modulation.The historical HTS paradigms valued the use of automationto only increase throughput; however, the