commentary

Chemical and the limits of reductionism

Randall T Peterson

Chemical biology and systems biology have grown and evolved in parallel during the past decade, but the mindsets of the two disciplines remain quite different. As the inevitable intersections between the disciplines become more frequent, chemical biology has an opportunity to assimilate the most powerful ideas from systems biology. Can the integrationist mindset of systems biology liberate chemical biology from the compulsion to reduce everything to individual small molecule–target pairings?

Anyone following rock and roll music over the biological necessitated the creation of Systematic screens for integration, not last three decades may have faced the challeng- systems biology as a discipline. Clearly, chemical pairing ing and sometimes entertaining task of keeping biology and systems biology do share much in Both systems biology and chemical biology track of Prince Rogers Nelson. This musician common with more traditional disciplines. But have turned to systematic, large-scale studies led fans through a complex series of name the new names appear to have endowed both as their discovery engines. Using many of the changes, adopting at various times the names disciplines with a feeling of newness that is same technologies, studies in both disciplines Prince, Jamie Starr, Camille, Christopher Tracey, attracting bright trainees, research funding and often begin by developing simple, robust assays Madhouse, The Artist Formerly Known as institutional investment (not to mention new and churning through large collections of Prince, and even at one point an unpronounce- journals). Will history view the emergence of small molecules, genes or proteins. However, able ‘love symbol’. Debate continues today about chemical biology and systems biology as inflec- the purposes are usually quite different in the whether the name changes reflected substantial tion points in scientific progress, or will the two disciplines. Systems biology seeks to use creative differences in a rapidly evolving artist terms simply be viewed as generation-specific comparison between conditions as a means of or simply a marketing strategy aimed at creating monikers for pharmacology and physiology? understanding relationships, revealing higher Publishing Group http://www.nature.com/naturechemicalbiology

8 the impression of newness. Regardless of what we call them, the disci- order network structure and modeling the com- In a similar way, the christening of new sci- plines of chemical biology and systems biology plexity. By contrast, chemical biology in general entific disciplines can spark debate about the encompass a great deal of progressive, cutting- is still dominated by the mindset of pairing indi- © 200 significance and meaning of the new names, edge science. The fact that the terms are poorly vidual compounds and targets. In fact, one of and neither chemical biology nor systems biol- defined and have vague boundaries can be an the often-quoted overarching goals of chemical ogy has been exempt. In a job interview with asset, encouraging innovation and overlap with biology—to identify a small-molecule partner a Nobel prize–winning pharmacologist, I once other disciplines. As the disciplines co-evolve for every gene product in the genome—seems unwittingly touched off a polite tirade by declar- and intersect, both will benefit from a frequent to reflect a ‘one compound/one target’ mindset. ing my interest in chemical biology. Like other exchange of ideas. One of the most obvious As a result, systematic chemical biology stud- pharmacologists long involved in the study of opportunities for this is the borrowing by chem- ies (for example, high-throughput screens) the -biology interface, he questioned ical biology of systems biology’s integrationist are frequently focused on grinding through whether the name chemical biology truly mindset. Systems biologists generally seek to large libraries to identify interactions between reflected a substantially different field of study replace the reductionist ‘one student/one gene’ specific small molecules and a single target or was simply an attempt to dress pharmacology approach with an integrative approach that (Fig. 1a). Additionally, our preferred descriptors up in new clothes. Similarly, some physiologists strives to understand entire systems in their for compounds depend on this simplification. who have long advocated integrative approaches complexity. This integrationist mindset has not We describe aspirin as a cyclooxygenase inhibi- question why the influx of new techniques into yet permeated chemical biology very deeply, tor, atorvastatin as a 3-hydroxy-3-methylglu- although it is beginning to do so. Assimilating taryl (HMG) coenzyme A reductase inhibitor, Randall T. Peterson is at the Massachusetts more integrationist thinking could have posi- and lithium as a glycogen synthase kinase 3β General Hospital, Harvard Medical School, tive effects on many aspects of chemical biol- (GSK3β) inhibitor. These descriptors are useful 149 13th Street, Charlestown, Massachusetts ogy, including the ways we utilize screening data, and carry some information, but in reality these 02129, USA, and the Broad Institute of MIT describe compounds and use animal models. small molecules do much more than inhibit a and Harvard, 7 Cambridge Center, Cambridge, Ultimately, the most important impact may be single enzyme, and neither their beneficial nor Massachusetts 02142, USA. to lessen our dependence on reducing biology to their negative effects in humans are explained e-mail: [email protected] a series of small molecule–target pairings. fully by their actions on a single enzyme.

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by the diversity of assays, which may use radically Assays different experimental conditions, compound a b 123456789 A doses or readouts and may be conducted by B

C Functional classes labs with differing data standards. Nevertheless, D E integration of a compound’s data across numer- F G ous assays creates a ‘biological fingerprint’ (also H I J called a ‘chemical genomic profile’) that serves as K L a functional descriptor for the compound, with M N more information than the structural or text O

Small molecules P Q descriptors we typically use (Fig. 1b). R S Biological fingerprints can be used to cal- T culate the degree of functional similarity Systems biology Chemical biology Biological fingerprints between two compounds. More importantly, by comparing across both small-molecule and Figure 1 Evolving uses for systematic data collection. (a) The large-scale, systematic screens of genomic screens, it may become increasingly systems biology and chemical biology generally have different objectives. Whereas systems biology feasible to determine the relationship between seeks to understand the complex relationship of one biological element (for example, protein) to all a compound’s effects and the effects of genetic others, chemical biology has focused on pairing individual small molecules with a single target. (b) By comparing small-molecule activities across a spectrum of assays, biological fingerprints can be perturbations. The power of combined chemi- established that reflect the true, often complex, activity of a small molecule. cal and genomic screens and their potential for determining small-molecule mechanisms of action have been highlighted by recent proof- So, how might a systems biology mindset help originally intended to discover compound- of-concept studies in yeast and Drosophila mel- us relinquish our dependence on forcing every target pairs, can be used to create an integra- anogaster cells6–9. Importantly, describing and small molecule into a neat compound-target tive picture of a small molecule’s biological comparing small molecules using biological fin- pair? Hopefully, it will provide tools and lan- activity1–5. Databases such as PubChem and gerprints does not require the simplified pairing guage to help us conceptualize the simultaneous ChemBank that collect systematic assay data of a compound with a single protein target, but effects of a small molecule on numerous targets. enable assessment of an individual compound’s rather reflects some of the complexity present in Several groups have begun to demonstrate that activity across diverse biological assays. Of the bioactivity of most small molecules. high-throughput screening data, even those course, interassay comparisons are complicated Although biological fingerprints may be the most accurate way of describing the true func- tion of a compound, there is danger that they may be the equivalent of an unpronounceable a Biology ‘love symbol’—unique, but too unwieldy for Chemical biology regular use. Until we find better ways to visual- ize and verbalize the richness of these biologi- cal fingerprints, their utility is likely to remain Reduction Integration Nature Publishing Group http://www.nature.com/naturechemicalbiology

8 restricted to sophisticated computational or predictive settings with minimal impact on how b Nature’s bias O O MeO NH we think about small-molecule mechanisms of © 200 HN O MeO H action on a daily basis. OMe O O OH

OMe

O O O O 6 O MeO O Spreading out along the reduction- O H integration continuum H OH H O O O O Albert Einstein once advised, “Make everything HO OH as simple as possible, but not simpler.” Systems All possible naturally Selected for ability to target Natural products with produced small molecules cell-autonomous processes cell-autonomous activity biology, too, has been fueled by growing aware- ness of the limitations of reductionism and the Chemical biology’s bias value of balancing reductionist studies with those that embrace biological complexity. In contrast, chemical biology continues to trend toward the reductionist end of the reduction- integration continuum (Fig. 2a). For example, chemical biology papers are more likely than other biology papers to rely wholly on in vitro All natural and synthetic Typically selected for activity Molecules whose in vivo studies, a hallmark of reductionism. In a sam- small molecules in in vitro assays activities are poorly defined pling of papers from last year, only 17% of papers in Nature Chemical Biology included Figure 2 Is chemical biology biased toward reductionism? (a) While biological studies span the continuum from reductionist to integrationist, chemical biology relies heavily on reductionist any in vivo experiments, versus 42% of papers approaches. This may be due in part to the tendency of natural products to inhibit essential cellular in Nature. Why do chemical biologists tend processes (and hence to be accessible to in vitro study). (b) In addition, the limited training of many to avoid in vivo studies? Are in vivo processes chemists in in vivo biology creates a second bias against integrative approaches. such as physiology, embryonic development

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ab In vitro discovery In vivo use In vivo discovery and use Lower cholesterol

Protein Desired Statin Reduced Cardiac X effect inflammation benefit Target Other HTS Protein protein Undesired Desired activities? Y X Small effect effect No molecule Protein Undesired Lower cardiac Z Ezetimibe effect cholesterol benefit

Figure 3 Bridging the in vitro–in vivo divide. (a) Discovering small molecules using in vitro screens often leads to molecules that cause undesirable effects in vivo. Although high-throughput screening (HTS) may identify a small molecule that inhibits the target protein in vitro, the small molecule may also inhibit other proteins that cause undesired effects (left). When both discovery and use occur in vivo, it is possible to identify small molecules that perform the desired function, sometimes through complementary activities against multiple protein targets (right). (b) Some clinically successful compounds function through beneficial promiscuity. Although statins lower cholesterol and provide a cardiac benefit, noncholesterol effects of the statins also appear to be essential. Lowering cholesterol alone appears to be insufficient to provide a cardiac benefit.

and disease progression less interesting topics effective therapies by combining the advantages multiple, complementary activities. So, while to chemical biologists? Are chemistry and small of high-throughput screening with the physi- in vitro screens reinforce the compound-target molecules inadequate experimental tools for in ological relevance of integrative, in vivo systems. pairing mindset, in vivo screens open the pos- vivo studies? Probably not. More likely, scientists The zebrafish, in particular, is proving to be a sibility of selecting for beneficial promiscuity. with training in chemistry and chemical biology fruitful model for in vivo screening. Medium- Small-molecule promiscuity has been viewed may have less exposure to and experience with in scale, phenotype-based screens in zebrafish by some as a shameful blemish on chemical biol- vivo systems and therefore choose in vitro exper- have identified small molecules with fascinat- ogy’s reputation, and not without reason. Lack iments that are more comfortable for them. In ing in vivo functions, including suppression of of specificity frequently limits the utility of small addition, many of the natural products used by a congenital vascular defect, reversal of a cell molecules as experimental tools17, and poorly chemical biologists have natural antimicrobial cycle defect, expansion of the hematopoietic understood promiscuity can lead to clinical activity and tend to target fundamental, cell- stem cell pool, regulation of iron homeostasis disasters. Undoubtedly, selectivity will continue autonomous processes (Fig. 2b). Together, these and protection against ototoxicity12–16. Some of to be considered a virtue. But can chemical biol- factors have drawn chemical biology toward the these molecules are being developed preclini- ogists be convinced to find an interest in small reductionist end of the continuum. cally, and because they were discovered on the molecules with well-defined functional activities Because chemical biology is currently con- basis of their in vivo activity, they appear more but poorly defined biochemical activities? tributing disproportionately little to the fields likely to be safe and efficacious than compounds Pressure to embrace promiscuous molecules of developmental biology, behavioral science, discovered using in vitro assays. may come from, of all places, the clinic. In the physiology and other integrative in vivo fields of last few years, a major shift in perspective has Nature Publishing Group http://www.nature.com/naturechemicalbiology

8 study, there is an unmet need for chemical biol- Virtue in promiscuity? occurred in oncology. Whereas selective kinase ogists to move into these areas. Several recent Like biological fingerprints, it’s conceivable that inhibitors for clinical oncology were the objec- examples have illustrated the potential for posi- incorporating more in vivo studies into chemi- tive a decade ago, many experts now feel that © 200 tive impact. In some cases, the outcome has been cal biology will diminish our dependence on kinase inhibitors that hit multiple kinases may new chemical tools for traditional biologists. For the one compound–one target mentality. By be advantageous in treating cancer18. But this example, James Chen’s research at Stanford has screening for function rather than inhibition embracing of small-molecule promiscuity is helped to overcome long-standing obstacles in of a specific target, chemical biologists may largely based on the unanticipated and poorly developmental biology by creating chemical discover compounds that accomplish a desired understood success of ‘dirty’ kinase inhibitors tools that conditionally activate or inactivate objective through a complex mixture of activi- in clinical trials. Rational approaches for devel- gene expression in zebrafish during embryonic ties. For example, imagine creating animal dis- oping new promiscuous inhibitors are largely development10. More traditional developmen- ease models of anxiety, cancer or congenital non-existent, but somewhere at the interface tal biologists are rapidly adopting these tools. In birth defects and conducting high-throughput between chemical biology and systems biol- other cases, in vivo biology is helping to remove screens with the animals to discover compounds ogy lie the tools for predicting what mélange long-standing obstacles for chemical biology. that functionally alleviate the anxiety, regress the of activities will be most effective for specific For example, the problem of small-molecule tumor or suppress the developmental defect. cancer types, and which small molecules could target identification was recently addressed The most effective hits from these screens may provide the optimal activity profile19. Other by showing that genetic suppressor screens in be those that have multiple in vivo targets, just as important clinical mysteries are also likely to Caenorhabditis elegans can identify the targets some of the most effective drugs work precisely be answered through an understanding of of new compounds discovered in phenotype- because they hit multiple targets simultaneously simultaneous effects on multiple targets. Why based screens11. (Fig. 3a). In vivo screens like these would be does lowering cholesterol with a statin offer Beyond target identification, animals (pri- difficult to replace with reductionist in vitro health benefits, while lowering cholesterol with marily worms, flies and fish) are being used by screens, not only because of the inherent diffi- numerous other drug classes offers little benefit chemical biologists as in vivo assay systems for culty in predicting the optimal target for disease (Fig. 3b)? How do drugs without conventional medium- to large-scale small-molecule screens. reversal, but also because an in vitro screen may targets (for example, inhaled anesthetics) func- In vivo screens promise to shorten the path to not have the ability to select for compounds with tion? The tools and mindsets of systems biology

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may enable us to describe with great precision analyses easier, but standardization may run Shedden, K. Pharm. Res. 24, 1791–1802 (2007). the in vivo biological effects of these compounds, contrary to the quest for chemical and experi- 4. Guha, R. & Schurer, S.C. J. Comput. Aided Mol. Des. 22, 367–384 (2008). despite the fact that simple compound-target mental novelty that is and should remain a 5. Zhou, Y. et al. J. Chem. Inf. Model. 47, 1386–1394 pairs have been elusive. hallmark of chemical biology. The depth with (2007). which systems-level thinking can penetrate 6. Hoon, S. et al. Nat. Chem. Biol. 4, 498–506 (2008). 7. Hillenmeyer, M.E. et al. Science 320, 362–365 The times they are a-changin’ chemical biology remains to be seen, but our (2008). Though assimilating the best ideas of systems willingness to assimilate new ways of thinking 8. Eggert, U.S. et al. PLoS Biol. 2, e379 (2004). 9. Lamb, J. et al. Science 313, 1929–1935 (2006). biology into chemical biology is appealing in will undoubtedly determine whether chemi- 10. Esengil, H. & Chen, J.K. Mol. Biosyst. 4, 300–308 theory, the technical and cultural impediments cal biology is more than just a new name for (2008). are daunting. Reductionism has been success- decades-old ideas. 11. Kwok, T.C. et al. Nature 441, 91–95 (2006). 12. Peterson, R.T. et al. Nat. Biotechnol. 22, 595–599 ful because of its ability to limit the complexity (2004). and variability of biological systems. Will new ACKNOWLEDGMENTS 13. Stern, H.M. et al. Nat. Chem. Biol. 1, 366–370 technical and computational tools allow us to I thank J. Chen, P. Clemons, D. Kokel, C. MacRae and (2005). G. Sorensen for their stimulating ideas and comments 14. North, T.E. et al. Nature 447, 1007–1011 (2007). handle the complexity better than in the past, 15. Yu, P.B. et al. Nat. Chem. Biol. 4, 33–41 (2008). on the manuscript, and S. Kim for technical assistance or will systems-level analyses create a morass? 16. Owens, K.N. et al. PLoS Genet. 4, e1000020 (2008). with manuscript preparation. 17. Feng, B.Y., Shelat, A., Doman, T.N., Guy, R.K. & Integrative approaches are also likely to require Shoichet, B.K. Nat. Chem. Biol. 1, 146–148 (2005). greater coordination and standardization than 1. Bender, A. et al. Comb. Chem. High Throughput Screen. 18. Fojo, T. Oncologist 13, 277–283 (2008). many chemical biologists may find comfort- 10, 719–731 (2007). 19. Zhang, X., Crespo, A. & Fernandez, A. Trends Biotechnol. 20 2. Seiler, K.P. et al. Nucleic Acids Res. 36, D351–D359 26, 295–301 (2008). able . Standardized sets of screening molecules, (2008). 20. Inglese, J., Shamu, C.E. & Guy, R.K. Nat. Chem. Biol. protocols, and so on would make systems-level 3. Rosania, G.R., Crippen, G., Woolf, P., States, D. & 3, 438–441 (2007). Nature Publishing Group http://www.nature.com/naturechemicalbiology 8 © 200

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