Abstract
From the start of the pharmaceutical research natural products played a key role in drug discovery and development. Over time many discoveries of fundamental new biology were triggered by the unique biological activity of natural products. Unprecedented chemical structures, novel chemotypes, often pave the way to investigate new biology and to explore new pathways and targets. This review summarizes the recent results in the area with a focus on research done in the laboratories of Novartis Institutes for BioMedical Research. We aim to put the technological advances in target identification techniques in the context to the current revival of phenotypic screening and the increasingly complex biological questions related to drug discovery.
Similar content being viewed by others
References
Akbulut Y, Gaunt HJ, Muraki K, Ludlow MJ, Amer MS, Bruns A, Vasudev NS, Radtke L, Willot M, Hahn S et al (2015) (−)-Englerin A is a potent and selective activator of TRPC4 and TRPC5 calcium channels. Angew Chem Int Ed Engl 54:3787–3791. doi:10.1002/anie.201411511
Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D et al (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483:603–607. doi:10.1038/nature11003
Brinkmann V, Billich A, Baumruker T, Heining P, Schmouder R, Francis G, Aradhye S, Burtin P (2010) Fingolimod (FTY720): discovery and development of an oral drug to treat multiple sclerosis. Nat Rev Drug Discov 9:883–897. doi:10.1038/nrd3248
Brotz-Oesterhelt H, Sass P (2014) Bacterial caseinolytic proteases as novel targets for antibacterial treatment. Int J Med Microbiol 304:23–30. doi:10.1016/j.ijmm.2013.09.001
Buerstner N, Roggo S, Ostermann N, Blank J, Delmas C, Freuler F, Gerhartz B, Hinniger A, Hoepfner D, Liechty B et al (2015) Gift from nature: cyclomarin A kills mycobacteria and malaria parasites using distinct modes of action. ChemBioChem. doi:10.1002/cbic.201500472
Burgett AW, Poulsen TB, Wangkanont K, Anderson DR, Kikuchi C, Shimada K, Okubo S, Fortner KC, Mimaki Y, Kuroda M et al (2011) Natural products reveal cancer cell dependence on oxysterol-binding proteins. Nat Chem Biol 7:639–647. doi:10.1038/nchembio.625
Carson C, Raman P, Tullai J, Xu L, Henault M, Thomas E, Yeola S, Lao J, McPate M, Verkuyl JM et al (2015) Englerin A agonizes the TRPC4/C5 cation channels to inhibit tumor cell line proliferation. PLoS ONE 10:e0127498. doi:10.1371/journal.pone.0127498
Chu J, Pelletier J (2014) Targeting the eIF4A RNA helicase as an anti-neoplastic approach. Biochim Biophys Acta. doi:10.1016/j.bbagrm.2014.09.006
Cully M (2014) Trial watch: next-generation antimalarial from phenotypic screen shows clinical promise. Nat Rev Drug Discov 13:717. doi:10.1038/nrd4457
Dantal J (2012) Everolimus: preventing organ rejection in adult kidney transplant recipients. Expert Opin Pharmacother 13:767–778. doi:10.1517/14656566.2012.662955
de Lichtervelde L, Antal CE, Boitano AE, Wang Y, Krastel P, Petersen F, Newton AC, Cooke MP, Schultz PG (2012) Euphohelioscopin A is a PKC activator capable of inducing macrophage differentiation. Chem Biol 19:994–1000. doi:10.1016/j.chembiol.2012.06.010
Eder J, Sedrani R, Wiesmann C (2014) The discovery of first-in-class drugs: origins and evolution. Nat Rev Drug Discov 13:577–587. doi:10.1038/nrd4336
Ferrari P, Vekey K, Galimberti M, Gallo GG, Selva E, Zerilli LF (1996) Antibiotics A21459 A and B, new inhibitors of bacterial protein synthesis. II. Structure elucidation. J Antibiot 49:150–154
Gao W, Kim JY, Anderson JR, Akopian T, Hong S, Jin YY, Kandror O, Kim JW, Lee IA, Lee SY et al (2015) The cyclic peptide ecumicin targeting ClpC1 is active against Mycobacterium tuberculosis in vivo. Antimicrob Agents Chemother 59:880–889. doi:10.1128/AAC.04054-14
Gao W, Kim JY, Chen SN, Cho SH, Choi J, Jaki BU, Jin YY, Lankin DC, Lee JE, Lee SY et al (2014) Discovery and characterization of the tuberculosis drug lead ecumicin. Org Lett 16:6044–6047. doi:10.1021/ol5026603
Giaever G, Shoemaker DD, Jones TW, Liang H, Winzeler EA, Astromoff A, Davis RW (1999) Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat Genet 21:278–283. doi:10.1038/6791
Goldberg EL, Romero-Aleshire MJ, Renkema KR, Ventevogel MS, Chew WM, Uhrlaub JL, Smithey MJ, Limesand KH, Sempowski GD, Brooks HL et al (2015) Lifespan-extending caloric restriction or mTOR inhibition impair adaptive immunity of old mice by distinct mechanisms. Aging Cell 14:130–138. doi:10.1111/acel.12280
Harrison DE, Strong R, Sharp ZD, Nelson JF, Astle CM, Flurkey K, Nadon NL, Wilkinson JE, Frenkel K, Carter CS et al (2009) Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature 460:392–395. doi:10.1038/nature08221
Hassan AQ, Kirby CA, Zhou W, Schuhmann T, Kityk R, Kipp DR, Baird J, Chen J, Chen Y, Chung F et al (2015) The novolactone natural product disrupts the allosteric regulation of Hsp70. Chem Biol 22:87–97. doi:10.1016/j.chembiol.2014.11.007
Hasskarl J (2014) Everolimus. Recent Results Cancer Res 201:373–392. doi:10.1007/978-3-642-54490-3_23
Hausenloy DJ, Boston-Griffiths EA, Yellon DM (2012) Cyclosporin A and cardioprotection: from investigative tool to therapeutic agent. Br J Pharmacol 165:1235–1245. doi:10.1111/j.1476-5381.2011.01700.x
Hirt SW, Bara C, Barten MJ, Deuse T, Doesch AO, Kaczmarek I, Schulz U, Stypmann J, Haneya A, Lehmkuhl HB (2013) Everolimus in heart transplantation: an update. J Transplant 2013:683964. doi:10.1155/2013/683964
Hoepfner D, Helliwell SB, Sadlish H, Schuierer S, Filipuzzi I, Brachat S, Bhullar B, Plikat U, Abraham Y, Altorfer M et al (2014) High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions. Microbiol Res 169:107–120. doi:10.1016/j.micres.2013.11.004
Hoepfner D, McNamara CW, Lim CS, Studer C, Riedl R, Aust T, McCormack SL, Plouffe DM, Meister S, Schuierer S et al (2012) Selective and specific inhibition of the Plasmodium falciparum lysyl-tRNA synthetase by the fungal secondary metabolite cladosporin. Cell Host Microbe 11:654–663. doi:10.1016/j.chom.2012.04.015
Hoffmann H, Kogler H, Heyse W, Matter H, Caspers M, Schummer D, Klemke-Jahn C, Bauer A, Penarier G, Debussche L et al (2015) Discovery, structure elucidation, and biological characterization of nannocystin A, a macrocyclic myxobacterial metabolite with potent antiproliferative properties. Angew Chem Int Ed Engl 54(35):10145–10148. doi:10.1002/anie.201411377
Jain V, Yogavel M, Oshima Y, Kikuchi H, Touquet B, Hakimi MA, Sharma A (2015) Structure of prolyl-tRNA synthetase-halofuginone complex provides basis for development of drugs against malaria and toxoplasmosis. Structure 23:819–829. doi:10.1016/j.str.2015.02.011
Junne T, Wong J, Studer C, Aust T, Bauer BW, Beibel M, Bhullar B, Bruccoleri R, Eichenberger J, Estoppey D et al (2015) Decatransin, a new natural product inhibiting protein translocation at the Sec61/SecYEG translocon. J Cell Sci 128:1217–1229. doi:10.1242/jcs.165746
Keller TL, Zocco D, Sundrud MS, Hendrick M, Edenius M, Yum J, Kim YJ, Lee HK, Cortese JF, Wirth DF et al (2012) Halofuginone and other febrifugine derivatives inhibit prolyl-tRNA synthetase. Nat Chem Biol 8:311–317. doi:10.1038/nchembio.790
Khan S, Sharma A, Belrhali H, Yogavel M, Sharma A (2014) Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin. J Struct Funct Genomics 15:63–71. doi:10.1007/s10969-014-9182-1
Krastel P, Roggo S, Schirle M, Ross NT, Perruccio F, Aspesi P Jr, Aust T, Buntin K, Estoppey D, Liechty B et al (2015) Nannocystin A: an elongation factor 1 inhibitor from myxobacteria with differential anti-cancer properties. Angew Chem Int Ed Engl 54:10149–10154. doi:10.1002/anie.201505069
Kurabachew M, Lu SH, Krastel P, Schmitt EK, Suresh BL, Goh A, Knox JE, Ma NL, Jiricek J, Beer D et al (2008) Lipiarmycin targets RNA polymerase and has good activity against multidrug-resistant strains of Mycobacterium tuberculosis. J Antimicrob Chemother 62:713–719. doi:10.1093/jac/dkn269
Lai K, Selinger DW, Solomon JM, Wu H, Schmitt E, Serluca FC, Curtis D, Benson JD (2013) Integrated compound profiling screens identify the mitochondrial electron transport chain as the molecular target of the natural products manassantin, sesquicillin, and arctigenin. ACS Chem Biol 8:257–267. doi:10.1021/cb300495e
LaMarche MJ, Leeds JA, Amaral A, Brewer JT, Bushell SM, Deng G, Dewhurst JM, Ding J, Dzink-Fox J, Gamber G et al (2012) Discovery of LFF571: an investigational agent for Clostridium difficile infection. J Med Chem 55:2376–2387. doi:10.1021/jm201685h
LaMarche MJ, Leeds JA, Dzink-Fox J, Gangl E, Krastel P, Neckermann G, Palestrant D, Patane MA, Rann EM, Tiamfook S et al (2012) Antibiotic optimization and chemical structure stabilization of thiomuracin A. J Med Chem 55:6934–6941. doi:10.1021/jm300783c
Leeds JA, Sachdeva M, Mullin S, Dzink-Fox J, Lamarche MJ (2012) Mechanism of action of and mechanism of reduced susceptibility to the novel anti-Clostridium difficile compound LFF571. Antimicrob Agents Chemother 56:4463–4465. doi:10.1128/AAC.06354-11
Leeds JA, Schmitt EK, Krastel P (2006) Recent developments in antibacterial drug discovery: microbe-derived natural products–from collection to the clinic. Expert Opin Investig Drugs 15:211–226. doi:10.1517/13543784.15.3.211
Leong FJ, Li R, Jain JP, Lefevre G, Magnusson B, Diagana TT, Pertel P (2014) A first-in-human randomized, double-blind, placebo-controlled, single- and multiple-ascending oral dose study of novel antimalarial Spiroindolone KAE609 (Cipargamin) to assess its safety, tolerability, and pharmacokinetics in healthy adult volunteers. Antimicrob Agents Chemother 58:6209–6214. doi:10.1128/AAC.03393-14
Mackinnon AL, Paavilainen VO, Sharma A, Hegde RS, Taunton J (2014) An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate. Elife 3:e01483. doi:10.7554/eLife.01483
Mali P, Esvelt KM, Church GM (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10:957–963. doi:10.1038/nmeth.2649
Mannick JB, Del Giudice G, Lattanzi M, Valiante NM, Praestgaard J, Huang B, Lonetto MA, Maecker HT, Kovarik J, Carson S et al (2014) mTOR inhibition improves immune function in the elderly. Sci Transl Med 6:268ra179. doi:10.1126/scitranslmed.3009892
Morris RP, Leeds JA, Naegeli HU, Oberer L, Memmert K, Weber E, LaMarche MJ, Parker CN, Burrer N, Esterow S et al (2009) Ribosomally synthesized thiopeptide antibiotics targeting elongation factor Tu. J Am Chem Soc 131:5946–5955. doi:10.1021/ja900488a
Mullane K, Lee C, Bressler A, Buitrago M, Weiss K, Dabovic K, Praestgaard J, Leeds JA, Blais J, Pertel P (2015) Multicenter, randomized clinical trial to compare the safety and efficacy of LFF571 and vancomycin for Clostridium difficile infections. Antimicrob Agents Chemother 59:1435–1440. doi:10.1128/AAC.04251-14
Nyfeler B, Hoepfner D, Palestrant D, Kirby CA, Whitehead L, Yu R, Deng G, Caughlan RE, Woods AL, Jones AK et al (2012) Identification of elongation factor G as the conserved cellular target of argyrin B. PLoS ONE 7:e42657. doi:10.1371/journal.pone.0042657
Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL (2007) Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat Rev Drug Discov 6:29–40. doi:10.1038/nrd2201
Petersen F (2006) Natural product research at Novartis Pharmaceuticals - a historical overview. In: Engel G, Herrling P (eds) Exploring the frontiers—in celebration of Albert Hofmann’s 100th birthday. Schwabe, Basel, pp 28–73
Powers MV, Clarke PA, Workman P (2008) Dual targeting of HSC70 and HSP72 inhibits HSP90 function and induces tumor-specific apoptosis. Cancer Cell 14:250–262. doi:10.1016/j.ccr.2008.08.002
Roemer T, Davies J, Giaever G, Nislow C (2012) Bugs, drugs and chemical genomics. Nat Chem Biol 8:46–56. doi:10.1038/nchembio.744
Rottmann M, McNamara C, Yeung BK, Lee MC, Zou B, Russell B, Seitz P, Plouffe DM, Dharia NV, Tan J et al (2010) Spiroindolones, a potent compound class for the treatment of malaria. Science 329:1175–1180. doi:10.1126/science.1193225
Sadlish H, Galicia-Vazquez G, Paris CG, Aust T, Bhullar B, Chang L, Helliwell SB, Hoepfner D, Knapp B, Riedl R et al (2013) Evidence for a functionally relevant rocaglamide binding site on the eIF4A-RNA complex. ACS Chem Biol 8:1519–1527. doi:10.1021/cb400158t
Santhosh S, Kumar P, Ramprasad V, Chaudhuri A (2015) Evolution of targeted therapies in cancer: opportunities and challenges in the clinic. Future Oncol 11:279–293. doi:10.2217/fon.14.198
Sasse F, Steinmetz H, Schupp T, Petersen F, Memmert K, Hofmann H, Heusser C, Brinkmann V, von Matt P, Hofle G et al (2002) Argyrins, immunosuppressive cyclic peptides from myxobacteria. I. Production, isolation, physico-chemical and biological properties. J Antibiot 55:543–551
Schirle M, Bantscheff M, Kuster B (2012) Mass spectrometry-based proteomics in preclinical drug discovery. Chem Biol 19:72–84. doi:10.1016/j.chembiol.2012.01.002
Schlecht R, Scholz SR, Dahmen H, Wegener A, Sirrenberg C, Musil D, Bomke J, Eggenweiler HM, Mayer MP, Bukau B (2013) Functional analysis of Hsp70 inhibitors. PLoS ONE 8:e78443. doi:10.1371/journal.pone.0078443
Schmitt EK, Riwanto M, Sambandamurthy V, Roggo S, Miault C, Zwingelstein C, Krastel P, Noble C, Beer D, Rao SP et al (2011) The natural product cyclomarin kills Mycobacterium tuberculosis by targeting the ClpC1 subunit of the caseinolytic protease. Angew Chem Int Ed Engl 50:5889–5891. doi:10.1002/anie.201101740
Singh R, Sharma M, Joshi P, Rawat DS (2008) Clinical status of anti-cancer agents derived from marine sources. Anticancer Agents Med Chem 8:603–617
Spillman NJ, Allen RJ, McNamara CW, Yeung BK, Winzeler EA, Diagana TT, Kirk K (2013) Na(+) regulation in the malaria parasite Plasmodium falciparum involves the cation ATPase PfATP4 and is a target of the spiroindolone antimalarials. Cell Host Microbe 13:227–237. doi:10.1016/j.chom.2012.12.006
Swinney DC, Anthony J (2011) How were new medicines discovered? Nat Rev Drug Discov 10:507–519. doi:10.1038/nrd3480
Trotter JF, Lizardo-Sanchez L (2014) Everolimus in liver transplantation. Curr Opin Organ Transpl 19:578–582. doi:10.1097/MOT.0000000000000127
Waller CF (2014) Imatinib mesylate. Recent Results Cancer Res 201:1–25. doi:10.1007/978-3-642-54490-3_1
White NJ, Pukrittayakamee S, Phyo AP, Rueangweerayut R, Nosten F, Jittamala P, Jeeyapant A, Jain JP, Lefevre G, Li R et al (2014) Spiroindolone KAE609 for falciparum and vivax malaria. N Engl J Med 371:403–410. doi:10.1056/NEJMoa1315860
Yeung BK, Zou B, Rottmann M, Lakshminarayana SB, Ang SH, Leong SY, Tan J, Wong J, Keller-Maerki S, Fischli C et al (2010) Spirotetrahydro beta-carbolines (spiroindolones): a new class of potent and orally efficacious compounds for the treatment of malaria. J Med Chem 53:5155–5164. doi:10.1021/jm100410f
Zeisel MB, Lupberger J, Fofana I, Baumert TF (2013) Host-targeting agents for prevention and treatment of chronic hepatitis C: perspectives and challenges. J Hepatol 58:375–384. doi:10.1016/j.jhep.2012.09.022
Acknowledgments
We would like to thank the management of our departments Developmental and Molecular Pathways and Center for Proteomic Chemistry for continued support and the freedom to explore novel biological space. Special thanks to the head of the Natural Products Unit Frank Petersen for careful reading of the manuscript and helpful suggestions.
Author information
Authors and Affiliations
Corresponding author
Additional information
Special Issue: Natural Product Discovery and Development in the Genomic Era. Dedicated to Professor Satoshi Ōmura for his numerous contributions to the field of natural products.
Rights and permissions
About this article
Cite this article
Schmitt, E.K., Hoepfner, D. & Krastel, P. Natural products as probes in pharmaceutical research. J Ind Microbiol Biotechnol 43, 249–260 (2016). https://doi.org/10.1007/s10295-015-1691-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10295-015-1691-9