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Chapter 2 - Exploring Biology with Small Organic Molecules

from Section one - Overviews

Published online by Cambridge University Press:  05 June 2012

Haian Fu
Affiliation:
Emory University, Atlanta
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Summary

From Chemical Genetics to Chemical Genomics

Small molecules have long been recognized as an invaluable part of human medicine. Well before chemistry, biology, and chemical genomics were established as scientific disciplines, people routinely used plants to treat and prevent illnesses. Not until the advent of modern science, however, were we able to isolate and identify the active ingredients that conferred on the flora around us such a vast array of effects. Along with synthetic and semisynthetic molecules, these naturally occurring compounds have formed the cornerstone of today's therapeutics and have provided a way of improving our understanding of fundamental biological processes.

Exploration of these processes using chemical genetics requires certain basic elements common to all studies: 1) a small molecule with good target specificity, 2) a protein of interest, 3) a phenotype that is being investigated, and 4) an assay or screen that will bring these elements together to provide useful information (Figure 2.1).

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Chemical Genomics , pp. 10 - 25
Publisher: Cambridge University Press
Print publication year: 2012

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References

Clamp, MFry, BKamal, MXie, XCuff, JLin, M. FKellis, MLindblad-Toh, KLander, E 2007 Distinguishing protein-coding and noncoding genes in the human genomeProc Natl Acad Sci U S A 104 19428Google Scholar
MacBeath, G 2001 Chemical genomics: what will it take and who gets to play?Genome Biol 2Google Scholar
Newman, D. JCragg, G. MSnader, K. M 2003 Natural products as sources of drugs over the period 1981–2002J Nat Prod 66 1022Google Scholar
Rouhi, A. M 2003 Rediscovering natural productsChem Eng News 81 77Google Scholar
Butler, M. S 2005 Natural products to drugs: natural product derived compounds in clinical trialsNat Prod Rep 22 162Google Scholar
Koehn, F. ECarter, G. T 2005 The evolving role of natural products in drug discoveryNat Rev Drug Discov 4 206Google Scholar
Kirschning, ATaft, FKnobloch, T 2007 Total synthesis approaches to natural product derivatives based on the combination of chemical synthesis and metabolic engineeringOrg Biomol Chem 5 3245Google Scholar
Kennedy, J 2008 Mutasynthesis, chemobiosynthesis, and back to semi-synthesis: combining synthetic chemistry and biosynthetic engineering for diversifying natural productsNat Prod Rep 25 25Google Scholar
Weissman, K. J 2007 Mutasynthesis – uniting chemistry and genetics for drug discoveryTrends Biotechnol 25 139Google Scholar
Schwecke, TAparicio, J. FMolnar, IKonig, AKhaw, L. EHaydock, S. FOliynyk, MCaffrey, PCortes, JLester, J. BBohm, G. AStaunton, JLeadlay, P. F 1995 The biosynthetic gene cluster for the polyketide immunosuppressant rapamycinProc Natl Acad Sci U S A 92 7839Google Scholar
Gregory, M. APetkovic, HLill, R. EMoss, S. JWilkinson, BGaisser, SLeadlay, P. FSheridan, R. M 2005 Mutasynthesis of rapamycin analogues through the manipulation of a gene governing starter unit biosynthesisAngew Chem Int Ed Engl 44 4757Google Scholar
Goss, R. JLanceron, S. EWise, N. JMoss, S. J 2006 Generating rapamycin analogues by directed biosynthesis: starter acid substrate specificity of mono-substituted cyclohexane carboxylic acidsOrg Biomol Chem 4 4071Google Scholar
Graziani, E. IRitacco, F. VSummers, M. YZabriskie, T. MYu, KBernan, V. SGreenstein, MCarter, G. T 2003 Novel sulfur-containing rapamycin analogs prepared by precursor-directed biosynthesisOrg Lett 5 2385Google Scholar
Eustaquio, A. SMoore, B. S 2008 Mutasynthesis of fluorosalinosporamide, a potent and reversible inhibitor of the proteasomeAngew Chem Int Ed Engl 47 3936Google Scholar
McGlinchey, R. PNett, MEustaquio, A. SAsolkar, R. NFenical, WMoore, B. S 2008 Engineered biosynthesis of antiprotealide and other unnatural salinosporamide proteasome inhibitorsJ Am Chem Soc 130 7822Google Scholar
Zhang, WTang, Y 2008 Combinatorial biosynthesis of natural productsJ Med Chem 51 2629Google Scholar
Breinbauer, RVetter, I. RWaldmann, H 2002 From protein domains to drug candidates – natural products as guiding principles in the design and synthesis of compound librariesAngew Chem Int Ed Engl 41 2879Google Scholar
Tan, D. SFoley, M. AShair, M. DSchreiber, S. L 1998 Stereoselective synthesis of over two million compounds having structural features both reminiscent of natural products and compatible with miniaturized cell-based assaysJ Am Chem Soc 120 8565Google Scholar
Zhu, JBienayme, H 2005 Multicomponent ReactionsWeinheim, GermanyWiley-VCH
Schreiber, S. L 2000 Target-oriented and diversity-oriented organic synthesis in drug discoveryScience 287 1964Google Scholar
Spring, D. R 2003 Diversity-oriented synthesis; a challenge for synthetic chemistsOrg Biomol Chem 1 3867Google Scholar
Tan, D. S 2005 Diversity-oriented synthesis: exploring the intersections between chemistry and biologyNat Chem Biol 1 74Google Scholar
Taylor, S. JTaylor, A. MSchreiber, S. L 2004 Synthetic strategy toward skeletal diversity via solid-supported, otherwise unstable reactive intermediatesAngew Chem Int Ed Engl 43 1681Google Scholar
Thomas, G. LSpandl, R. JGlansdorp, F. GWelch, MBender, ACockfield, JLindsay, J. ABryant, CBrown, D. FLoiseleur, ORudyk, HLadlow, MSpring, D. R 2008 Anti-MRSA agent discovery using diversity-oriented synthesisAngew Chem Int Ed Engl 47 2808Google Scholar
Comer, ERohan, EDeng, LPorco, J. A 2007 An approach to skeletal diversity using functional group pairing of multifunctional scaffoldsOrg Lett 9 2123Google Scholar
Wender, P. AVerma, V. APaxton, T. JPillow, T. H 2008 Function-oriented synthesis, step economy, and drug designAcc Chem Res 41 40Google Scholar
Cordier, CMorton, DMurrison, SNelson, AO’Leary-Steele, C 2008 Natural products as an inspiration in the diversity-oriented synthesis of bioactive compound librariesNat Prod Rep 25 719Google Scholar
Noren-Muller, AReis-Correa, IPrinz, HRosenbaum, CSaxena, KSchwalbe, H. JVestweber, DCagna, GSchunk, SSchwarz, OSchiewe, HWaldmann, H 2006 Discovery of protein phosphatase inhibitor classes by biology-oriented synthesisProc Natl Acad Sci U S A 103 10606Google Scholar
Lessmann, TLeuenberger, M. GMenninger, SLopez-Canet, MMuller, OHummer, SBormann, JKorn, KFava, EZerial, MMayer, T. UWaldmann, H 2007 Natural product-derived modulators of cell cycle progression and viral entry by enantioselective oxa Diels-Alder reactions on the solid phaseChem Biol 14 443Google Scholar
Noren-Muller, AWilk, WSaxena, KSchwalbe, HKaiser, MWaldmann, H 2008 Discovery of a new class of inhibitors of Mycobacterium tuberculosis protein tyrosine phosphatase B by biology-oriented synthesisAngew Chem Int Ed Engl 47 5973Google Scholar
Dean, P. M 2007 Chemical genomics: a challenge for de novo drug designMol Biotechnol 37 237Google Scholar
Arkin, M. RWells, J. A 2004 Small-molecule inhibitors of protein-protein interactions: progressing towards the dreamNat Rev Drug Discov 3 301Google Scholar
Chene, P 2006 Drugs targeting protein-protein interactionsChemMedChem 1 400Google Scholar
Wells, J. AMcClendon, C. L 2007 Reaching for high-hanging fruit in drug discovery at protein-protein interfacesNature 450 1001Google Scholar
Gestwicki, J. EMarinec, P. S 2007 Chemical control over protein-protein interactions: beyond inhibitorsComb Chem High Throughput Screen 10 667Google Scholar
Clackson, T 2006 Dissecting the functions of proteins and pathways using chemically induced dimerizationChem Biol Drug Des 67 440Google Scholar
Clackson, T 2007 Controlling protein-protein interactions using chemical inducers and disrupters of dimerizationChemical BiologySchreiber, S. LKapoor, T. MWess, GWeinheim, GermanyWiley-VCH
Corson, T. WAberle, NCrews, C. M 2008 Design and applications of bifunctional molecules: why two heads are better than oneACS Chem Biol 3 677Google Scholar
Sakamoto, K. MKim, K. BKumagai, AMercurio, FCrews, C. MDeshaies, R. J 2001 Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradationProc Natl Acad Sci U S A 98 8554Google Scholar
Schneekloth, J. SFonseca, F. NKoldobskiy, MMandal, ADeshaies, RSakamoto, KCrews, C. M 2004 Chemical genetic control of protein levels: selective in vivo targeted degradationJ Am Chem Soc 126 3748Google Scholar
Lee, HPuppala, DChoi, E.-YSwanson, HKim, K.-B 2007 Targeted degradation of the aryl hydrocarbon receptor by the PROTAC approach: a useful chemical genetic toolChemBioChem 8 2058Google Scholar
Koide, KFinkelstein, J. MBall, ZVerdine, G 2001 A synthetic library of cell-permeable moleculesJ Am Chem Soc 123 398Google Scholar
Kanoh, NHonda, KSimizu, SMuroi, MOsada, H 2005 Photo-cross-linked small-molecule affinity matrix for facilitating forward and reverse chemical geneticsAngew Chem Int Ed Engl 44 3559Google Scholar
Kotzyba-Hibert, FKapfer, IGoeldner, M 1995 Recent trends in photoaffinity labelingAngew Chem Int Ed Engl 34 1296Google Scholar
Fuwa, HTakahashi, YKonno, YWatanabe, NMiyashita, HSasaki, MNatsugari, HKan, TFukuyama, TTomita, TIwatsubo, T 2007 Divergent synthesis of multifunctional molecular probes to elucidate the enzyme specificity of dipeptidic gamma-secretase inhibitorsACS Chem Biol 2 408Google Scholar
Dorman, GPrestwich, G. D 2000 Using photolabile ligands in drug discovery and developmentTrends Biotechnol 18 64Google Scholar
Lim, H. SCai, DArcher, C. TKodadek, T 2007 Periodate-triggered cross-linking reveals Sug2/Rpt4 as the molecular target of a peptoid inhibitor of the 19S proteasome regulatory particleJ Am Chem Soc 129 12936Google Scholar
Peterson, J. RMitchison, T. J 2002 Small molecules, big impact: a history of chemical inhibitors and the cytoskeletonChem Biol 9 1275Google Scholar
Levine, M 1951 The action of colchicine on cell division in human cancer, animal, and plant tissuesAnn N Y Acad Sci 51 1365Google Scholar
Borisy, G. GTaylor, E. W 1967 The mechanism of action of colchicine. Binding of colchincine-3H to cellular proteinJ Cell Biol 34 525Google Scholar
Taylor, E. W 1965 The mechanism of colchicine inhibition of mitosis. I. Kinetics of inhibition and the binding of H3-colchicineJ Cell Biol 25 145Google Scholar
Weisenberg, R. CBorisy, G. GTaylor, E. W 1968 The colchicine-binding protein of mammalian brain and its relation to microtubulesBiochemistry 7 4466Google Scholar
Mohri, H 1968 Amino-acid composition of “tubulin” constituting microtubules of sperm flagellaNature 217 1053Google Scholar
Horwitz, S 1994 Taxol (paclitaxel): mechanisms of actionAnn Oncol 5 S3Google Scholar
Altmann, K. HPfeiffer, BArseniyadis, SPratt, B. ANicolaou, K. C 2007 The chemistry and biology of epothilones – the wheel keeps turningChemMedChem 2 396Google Scholar
Donovan, DVahdat, L. T 2008 Epothilones: clinical update and future directionsOncology (Williston Park) 22 408Google Scholar
Mayer, T. UKapoor, T. MHaggarty, S. JKing, R. WSchreiber, S. LMitchison, T. J 1999 Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screenScience 286 971Google Scholar
Yan, YSardana, VXu, BHomnick, CHalczenko, WBuser, C.A.Schaber, MHartman, G. DHuber, H. EKuo, L. C 2004 Inhibition of a mitotic motor protein: where, how, and conformational consequencesJ Mol Biol 335 547Google Scholar
Kapoor, T. MMayer, T. UCoughlin, M. LMitchison, T. J 2000 Probing spindle assembly mechanisms with monastrol, a small molecule inhibitor of the mitotic kinesin, Eg5J Cell Biol 150 975Google Scholar
Ingber, DFujita, TKishimoto, SSudo, KKanamaru, TBrem, HFolkman, J 1990 Synthetic analogues of fumagillin that inhibit angiogenesis and suppress tumour growthNature 348 555Google Scholar
Sin, NMeng, LWang, M.Q.Wen, J. JBornmann, W. GCrews, C. M 1997 The anti-angiogenic agent fumagillin covalently binds and inhibits the methionine aminopeptidase, MetAP-2Proc Natl Acad Sci U S A 94 6099Google Scholar
Griffith, E. CSu, ZTurk, B. EChen, SChang, Y. HWu, ZBiemann, KLiu, J. O 1997 Methionine aminopeptidase (type 2) is the common target for angiogenesis inhibitors AGM-1470 and ovalicinChem Biol 4 461Google Scholar
Yeh, J. RMohan, RCrews, C.M. 2000 The antiangiogenic agent TNP-470 requires p53 and p21CIP/WAF for endothelial cell growth arrestProc Natl Acad Sci U S A 97 12782Google Scholar
Zhang, YYeh, J. RMara, AJu, RHines, J. FCirone, PGriesbach, H. LSchneider, ISlusarski, D. CHolley, S. ACrews, C. M 2006 A chemical and genetic approach to the mode of action of fumagillinChem Biol 13 1001Google Scholar
Cirone, PLin, SGriesbach, H. LZhang, YSlusarski, D. CCrews, C. M 2008 A role for planar cell polarity signaling in angiogenesisAngiogenesis 11 347Google Scholar
Zheng, X. SChan, T. FZhou, H. H 2004 Genetic and genomic approaches to identify and study the targets of bioactive small moleculesChem Biol 11 609Google Scholar
Heitman, JMovva, N. RHall, M. N 1991 Targets for cell cycle arrest by the immunosuppressant rapamycin in yeastScience 253 905Google Scholar
Miyamoto, YMachida, KMizunuma, MEmoto, YSato, NMiyahara, KHirata, DUsui, TTakahashi, HOsada, HMiyakawa, T 2002 Identification of isoleucyl-tRNA synthetase as a target of the G1-specific inhibitor reveromycin AJ Biol Chem 277 28810Google Scholar
Sundberg, S. A. 2000 High-throughput and ultra-high-throughput screening: solution- and cell-based approachesCurr Opin Biotechnol 11 47Google Scholar
Zhang, J. HChung, T. DOldenburg, K. R 1999 A simple statistical parameter for use in evaluation and validation of high throughput screening assaysJ Biomol Screen 4 67Google Scholar
Auld, D. SThorne, NNguyen, D. TInglese, J 2008 A specific mechanism for nonspecific activation in reporter-gene assaysACS Chem Biol 3 463Google Scholar
Kwok, T. CRicker, NFraser, RChan, A. WBurns, AStanley, E. FMcCourt, PCutler, S. RRoy, P. J 2006 A small-molecule screen in yields a new calcium channel antagonistNature 441 91Google Scholar
MacRae, C. APeterson, R. T 2003 Zebrafish-based small molecule discoveryChem Biol 10 901Google Scholar
Peterson, R. TLink, B. ADowling, J. ESchreiber, S. L 2000 Small molecule developmental screens reveal the logic and timing of vertebrate developmentProc Natl Acad Sci U S A 97 12965Google Scholar
Khersonsky, S. MJung, D. WKang, T. WWalsh, D. PMoon, H. SJo, HJacobson, E. MShetty, VNeubert, T. AChang, Y. T 2003 Facilitated forward chemical genetics using a tagged triazine library and zebrafish embryo screeningJ Am Chem Soc 125 11804Google Scholar
Mitsopoulos, GWalsh, D. PChang, Y. T 2004 Tagged library approach to chemical genomics and proteomicsCurr Opin Chem Biol 8 26Google Scholar
MacBeath, GKoehler, A. NSchreiber, S. L 1999 Printing small molecules as microarrays and detecting protein-ligand interactions en masseJ Am Chem Soc 121 7967Google Scholar
Winssinger, NPianowski, ZDebaene, F 2007 Probing biology with small molecule microarrays (SMM)Top Curr Chem 278 311Google Scholar
Hergenrother, P. JDepew, K. MSchreiber, S. L 2000 Small-molecule microarrays: covalent attachment and screening of alcohol-containing small molecules on glass slidesJ Am Chem Soc 122 7849Google Scholar
Bryan, M. CFazio, FLee, H. KHuang, C. YChang, ABest, M. DCalarese, D. ABlixt, OPaulson, J. CBurton, DWilson, I. AWong, C. H 2004 Covalent display of oligosaccharide arrays in microtiter platesJ Am Chem Soc 126 8640Google Scholar
Kanoh, NKumashiro, SSimizu, SKondoh, YHatakeyama, STashiro, HOsada, H 2003 Immobilization of natural products on glass slides by using a photoaffinity reaction and the detection of protein-small-molecule interactionsAngew Chem Int Ed Engl 42 5584Google Scholar
Kanoh, NAsami, AKawatani, MHonda, KKumashiro, STakayama, HSimizu, SAmemiya, TKondoh, YHatakeyama, STsuganezawa, KUtata, RTanaka, AYokoyama, STashiro, HOsada, H 2006 Photo-cross-linked small-molecule microarrays as chemical genomic tools for dissecting protein-ligand interactionsChem Asian J 1 789Google Scholar
Dilly, S. JBell, M. JClark, A. JMarsh, ANapier, R. MSergeant, M. JThompson, A. JTaylor, P. C 2007 A photoimmobilisation strategy that maximises exploration of chemical space in small molecule affinity selection and target discoveryChem Commun (Camb)2808Google Scholar
Bradner, J. EMcPherson, O. MMazitschek, RBarnes-Seeman, DShen, J. PDhaliwal, JStevenson, K. EDuffner, J. LPark, S. BNeuberg, D. SNghiem, PSchreiber, S. LKoehler, A. N 2006 A robust small-molecule microarray platform for screening cell lysatesChem Biol 13 493Google Scholar
Bradner, J. EMcPherson, O. MKoehler, A. N 2006 A method for the covalent capture and screening of diverse small molecules in a microarray formatNat Protoc 1 2344Google Scholar
Vegas, A. JFuller, J. HKoehler, A. N 2008 Small-molecule microarrays as tools in ligand discoveryChem Soc Rev 37 1385Google Scholar
Bailey, S. NSabatini, D. MStockwell, B. R 2004 Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screensProc Natl Acad Sci U S A 101 16144Google Scholar
Schmitz, KHaggarty, S. JMcPherson, O. MClardy, JKoehler, A. N 2007 Detecting binding interactions using microarrays of natural product extractsJ Am Chem Soc 129 11346Google Scholar
Dove, A 2007 High-throughput screening goes to schoolNature Methods 4 523Google Scholar
Kaiser, J 2008 Industrial-style screening meets academic biologyScience 321 764Google Scholar

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