Organic Synthesis Toward Small-Molecule Probes and Drugs

PCA ETR:PERSPECTIVE FEATURE: SPECIAL

Organic synthesis toward small-molecule probes and drugs

Stuart L. Schreiber1 Howard Hughes Medical Institute, Broad Institute of Harvard and MIT, Cambridge, MA 02142; and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138

Edited by Jack Halpern, University of Chicago, Chicago, IL, and approved March 10, 2011 (received for review February 28, 2011)

“Organic synthesis” is a compound-creating activity often focused on biologically active small molecules. This special issue of PNAS explores innovations and trends in the ﬁeld that are enabling the synthesis of new types of small-molecule probes and drugs. This perspective article frames the research described in the special issue but also explores how these modern capabilities can both foster a new and more extensive view of basic research in the academy and promote the linkage of life-science research to the discovery of novel types of small-molecule therapeutics [Schreiber SL (2009) Chem Bio Chem 10:26–29]. This new view of basic research aims to bridge the chasm between basic scientiﬁc discoveries in life sciences and new drugs that treat the root cause of human disease—recently referred to as the “valley of death” for drug discovery. This perspective article describes new roles that modern organic chemistry will need to play in overcoming this challenge.

Organic Synthesis of Small-Molecule use of dominant drug-resistant alleles that cesses may be the focus of future drug- Probes and Drugs encode fully functional protein targets of discovery efforts (21). Chemists and biologists have been ex- small-molecule modulators but that have When highly selective probes are com- ploring the functions of small molecules side chains that prevent binding by the bined with new methods to characterize in living systems for over a century, be- “native” small molecule and can, there- cells comprehensively, including the ge- ginning with the discovery of glucose, fore, be used to determine the relevance netic features of different cell lines, cor- amino acids, vitamins, hormones, neuro- of the target to the small molecule’s cel- relations can be derived that impact early transmitters, lipid mediators, and many lular activities (12). drug discovery. For example, correlations others. Especially during the second half These methods, however, require the between genetic variation and sensitivity of the 20th century, small molecules genetic engineering of model systems. The toward highly selective small-molecule have been used increasingly as probes greatest advances have been in the meth- probes may facilitate the development of (“tool compounds”) of life processes. ods that enable the discovery of small drugs tailored for the genetic features Notable early examples include the use of molecules targeting native proteins in of disease associated with individual small-molecule neurotoxins and neuro- cells and animals. Here, modern organic patients. Although this is perhaps most transmitters to probe ion channels and synthesis is playing an increasingly evident in diseases such as cancer where neurotransmission (1, 2), phorbol esters to prominent role. the penetrance of somatic mutations is probe protein kinases and signal trans- Organic synthesis is yielding probes of often high (22, 23), new approaches have duction (3, 4), and colchicine and cy- new types of targets and processes, in- been described that reveal such correla- tochalasins to illuminate the molecular cluding ones historically considered chal- tions in heritable disease as well (24). components of the cytoskeleton (5, 6). lenging, and these are informing drug Strategies Used by Organic Chemists Understanding the types of targets and discovery by testing new concepts in Organic synthesis can contribute to the processes that can be modulated with physiology with small molecules. Whereas small molecules helped define the princi- discovery of biologically active small mol- processes including intracellular signal ecules in several ways. By yielding struc- ples that underlie the rational discovery of transduction, gene expression, and protein small-molecule therapeutics (7). turally diverse small molecules having homeostasis were considered challenging features well suited for binding macro- This outline of small-molecule science is just 20 y earlier, small-molecule probes being developed more fully in the 21st molecules, it delivers starting points for of protein kinases, protein phosphatases, century (8). New approaches that ensure probes or drugs. Structure/activity rela- chromatin-modifying enzymes, and the exquisite specificity of small-molecule/ tionships resulting from the strategic proteasome demonstrated in the 1990s that macromolecule interactions are enabling synthesis of analogs are central to the these targets can be modulated with small inferences to be drawn with greater con- identification of optimized variants of the fi fidence, including the “bump/hole strat- molecules with outstanding selectivity starting compounds. Ef cient syntheses of egy” (9) used with protein phosphatases and potency (13, 14). These same target the optimized variants are essential for and kinases (10, 11). In this approach, classes are today central to many if not the practical applications of probes and drugs. researchers introduce by mutation a majority of drug-discovery efforts. More The research reports from authors in this “hole” in the drug target, typically by de- recent studies showing that small mole- special issue focus on advances in each creasing the size or increasing the flexi- cules can be discovered that (i) modulate of these three facets of organic synthesis. bility of an amino acid side chain at a site the cellular functions of extracellular Strikingly, the contributions illustrate, contacting the small-molecule modulator. growth factors (15) and intracellular tran- overall, two primary strategies for discov- A complementary substituent is added scription factors (16), proteins lacking ering probes and drugs. to the small molecule (the “bump”) that enzymatic activities, and (ii) disrupt pro- occupies the newly created hole in the tein/protein interactions (17, 18), activate protein encoded by the dominant drug- or inactivate autophagy (19), or cause cell Author contributions: S.L.S. wrote the paper. sensitive allele. This key substituent also types to adopt features characteristic of The author declares no conflict of interest. prevents binding to the native drug target. other cell types (“transdifferentiation”) This article is a PNAS Direct Submission. Related to this is the increasingly common (20) suggest that these targets and pro- 1E-mail: [email protected].

www.pnas.org/cgi/doi/10.1073/pnas.1103205108 PNAS | April 26, 2011 | vol. 108 | no. 17 | 6699–6702 Downloaded by guest on October 2, 2021 The first strategy is inspired by naturally occurring small molecules named “natural products.” For many years chemists have synthesized the natural products themselves with an eye toward advancing the capabilities of organic synthesis. This issue highlights instead short and modular syntheses of structural variants of specific natural products with an eye toward the discovery of small molecules having improved or novel properties as probes or drugs. Fig. 1. Advances in diastereoselective catalysis facilitated the discovery of eribulin. Variations on No- The second strategy is inspired by the zaki–Hiyama–Kishi reactions using chiral catalysts resulted in unprecedented control of stereochemistry structural complexity and diversity of the during key convergent couplings involving the formation of carbon/carbon bonds. These coupling re- entire ensemble of natural products, rather actions were central to an efficient synthesis of eribulin, a novel drug recently approved for the than by specific ones. Here, chemists use treatment of advanced breast cancer. modular syntheses of compounds having features such as intermediate ratios of atoms 3 2 novel structural elements, each introduced in naturally occurring small molecules. with sp or sp hybridization, multiple ster- by chemical synthesis, they acquired bi- These include the features that correlate eogenic elements, and rigidifying skeletal ological properties necessary for use in with highly selective binding by small elements. These features enable the discov- humans. Most strikingly, the daunting molecules recently reported by another ery of modulators of many disparate aspects challenge of synthesizing such a complex contributing author of this special issue, of biology, including ones currently viewed drug with the efficiency required for Paul Clemons. The Clemons study illus- as challenging. Chemists are learning to patient use worldwide was enabled by the trated that selective compounds (ones that incorporate these features strategically to development of new and powerful chem- bind only 1 of >100, sequence-unrelated facilitate downstream optimization and ical transformations, including carbon/ proteins) have an increased proportion manufacturing. carbon bond-forming reactions of large of atoms with sp3 hybridization, an in- Even though these synthetic chemistry efforts are relatively recent, data are be- synthetic fragments. The reactions are termediate degree of stereochemical ginning to emerge that enable retrospective enabled by transition metal catalysts that complexity, and rigidifying skeletal analyses of them. This special feature also deliver outstanding control of diaster- elements (29). illustrates computational science aimed eoselectivity. This new capability of or- The compound discovered by Rottmann at, among others, providing guiding prin- ganic synthesis enables systematic vari- et al. resulted from a short, modular di- ation of stereochemistry at a large number versity synthesis strategy (“build/couple/ ciples for improving the rate of success ” in either of the two paths being explored. of the stereogenic atoms in eribulin, pair ) that entails syntheses (or purchase) Two recent and striking advances of thereby illuminating structure/activity of small building blocks, including chiral these concepts in drug discovery are de- relationships (Fig. 1). ones, coupling them intermolecularly and scribed next. These vignettes have been pairing remaining functional groups in- Vignette: Organic Synthesis Exploring selected to illustrate the two approaches tramolecularly to yield rigidifying rings Novel Structural Features of High- noted above. (Fig. 2) (30). This strategy provides ster- Performance Hits in Screens and eochemically and skeletally diverse com- Vignette: Organic Synthesis Exploring Yielding a Promising Starting Point for pounds in a small number of steps. It is Structure/Activity Relationships of a New Mechanism-of-Action Malaria especially useful in optimization efforts a Complex Natural Product and Drug (medicinal chemistry in drug discovery Yielding a New Breast Cancer Drug An interdisciplinary effort involving syn- efforts) because it enables nearly every fi The US Food and Drug Administration thetic organic chemists and infectious atom to be modi ed without having to approved in late 2010 a new drug for disease biologists resulted in the discovery develop new synthetic pathways. Each as- treatment of metastatic breast cancers (25). of a small molecule that kills malarial pect of this synthetic strategy was used Eribulin’s structural complexity is un- parasites by a novel mechanism-of-action brilliantly in this promising advance in rivaled for a completely synthetic drug, (27). This study provides a striking exam- malaria drug discovery. and its discovery and large-scale man- ple of organic synthesis yielding modest- ufacturing represent a landmark for the sized collections of highly novel small Special Issue field of organic synthesis (Fig. 1). The molecules for challenging small-molecule This special issue of PNAS includes con- inspiration for eribulin comes from an screens. Only several months earlier, a tributions from 20 leading scientists in even more complex natural product, hal- malaria drug discovery effort was report- organic synthesis and related disciplines. ichondrin B, which was isolated from ed taking a similar approach but using The contributions highlight short and a marine sponge. One of the authors of >2 million candidate compounds having modular syntheses of structural variants this special issue, Yoshito Kishi, pioneered conventional structural features—most of natural products having novel proper- the advance of eribulin through collabo- notably enriched in heterocyclic rings ties as probes and drugs. They also de- rations at Harvard University and the and atoms having sp2 hybridzation—that scribe modular syntheses of compounds Eisai Research Institute (26). Exploiting yielded active compounds, but none that both poised for optimization and having their ability to synthesize halichondrin B have been advanced as drug candidates stereochemical complexity and skeletal and its structural variants, these chemists (28). In contrast, Rottmann et al. discov- diversity. They describe numerous illus- determined the influence of nearly every ered an advanced drug candidate having trations of the identification of small key structural feature found in halichon- antiparasitic activity via a new mechanism- molecules having novel biological acti- drin B. They discovered that a large com- of-action from merely 10,000 diverse vities. This special feature also highlights ponent of the natural substance could compounds synthesized by collaborating research at the interface of organic syn- be eliminated and that by adding back chemists to have structural features found thesis and computational science. These

6700 | www.pnas.org/cgi/doi/10.1073/pnas.1103205108 Schreiber Downloaded by guest on October 2, 2021 specificity in animals, may also have the potential to help redefine the scope of “basic research” in the academy with important consequences for drug discovery in the future. Here, I offer a proposal for achieving this goal (Fig. 3). Role of Organic Synthesis in Redefining Basic Research and Bridging the “Valley of Death” Academic research has provided many insights into biology that have medical Fig. 2. Build/couple/pair strategy of diversity synthesis yielding, following optimization studies of an potential. However, academic research initial “hit” in a live/dead malarial parasite screen, a promising malaria drug candidate having a novel often does not provide enough infor- mechanism of action. This strategy in organic synthesis can yield candidate probes or drugs having mation (“validation”) to help the phar- structural features that correlate with highly selective binding, including to proteins lacking enzymatic “ ” maceutical industry prioritize which activity. It can also yield compounds well suited for optimization ( follow-up chemistry for probes and insights merit the enormous investment “medicinal chemistry” for drugs). In this example, chemists synthesized or purchased building blocks (only two of many shown) having “orthogonal” functionality that permitted intermolecular coupling required to develop drugs. The United followed by intramolecular pairing of indole and imine functionality. Novel spirocyclic products of the States Cures Acceleration Network indicated Pictet–Spengler reaction yielded a starting point for a drug discovery effort in malaria. The (CAN) Act explicitly calls out this chasm ease of optimization of the starting point facilitated the discovery of an extraordinary compound that between basic scientific discoveries and eliminates the malaria parasite in an animal model by a novel mechanism of action (27). new treatments—labeling it the valley of death (31). CAN legislation was created to efforts are providing guiding principles Beyond the Special Issue: Organic provide funding necessary to bridge the for improving the rate of success in Synthesis in the Future valley of death. However, effective strategies are needed for CAN and other scien- either of the two paths being explored. The advances in organic synthesis outlined tific support mechanisms to achieve this Although many of the contributed papers in this special issue are facilitating the important goal. stress the foundational role of three discovery of powerful probes with in- Advances in organic synthesis and the additional areas of organic synthesis, — creasing frequency including ones that increased focus on the science of drug dis- (i) synthetic methodology, (ii)total modulate historically challenging targets covery in the academy in general provide synthesis, and (iii) medicinal chemistry, and processes. However, increasingly so- a useful foundation for bridging this gap the papers do not focus on these areas phisticated small-molecule probes, for in knowledge. Modern, interdisciplinary per se. example, ones that function with high projects are enabling basic research to progress to a more advanced stage where emerging concepts in human disease can be tested with small-molecule probes or drugs Conventional academic project: one approach / one method in physiologically relevant conditions.

basic insight, Sort through many insights; attempt to select The ability to manipulate DNA or research publication ones with potential for drug discovery RNA in cells and animals provides ex- Pharma traordinary tools to infer the functions of valley of death genes. However, these inferences often 21st century: crossing over the valley of death by redefining basic research lead to uncertainties in terms of the effects of small-molecule drugs targeting not DNA identify or RNA, but proteins encoded by genes. Multiple drug novel strands of candidate; drug This is all too familiar to drug developers, O disease perform approaches Me H who invest enormous time, effort, and N clinical trial resources only to determine in many in- Me O O O stances that the hypotheses lack medical H Multiple small-molecule probe: relevance. The frequent failure of drug strands of in vivo proof-of-concept technology candidates in phase 2 and phase 3 clinical capabilities trials due to unexpected lack of efficacy or unanticipated mechanism-based toxicity is the painful consequence. Testing Use small molecules to test emerging concepts in human disease in physiologically relevant in vivo emerging concepts with highly selective probes (or drugs in some cases) in defined models of human disease would enable Fig. 3. Proposal for bridging the valley of death. (Upper) Current academic research yields concepts pharmaceutical companies to prioritize potentially related to human health, but their relevance to human clinical outcomes is difficult drug-development investments with much to assess—thereby contributing to the valley of death (31). (Lower) Building on and expanding greater confidence. The impact of invest- recent models of academic research [for example, the National Institutes of Health-sponsored Molecular ments in basic research would be enhanced Libraries Probe Centers Network (MLPCN) and Centers of Excellence in Chemical Methodology and Library considerably. Design (CMLD)] provide a solution, where basic research spans new concepts in human disease that are To redefine basic research and to impact tested using small molecules in physiologically relevant settings. Here, it is anticipated that small- molecule probes (or drugs) with mechanisms of action that are rigorously established are used in disease therapeutic discovery as described above, models to test hypotheses. Positive outcomes provide much greater confidence in the merits of a full drug actually crossing over the valley of death by discovery and development program by, for example, the pharmaceutical industry. In some instances, for using small-molecule compounds to test example in rare and neglected diseases or ones requiring new approaches to clinical research, academic hypotheses (Fig. 3), future research un- efforts might also entail the development of the clinical candidate. dertakings would be structured in ways not

Schreiber PNAS | April 26, 2011 | vol. 108 | no. 17 | 6701 Downloaded by guest on October 2, 2021 readily funded currently. These under- small molecules having novel biologi- iii) Organic synthesis projects should be takings would tackle audacious challenges cal activities. Novel small molecules selected carefully with a critical anal- of relevance to human disease, incorporate available only via modern organic syn- ysis of the potential impact on hu- modern methods of understanding targets thesis should be made widely and freely man health as a key factor. These and mechanisms of action of tool com- available, especially for inclusion in projects provide a forum for advanc- pounds, and deliver advanced probes or ing an understanding of the core even “proof-of-concept drugs” that function small-molecule screening collections. in disease models. These models of disease ii) A disciplined approach to yielding principles of organic chemistry as ef- include human primary cells in three- probes and drugs that target the root fectively as projects less connected diminsional cocultures or organ cultures cause of disease,ratherthananoppor- to human health. However, they of- and genetically defined animals engineered tunistic one that exploits what is cur- fer the potential for extending our to mimic the precise basis of human disease. rently feasible, will advance the sci- definition of basic research and for Modern organic synthesis in the acad- ence of drug discovery. In some cases, actually bridging the valley of death. emy can contribute to this goal by providing this will require that organic synthesis Organic synthesis is a venerable field the following enhanced capabilities and be directed toward extremely challeng- materials: that is redefining itself, hopefully in a way ing drug targets and processes, ones that will accelerate the discovery of future i) Improved methods and strategies in viewed today as difficult to modulate therapeutics. The continued growth, re- organic synthesis will be needed, likely with small-molecule drugs but revealed direction, and evolution of the field is es- guided by advances in computational by human biology to be essential for sential for scientists to realize the promise science, to accelerate the discovery of safe and effective therapies. of human biology in the 21st century.

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