Counting on natural products for drug design
Abstract
Natural products and their molecular frameworks have a long tradition as valuable starting points for medicinal chemistry and drug discovery. Recently, there has been a revitalization of interest in the inclusion of these chemotypes in compound collections for screening and achieving selective target modulation. Here we discuss natural-product-inspired drug discovery with a focus on recent advances in the design of synthetically tractable small molecules that mimic nature's chemistry. We highlight the potential of innovative computational tools in processing structurally complex natural products to predict their macromolecular targets and attempt to forecast the role that natural-product-derived fragments and fragment-like natural products will play in next-generation drug discovery.
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Natural compounds have shown advantages in terms of safety, effectiveness, and convenience in disease treatment.
“Natural compounds have shown advantages in terms of safety, effectiveness, and convenience in disease treatment31”
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Cites
Network pharmacology: the next paradigm in drug discovery
Hopkins, A. L. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.118 · Cited by 4,622 · see citing works
Baell, J. B., & Holloway, G. A. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm901137j · Cited by 3,963 · see citing works
Drug-like properties and the causes of poor solubility and poor permeability
Lipinski, C. A. (2000) · Journal of Pharmacological and Toxicological Methods · doi:10.1016/s1056-8719(00)00107-6 · Cited by 3,776 · see citing works
DrugBank: a knowledgebase for drugs, drug actions and drug targets
Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., & Hassanali, M. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm958 · Cited by 2,852 · see citing works
The re-emergence of natural products for drug discovery in the genomics era
Harvey, A. L., Edrada‐Ebel, R., & Quinn, R. J. (2015) · Nature Reviews Drug Discovery · doi:10.1038/nrd4510 · Cited by 2,601 · see citing works
The evolving role of natural products in drug discovery
Koehn, F. E., & Carter, G. T. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1657 · Cited by 2,579 · see citing works
Relating protein pharmacology by ligand chemistry
Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., & Shoichet, B. K. (2007) · Nature Biotechnology · doi:10.1038/nbt1284 · Cited by 2,402 · see citing works
Quantifying the chemical beauty of drugs
Bickerton, G. R., Paolini, G. V., Besnard, J., Mureşan, S., & Hopkins, A. L. (2012) · Nature Chemistry · doi:10.1038/nchem.1243 · Cited by 2,301 · see citing works
Natural products in drug discovery
Harvey, A. L. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.07.004 · Cited by 1,836 · see citing works
SwissTargetPrediction: a web server for target prediction of bioactive small molecules
Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O. A., & Zoete, V. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku293 · Cited by 1,811 · see citing works
Predicting new molecular targets for known drugs
Keiser, M. J., Setola, V., Irwin, J. J., Laggner, C., Abbas, A. I., Hufeisen, S. J., Jensen, N. H., Kuijer, M. B., Matos, R. C., Tran, T. B., et al. (2009) · Nature · doi:10.1038/nature08506 · Cited by 1,667 · see citing works
The ChEMBL bioactivity database: an update
Bento, A. P., Gaulton, A., Hersey, A., Bellis, L. J., Chambers, J. K., Davies, M., Krüger, F. A., Light, Y., Mak, L., McGlinchey, S., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1031 · Cited by 1,487 · see citing works
A ‘Rule of Three’ for fragment-based lead discovery?
Congreve, M., Carr, R. A. E., Murray, C. W., & Jhoti, H. (2003) · Drug Discovery Today · doi:10.1016/s1359-6446(03)02831-9 · Cited by 1,365 · see citing works
The role of ligand efficiency metrics in drug discovery
Hopkins, A. L., Keserü, G. M., Leeson, P. D., Rees, D. C., & Reynolds, C. H. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4163 · Cited by 1,181 · see citing works
PASS: prediction of activity spectra for biologically active substances
Lagunin, A. A., Stepanchikova, A. V., Filimonov, D. A., & Poroikov, V. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.8.747 · Cited by 1,164 · see citing works
Chemistry: Chemical con artists foil drug discovery
Baell, J. B., & Walters, M. A. (2014) · Nature · doi:10.1038/513481a · Cited by 1,048 · see citing works
Walters, W. P., Stahl, M. T., & Murcko, M. A. (1998) · Drug Discovery Today · doi:10.1016/s1359-6446(97)01163-x · Cited by 996 · see citing works
Large-scale prediction and testing of drug activity on side-effect targets
Lounkine, E., Keiser, M. J., Whitebread, S., Mikhailov, D., Hamon, J., Jenkins, J. L., Lavan, P., Weber, E., Doak, A. K., Côté, S., et al. (2012) · Nature · doi:10.1038/nature11159 · Cited by 880 · see citing works
Natural products: An evolving role in future drug discovery
Mishra, B. B., & Tiwari, V. K. (2011) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2011.07.057 · Cited by 866 · see citing works
The promise and peril of chemical probes
Arrowsmith, C. H., Audia, J. E., Austin, C., Baell, J., Bennett, J., Blagg, J., Bountra, C., Brennan, P. E., Brown, P. J., Bunnage, M. E., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1867 · Cited by 839 · see citing works
An analysis of FDA-approved drugs: natural products and their derivatives
Patridge, E. V., Gareiss, P. C., Kinch, M. S., & Hoyer, D. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.01.009 · Cited by 836 · see citing works
Chen, C. Y. (2011) · PLoS ONE · doi:10.1371/journal.pone.0015939 · Cited by 807 · see citing works
The rise of fragment-based drug discovery
Murray, C. W., & Rees, D. C. (2009) · Nature Chemistry · doi:10.1038/nchem.217 · Cited by 803 · see citing works
Lewell, X. Q., Judd, D. B., Watson, S. P., & Hann, M. M. (1998) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci970429i · Cited by 695 · see citing works
Drug–target interaction prediction: databases, web servers and computational models
Chen, X., Yan, C. C., Zhang, X., Zhang, X., Dai, F., Yin, J., & Zhang, Y. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbv066 · Cited by 658 · see citing works
From Nature to Drug Discovery: The Indole Scaffold as a ‘Privileged Structure’
Alves, F. R. S., Barreiro, E. J., & Fraga, C. A. M. (2009) · Mini-Reviews in Medicinal Chemistry · doi:10.2174/138955709788452649 · Cited by 606 · see citing works
Talalay, P., Long, M. J., & Prochaska, H. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.21.8261 · Cited by 595 · see citing works
SuperPred: update on drug classification and target prediction
Nickel, J., Gohlke, B.-O., Erehman, J., Banerjee, P., Rong, W. W., Goede, A., Dunkel, M., & Preißner, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku477 · Cited by 591 · see citing works
Macrocyclic Drugs and Clinical Candidates: What Can Medicinal Chemists Learn from Their Properties?
Giordanetto, F., & Kihlberg, J. O. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm400887j · Cited by 573 · see citing works
Antonchick, A. P., Gerding‐Reimers, C., Catarinella, M., Schürmann, M., Preut, H., Ziegler, S., Rauh, D., & Waldmann, H. (2010) · Nature Chemistry · doi:10.1038/nchem.730 · Cited by 570 · see citing works
Toward more realistic drug-target interaction predictions
Pahikkala, T., Airola, A., Pietilä, S., Shakyawar, S. K., Szwajda, A., Tang, J. P., & Aittokallio, T. A. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu010 · Cited by 564 · see citing works
Koch, М. A., Schuffenhauer, A., Scheck, M., Wetzel, S., Casaulta, M., Odermatt, A., Ertl, P., & Waldmann, H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503647102 · Cited by 544 · see citing works
Predicting drug metabolism: experiment and/or computation?
Kirchmair, J., Göller, A. H., Lang, D. H., Kunze, J., Testa, B., Wilson, I. D., Glen, R. C., & Schneider, G. (2015) · Nature Reviews Drug Discovery · doi:10.1038/nrd4581 · Cited by 507 · see citing works
Self-citationComputational approaches to natural product discovery
Medema, M. H., & Fischbach, M. A. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1884 · Cited by 495 · see citing works
Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs
Seidler, J. A., McGovern, S. L., Doman, T. N., & Shoichet, B. K. (2003) · Journal of Medicinal Chemistry · doi:10.1021/jm030191r · Cited by 477 · see citing works
Why Drugs Fail - A Study on Side Effects in New Chemical Entities
Schuster, D., Laggner, C., & Langer, T. (2005) · Current Pharmaceutical Design · doi:10.2174/138161205774414510 · Cited by 417 · see citing works
Charting, Navigating, and Populating Natural Product Chemical Space for Drug Discovery
Lachance, H., Wetzel, S., Kumar, K., & Waldmann, H. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300288g · Cited by 403 · see citing works
Reactive compounds and in vitro false positives in HTS
Rishton, G. M. (1997) · Drug Discovery Today · doi:10.1016/s1359-6446(97)01083-0 · Cited by 348 · see citing works
Clemons, P. A., Bodycombe, N. E., Carrinski, H. A., Wilson, J. A., Shamji, A. F., Wagner, B. K., Koehler, A. N., & Schreiber, S. L. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012741107 · Cited by 343 · see citing works
Multi-target approach for natural products in inflammation
Koeberle, A., & Werz, O. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.08.006 · Cited by 327 · see citing works
Huigens, R. W., Morrison, K. C., Hicklin, R. W., Flood, T. A., Richter, M. F., & Hergenrother, P. J. (2013) · Nature Chemistry · doi:10.1038/nchem.1549 · Cited by 323 · see citing works
Natural-product-derived fragments for fragment-based ligand discovery
Over, B., Wetzel, S., Grütter, C., Nakai, Y., Renner, S., Rauh, D., & Waldmann, H. (2012) · Nature Chemistry · doi:10.1038/nchem.1506 · Cited by 301 · see citing works
Synthesis of Natural Product Inspired Compound Collections
Kumar, K., & Waldmann, H. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200803437 · Cited by 301 · see citing works
Lee, M., & Schneider, G. (2001) · Journal of Combinatorial Chemistry · doi:10.1021/cc000097l · Cited by 291 · see citing works
Self-citationFAF-Drugs3: a web server for compound property calculation and chemical library design
Lagorce, D., Spérandio, O., Baell, J. B., Miteva, M. A., & Villoutreix, B. O. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv353 · Cited by 277 · see citing works
Translating biosynthetic gene clusters into fungal armor and weaponry
Keller, N. P. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1897 · Cited by 277 · see citing works
Aptula, A. O., & Roberts, D. W. (2006) · Chemical Research in Toxicology · doi:10.1021/tx0601004 · Cited by 262 · see citing works
Industrial natural product chemistry for drug discovery and development
Bauer, A., & Brönstrup, M. (2013) · Natural Product Reports · doi:10.1039/c3np70058e · Cited by 256 · see citing works
Ertl, P., Jelfs, S. P., Mühlbacher, J., Schuffenhauer, A., & Selzer, P. M. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060217p · Cited by 252 · see citing works
Botanical Drugs, Synergy, and Network Pharmacology: Forth and Back to Intelligent Mixtures
Gertsch, J. (2011) · Planta Medica · doi:10.1055/s-0030-1270904 · Cited by 251 · see citing works
Roche, O., Schneider, P., Zuegge, J., Guba, W., Kansy, M., Alanine, A. I., Bleicher, K., Danel, F., Gutknecht, E.-M., Rogers‐Evans, M., et al. (2001) · Journal of Medicinal Chemistry · doi:10.1021/jm010934d · Cited by 249 · see citing works
Self-citationNew Horizons for Old Drugs and Drug Leads
Cragg, G. M. L., Grothaus, P. G., & Newman, D. J. (2014) · Journal of Natural Products · doi:10.1021/np5000796 · Cited by 247 · see citing works
Biology-Oriented Synthesis: Harnessing the Power of Evolution
van Hattum, H., & Waldmann, H. (2014) · Journal of the American Chemical Society · doi:10.1021/ja505861d · Cited by 246 · see citing works
Bioactivity-Guided Navigation of Chemical Space
Bon, R. S., & Waldmann, H. (2010) · Accounts of Chemical Research · doi:10.1021/ar100014h · Cited by 246 · see citing works
Interactive exploration of chemical space with Scaffold Hunter
Wetzel, S., Klein, K., Renner, S., Rauh, D., Oprea, T. I., Mutzel, P., & Waldmann, H. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.187 · Cited by 227 · see citing works
Strategic Pooling of Compounds for High-Throughput Screening
Hann, M. M., Hudson, B. D., Lewell, X. Q., Lifely, R., Miller, L., & Ramsden, N. G. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci990423o · Cited by 227 · see citing works
Reker, D., Rodrigues, T., Schneider, P., & Schneider, G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320001111 · Cited by 226 · see citing works
Self-citationStoichiometry and Physical Chemistry of Promiscuous Aggregate-Based Inhibitors
Coan, K. E. D., & Shoichet, B. K. (2008) · Journal of the American Chemical Society · doi:10.1021/ja802977h · Cited by 222 · see citing works
Scaffold diversity of natural products: inspiration for combinatorial library design
Grabowski, K., Baringhaus, K. H., & Schneider, G. (2008) · Natural Product Reports · doi:10.1039/b715668p · Cited by 220 · see citing works
Self-citationNatural products as starting points for the synthesis of complex and diverse compounds
Morrison, K. C., & Hergenrother, P. J. (2013) · Natural Product Reports · doi:10.1039/c3np70063a · Cited by 219 · see citing works
ChemGPS-NP: Tuned for Navigation in Biologically Relevant Chemical Space
Larsson, J., Gottfries, J., Mureşan, S., & Backlund, A. (2007) · Journal of Natural Products · doi:10.1021/np070002y · Cited by 209 · see citing works
Reinvigorating natural product combinatorial biosynthesis with synthetic biology
Kim, E., Moore, B. S., & Yoon, Y. J. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1893 · Cited by 207 · see citing works
Amslinger, S. (2010) · ChemMedChem · doi:10.1002/cmdc.200900499 · Cited by 204 · see citing works
Filimonov, D. A., Poroikov, V., Borodina, Y. V., & Gloriozova, T. A. (1999) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci980335o · Cited by 198 · see citing works
Developing a Drug-like Natural Product Library
Quinn, R. J., Carroll, A. R., Pham, N. B., et al. (2008) · Journal of Natural Products · doi:10.1021/np070526y · Cited by 194 · see citing works
New natural products as new leads for antibacterial drug discovery
Brown, D. G., Lister, T., & May‐Dracka, T. L. (2013) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2013.12.059 · Cited by 187 · see citing works
(−)‐Englerin A is a Potent and Selective Activator of TRPC4 and TRPC5 Calcium Channels
Akbulut, Y., Gaunt, H. J., Muraki, K., Ludlow, M. J., Amer, M. S., Bruns, A. F., Vasudev, N. S., Radtke, L., Willot, M., Hahn, S., et al. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201411511 · Cited by 186 · see citing works
Multi-Targeted Natural Products Evaluation Based on Biological Activity Prediction with PASS
Lagunin, A., Filimonov, D., & Poroikov, V. (2010) · Current Pharmaceutical Design · doi:10.2174/138161210791164063 · Cited by 179 · see citing works
Multitarget approach for natural products in inflammation
Jude, S., & Gopi, S. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819218-4.00004-3 · Cited by 176 · see citing works
Virtual screening for the discovery of bioactive natural products
Rollinger, J. M., Stuppner, H., & Langer, T. (2007) · Birkhäuser Basel eBooks · doi:10.1007/978-3-7643-8117-2_6 · Cited by 168 · see citing works
Jöst, C., Nitsche, C., Scholz, T., Roux, L., & Klein, C. D. P. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5006918 · Cited by 167 · see citing works
Reutlinger, M., Koch, C. P., Reker, D., Todoroff, N. K., Schneider, P., Rodrigues, T., & Schneider, G. (2013) · Molecular Informatics · doi:10.1002/minf.201200141 · Cited by 166 · see citing works
Self-citationAvonto, C., Taglialatela‐Scafati, O., Pollastro, F., Minassi, A., Marzo, V. D., PETROCELLIS, L. D., & Appendino, G. (2010) · Angewandte Chemie International Edition · doi:10.1002/anie.201005959 · Cited by 158 · see citing works
Rollinger, J. M., Schuster, D., Danzl, B., Schwaiger, S., Markt, P., Schmidtke, M., Gertsch, J., Raduner, S., Wolber, G., Langer, T., et al. (2008) · Planta Medica · doi:10.1055/s-0028-1088397 · Cited by 141 · see citing works
Bioactivity-guided mapping and navigation of chemical space
Renner, S., van Otterlo, W. A. L., Domínguez, M., Möcklinghoff, S., Hofmann, B., Wetzel, S., Schuffenhauer, A., Ertl, P., Oprea, T. I., Steinhilber, D., et al. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.188 · Cited by 141 · see citing works
Revealing the macromolecular targets of complex natural products
Reker, D., Perna, A. M., Rodrigues, T., Schneider, P., Reutlinger, M., Mönch, B., Koeberle, A., Lamers, C., Gabler, M., Steinmetz, H., et al. (2014) · Nature Chemistry · doi:10.1038/nchem.2095 · Cited by 135 · see citing works
Self-citationBeckmann, H. S. G., Nie, F., Hagerman, C. E., Johansson, H., Tan, Y. S., Wilcke, D., & Spring, D. R. (2013) · Nature Chemistry · doi:10.1038/nchem.1729 · Cited by 135 · see citing works
Honokiol: A non-adipogenic PPARγ agonist from nature
Atanasov, A., Wang, J. N., Gu, S.-P., Bu, J., Kramer, M. P., Baumgartner, L., Fakhrudin, N., Ladurner, A., Malainer, C., Vuorinen, A., et al. (2013) · Biochimica et Biophysica Acta · doi:10.1016/j.bbagen.2013.06.021 · Cited by 130 · see citing works
Natural Products in Drug Discovery: Present Status and Perspectives
Molinari, G. (2009) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-1132-2_2 · Cited by 129 · see citing works
Narayan, R., Bauer, J. O., Strohmann, C., et al. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201307392 · Cited by 126 · see citing works
Drug discovery in the next decade: innovation needed ASAP
Bennani, Y. L. (2011) · Drug Discovery Today · doi:10.1016/j.drudis.2011.06.004 · Cited by 119 · see citing works
Binding of Quinolizidine Alkaloids to Nicotinic and Muscarinic Acetylcholine Receptors
Schmeller, T., Sauerwein, M., Sporer, F., et al. (1994) · Journal of Natural Products · doi:10.1021/np50111a026 · Cited by 115 · see citing works
Natural product-likeness score revisited: an open-source, open-data implementation
Jayaseelan, K. V., Moreno, P. A., Truszkowski, A., et al. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-106 · Cited by 102 · see citing works
Drug–target interaction prediction via chemogenomic space: learning-based methods
Mousavian, Z., & Masoudi‐Nejad, A. (2014) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1517/17425255.2014.950222 · Cited by 101 · see citing works
Du, L., Robles, A. J., King, J. B., Powell, D. R., Miller, A. N., Mooberry, S. L., & Cichewicz, R. H. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201306549 · Cited by 101 · see citing works
Probing chemical space with alkaloid-inspired libraries
McLeod, M. C., Singh, G., Plampin, J. N., et al. (2014) · Nature Chemistry · doi:10.1038/nchem.1844 · Cited by 96 · see citing works
Rationally Designed Multi-Targeted Agents Against Neurodegenerative Diseases
Geldenhuys, W. J., & der Schyf, C. J. V. (2013) · Current Medicinal Chemistry · doi:10.2174/09298673113209990112 · Cited by 92 · see citing works
Multi‐Objective Molecular De Novo Design by Adaptive Fragment Prioritization
Reutlinger, M., Rodrigues, T., Schneider, P., & Schneider, G. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201310864 · Cited by 90 · see citing works
Self-citationAn Enantioselective Inverse‐Electron‐Demand Imino Diels–Alder Reaction
Eschenbrenner‐Lux, V., Küchler, P., Ziegler, S., et al. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201309022 · Cited by 89 · see citing works
DeLorbe, J. E., Clements, J. H., Whiddon, B. B., & Martin, S. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100142y · Cited by 88 · see citing works
Natural product-like synthetic libraries
Thomas, G. L., & Johannes, C. W. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.05.022 · Cited by 82 · see citing works
Inflation of correlation in the pursuit of drug-likeness
Kenny, P. W., & Montanari, C. A. (2013) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-012-9631-5 · Cited by 80 · see citing works
Discovery of Neuritogenic Compound Classes Inspired by Natural Products
Dakas, P., Parga, J. A., Höing, S., et al. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201302045 · Cited by 77 · see citing works
Fakhrudin, N., Ladurner, A., Atanasov, A. G., et al. (2010) · Molecular Pharmacology · doi:10.1124/mol.109.062141 · Cited by 75 · see citing works
Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens
Barelier, S., Eidam, O., Fish, I., et al. (2014) · ACS Chemical Biology · doi:10.1021/cb5001636 · Cited by 75 · see citing works
Predicting Targeted Polypharmacology for Drug Repositioning and Multi- Target Drug Discovery
Liu, X., Zhu, F., H., X., Shi, Z., Yang, S., Wei, Y., & Chen, Y. (2013) · Current Medicinal Chemistry · doi:10.2174/0929867311320130005 · Cited by 74 · see citing works
Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery
Reutlinger, M., & Schneider, G. (2012) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2011.12.006 · Cited by 72 · see citing works
Self-citationTakayama, H., Jia, Z., Kremer, L., Bauer, J. O., Carsten Strohmann, B., Ziegler, S., Antonchick, A. P., & Waldmann, H. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201306948 · Cited by 72 · see citing works
Voigt, T., Gerding‐Reimers, C., Tran, T. T. N., Bergmann, S., Lachance, H., Schölermann, B., Brockmeyer, A., Janning, P., Ziegler, S., & Waldmann, H. (2012) · Angewandte Chemie International Edition · doi:10.1002/anie.201205728 · Cited by 72 · see citing works
Colloidal Aggregation and the in Vitro Activity of Traditional Chinese Medicines
Duan, D., Doak, A. K., Nedyalkova, L., & Shoichet, B. K. (2015) · ACS Chemical Biology · doi:10.1021/cb5009487 · Cited by 71 · see citing works
Hübel, K., Leßmann, T., & Waldmann, H. (2008) · Chemical Society Reviews · doi:10.1039/b704729k · Cited by 70 · see citing works
Reutlinger, M., Rodrigues, T., Schneider, P., & Schneider, G. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201307786 · Cited by 69 · see citing works
Self-citationEfficient discovery of bioactive scaffolds by activity-directed synthesis
Karageorgis, G., Warriner, S. L., & Nelson, A. S. (2014) · Nature Chemistry · doi:10.1038/nchem.2034 · Cited by 67 · see citing works
Revealing the Macromolecular Targets of Fragment‐Like Natural Products
Rodrigues, T., Reker, D., Kunze, J., Schneider, P., & Schneider, G. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201504241 · Cited by 66 · see citing works
Self-citationBauer, J., Waltenberger, B., Noha, S. M., et al. (2012) · ChemMedChem · doi:10.1002/cmdc.201200345 · Cited by 65 · see citing works
Identification of Pim Kinases as Novel Targets for PJ34 with Confounding Effects in PARP Biology
Antolín, A. A., Jalencas, X., Yélamos, J., & Mestres, J. (2012) · ACS Chemical Biology · doi:10.1021/cb300317y · Cited by 64 · see citing works
Švenda, J., Sheremet, M., Kremer, L., Maier, L., Bauer, J. O., Carsten Strohmann, B., Ziegler, S., Kumar, K., & Waldmann, H. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201500112 · Cited by 62 · see citing works
Nanomolar Inhibitors of the Transcription Factor STAT5b with High Selectivity over STAT5a
Elumalai, N., Berg, A., Natarajan, K., Scharow, A., & Berg, T. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201410672 · Cited by 61 · see citing works
Zhang, J., Wu, J., Hong, B., et al. (2014) · Nature Communications · doi:10.1038/ncomms5614 · Cited by 60 · see citing works
Ask the Experts: Past, Present and Future of the Rule of Five
Baell, J. B., Congreve, M., Leeson, P. D., et al. (2013) · Future Medicinal Chemistry · doi:10.4155/fmc.13.61 · Cited by 58 · see citing works
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Schuster, D., & Wolber, G. (2010) · Current Pharmaceutical Design · doi:10.2174/138161210791164072 · Cited by 57 · see citing works
Stabilization of Protein–Protein Interactions in chemical biology and drug discovery
Bier, D., Thiel, P., Briels, J. M., & Ottmann, C. (2015) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2015.05.002 · Cited by 53 · see citing works
Chemogenomic Approaches to Infer Drug–Target Interaction Networks
Yamanishi, Y. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-107-3_9 · Cited by 47 · see citing works
Accessing target information by virtual parallel screening—The impact on natural product research
Rollinger, J. M. (2008) · Phytochemistry Letters · doi:10.1016/j.phytol.2008.12.002 · Cited by 45 · see citing works
Machine Learning Estimates of Natural Product Conformational Energies
Rupp, M., Bauer, M. R., Wilcken, R., Lange, A., Reutlinger, M., Boeckler, F. M., & Schneider, G. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003400 · Cited by 44 · see citing works
Self-citationParkinson, E. I., Bair, J. S., Nakamura, B. A., Lee, H. Y., Kuttab, H. I., Southgate, E. H., Lezmi, S., Lau, G. W., & Hergenrother, P. J. (2015) · Nature Communications · doi:10.1038/ncomms7947 · Cited by 43 · see citing works
Schuster, D., Spetea, M., Music, M., Rief, S., Fink, M., Kirchmair, J., Schütz, J., Wolber, G., Langer, T., Stuppner, H., et al. (2010) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2010.05.071 · Cited by 43 · see citing works
Do, Q., Lamy, C., Renimel, I., et al. (2007) · Planta Medica · doi:10.1055/s-2007-990216 · Cited by 39 · see citing works
Zimmermann, T. J., Roy, S., Martinez, N. E., Ziegler, S., Hedberg, C., & Waldmann, H. (2013) · ChemBioChem · doi:10.1002/cbic.201200711 · Cited by 39 · see citing works
A Natural‐Product Switch for a Dynamic Protein Interface
Scheepstra, M., Nieto, L., Hirsch, A. K. H., Fuchs, S., Leysen, S., Lam, C. V., Panhuis, L. I. H., van Boeckel, C. A. A., Wienk, H., Boelens, R., et al. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201403773 · Cited by 38 · see citing works
Spotting and designing promiscuous ligands for drug discovery
Schneider, P., Röthlisberger, M., Reker, D., & Schneider, G. (2015) · Chemical Communications · doi:10.1039/c5cc07506h · Cited by 37 · see citing works
Self-citationDeorphaning pyrrolopyrazines as potent multi-target antimalarial agents.
Reker, D., Seet, M., Pillong, M., Koch, C. P., Schneider, P., Witschel, M., Rottmann, M., Freymond, C., Brun, R., Schweizer, B., et al. (2014) · Angewandte Chemie · doi:10.1002/anie.201311162 · Cited by 36 · see citing works
Self-citationVuorinen, A., Nashev, L. G., Odermatt, A., et al. (2013) · Molecular Informatics · doi:10.1002/minf.201300063 · Cited by 34 · see citing works
Mak, L., Liggi, S., Tan, L., et al. (2012) · Current Pharmaceutical Design · doi:10.2174/138161213804581855 · Cited by 30 · see citing works
Truncated militarinone fragments identified by total chemical synthesis induce neurite outgrowth
Schmid, F., Jessen, H. J., Burch, P., & Gademann, K. (2012) · MedChemComm · doi:10.1039/c2md20181j · Cited by 26 · see citing works
Tramadol--a true natural product?
Kusari, S., Tatsimo, S. J. N., Zühlke, S., Talontsi, F. M., Kouam, S., & Spiteller, M. (2014) · Angewandte Chemie · doi:10.1002/anie.201406639 · Cited by 26 · see citing works
‘Fuzziness’ in pharmacophore-based virtual screening and de novo design
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Ntie‐Kang, F., Lifongo, L. L., Judson, P. N., et al. (2014) · Journal of Molecular Modeling · doi:10.1007/s00894-014-2069-z · Cited by 22 · see citing works
Chemogenomic Strategies to Expand the Bioactive Chemical Space
Jacoby, E., & Mozzarelli, A. (2009) · Current Medicinal Chemistry · doi:10.2174/092986709789712862 · Cited by 21 · see citing works
Gupta, P. K., Barone, G. W., Gurley, B. J., et al. (2015) · Drug Metabolism and Disposition · doi:10.1124/dmd.114.059410 · Cited by 17 · see citing works
Polymer supported synthesis of a natural product-inspired oxepane library
Basu, S., & Waldmann, H. (2014) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2014.05.039 · Cited by 17 · see citing works
Structural enrichment of HTS compounds from available commercial libraries
Petrova, T., Chuprina, A., Parkesh, R., & Pushechnikov, A. O. (2012) · MedChemComm · doi:10.1039/c2md00302c · Cited by 16 · see citing works
Medicinal chemistry matters – a call for discipline in our discipline
Johnstone, C. (2012) · Drug Discovery Today · doi:10.1016/j.drudis.2012.01.010 · Cited by 16 · see citing works
Lewell, X. Q., Judd, D. B., WATSON, S. P., et al. (1998) · ChemInform · doi:10.1002/chin.199836303 · Cited by 15 · see citing works
Lowe, D. (2014) · Nature Chemistry · doi:10.1038/nchem.2074 · Cited by 14 · see citing works
Venkatraman, P. (2010) · Mini-Reviews in Medicinal Chemistry · doi:10.2174/138955710791384090 · Cited by 11 · see citing works
Molecular Targets of Natural Drug Substances: Idiosyncrasies and Preferences
Imming, P. (2010) · Planta Medica · doi:10.1055/s-0030-1250236 · Cited by 6 · see citing works
Coping with Polypharmacology by Computational Medicinal Chemistry
Schneider, G., Reker, D., Rodrigues, T., et al. (2014) · CHIMIA International Journal for Chemistry · doi:10.2533/chimia.2014.648 · Cited by 6 · see citing works
Self-citationHirai, G. (2014) · The Chemical Record · doi:10.1002/tcr.201402074 · Cited by 5 · see citing works
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Generative molecular design in low data regimes
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Self-citationModeling the expansion of virtual screening libraries
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Reactive-cysteine profiling for drug discovery
Maurais, A. J., & Weerapana, E. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.02.010 · Cited by 167 · see citing works
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker
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Ma, Q., Wang, S., Xue, H., Ni, L., Yuan, P., Shen, Y., Zheng, B., Wang, Q., Zhang, J., Wang, H., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61938-0 · Cited by 15 · see citing works
“Moreover,theiruseintraditionalmedicineprovideshelpfulreferences for ef fi ciency and safety 31 .”
Spampinato, M., Carota, G., Sferrazzo, G., Fuochi, V., Distefano, A., Ronsisvalle, S., Sipala, F., Giuffrida, R., Furneri, P. M., Di Rosa, M., et al. (2022) · Pharmaceutics · doi:10.3390/pharmaceutics14122845 · Cited by 14 · see citing works
- Authors
- Rodrigues, T., Reker, D., Schneider, P., & Schneider, G.
- Affiliations
- ETH Zurich (CH)
- Corresponding author
- Schneider, Gisbert
- Venue
- Nature Chemistry
- Published
- 2016-04-25
- Volume
- 8
- Issue
- 6
- Pages
- 531-541
- ISSN
- 1755-4330 (ISSN-L)
- 1755-4349
- OpenAlex
- W2345198528
- Cited by
- 1,250
- References
- 142
- Citations by year
- 2026: 84 · 2025: 129 · 2024: 136 · 2023: 131 · 2022: 166 · 2021: 150 · 2020: 135 · 2019: 120 · 2018: 90 · 2017: 77 · 2016: 30
- FWCI
- 8.19
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioactive natural compounds
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- natural products, natural product-inspired drug design, fragment-based drug discovery, privileged scaffolds, machine learning, target prediction, synthetic accessibility, molecular fragments, chemotypes, drug selectivity
- MeSH terms
- Rosuvastatin Calcium, Biological Products, Chemistry, Pharmaceutical, Drug Design, Molecular Structure, Macromolecular Substances, Drug Discovery
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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