Exploring Chemical Space

Frontier of Chemistry

Shuli Mao 04/12/2008

Shuli Mao @ Wipf Group Page 1 of 40 4/15/2008 What is chemical space?

Chemical space is the space spanned by all possible (i.e. energetically stable) stoichiometrical combinations of electrons and atomic nuclei and topologies (isomers) in molecules and compounds in general. -----wilkipedia

Chemical space is defined as the total descriptor space that encompasses all the small carbon-based molecules that could in principle be created. (Descriptors: molecular mass, liphophilicity and topological features, etc.) -----Dobson, C. M. Chemical space and biology Nature 2004, 432, 824.

Shuli Mao @ Wipf Group Page 2 of 40 4/15/2008 Why we need to explore chemical space?

The estimated number of small carbon-based compounds is on the order of 1060. However, only a minute fraction of this chemical space has been explored. Given the vastness of chemical space, we need to explore chemical space efficiently to find biologically relevant chemical space (space in which biologically active compounds reside).

Dobson, C. M. Chemical space and biology Nature 2004, 432, 824.

• To understand biological systems especially in unknown area

• To develop potential drugs From 1994 to 2001, only 22 drugs that modulate new targets were approved. So far, less than 500 human proteins have been targeted by current drugs, which is a small portion of human proteins.

Lipinski, C; Hopkins, A. Navigating chemical space for biology and medicine Nature 2004, 432, 855.

Shuli Mao @ Wipf Group Page 3 of 40 4/15/2008 How to explore chemical space?

Three approaches:

(A) Target-Oriented Synthesis (B) Focused Synthesis (Medicinal Chemistry/ Combinatorial Chemistry) (C) Diversity-Oriented Synthesis

Burke, M. D.; Schreiber, S. L. A planning strategy for diversity-oriented synthesis Angew. Chem. Int. Ed. 2004, 43, 46.

Shuli Mao @ Wipf Group Page 4 of 40 4/15/2008 Comparison of Three Approaches

(A) Target-Oriented Synthesis (B) Focused Synthesis (Medicinal Chemistry/ Combinatorial Chemistry) (C) Diversity-Oriented Synthesis

Thomas, G. L.; Wyatt, E. E.; Spring, D. R. Enriching chemical space with diversity-oriented synthesis Curr Opin Drug Dis Dev 2006, 9, 700.

Shuli Mao @ Wipf Group Page 5 of 40 4/15/2008 Combinatorial Chemistry

The rapid synthesis and screening of a large number of different compounds at the same time - instead of one-at-a-time-manner- to identify agents with desired functional properties

Shuli Mao @ Wipf Group Page 6 of 40 4/15/2008 Classical VS. Combinatorial Approach

Classical approach: one at a time

Combinatorial approach: many at a time

www.aae.enscm.fr/anciens/94-mc/combchem.htm

Shuli Mao @ Wipf Group Page 7 of 40 4/15/2008 Synthetic Strategies towards Combinatorial Libraries

(A) Split-pool synthesis

Furka and co-workers pioneered the split-pool synthesis method for the synthesis of large peptide libraries in 1988; this approach is termed divide, couple and recombine synthesis by other workers

(B) Parallel synthesis

Jung, G. Combinatorial Chemistry:synthesis, analysis, screening; 1999

Shuli Mao @ Wipf Group Page 8 of 40 4/15/2008 Split-Pool Synthesis (One-Bead-One-Compound)

Shuli Mao @ Wipf Group Page 9 of 40 4/15/2008 Parallel Synthesis (One-Vessel-One-Compound)

Shuli Mao @ Wipf Group Page 10 of 40 4/15/2008 Synthetic Methodology for Organic Library Construction

• Solid-Phase Synthesis • Solution-Phase Synthesis

Solid-phase synthesis Solution-phase synthesis

Heterogeneous Homogeneous

Shuli Mao @ Wipf Group Page 11 of 40 4/15/2008 Solid-Phase Synthesis

Compound under construction is covalently attached to a swollen insoluble solid support (usually a resin bead) by a linker that can be cleaved under specific conditions with an appropriate reagent to give the target compound in solution later on.

Kennedy, J. P.; Williams, L.; Bridges, T. M.; Daniels, R. N.; Weaver, D.; Lindsley, C. W. Application of combinatorial science on modern drug discovery J. Com. Chem. 2008, ASAP.

Shuli Mao @ Wipf Group Page 12 of 40 4/15/2008 Solid-Phase Peptide Synthesis (SPPS)

“Merrifield’s publication of SPPS method completely revolutionized the field, both from the perspective of accelerating research and discovery, and also because of its now widespread use for the manufacture of peptides for use as active pharmaceutical ingredients (APIs).”

Peptide APIs: yearly sales in excess of $12 billion with a growth rate of ~4% and majority (>50%) are prepared via SPPS

Leuprolide: a blockbuster drug with worldwide sales in excess of $2 billion/year is prepared via SPPS Leuprolide

Verlander, M. Industrial applications of solid-phase peptide synthesis-a status report Int. J. Pep. Res. Ther. 2007, 13, 75.

Shuli Mao @ Wipf Group Page 13 of 40 4/15/2008 Microwave-Assisted SPPS

Easy reagent separation; Eliminates losses of product during filtration, recrystallization; MW heating used to minimize reaction time, Completion of reaction by excess reagents; improve peptide yield and Each step can be monitored by Nihydrin test reduce epimerization problem

Katritzky, A. R. Microwave-assisted solid-phase peptide synthesis utilizing N-Fmoc-protected (α-aminoacyl)benzotriazoles Chem. Bio. Drug. Des. 2007, 70, 465.

Shuli Mao @ Wipf Group Page 14 of 40 4/15/2008 Solid-Phase Synthesis of Dysidiolide Analogs as Phosphastase Inhibitors

O O O H O

O O 1) TMS OTf EtP -Ph I, nBuLi 2) PTS A 3 endo:exo= 91:9 endo:endo’ = 95:5 OHC dr = 87:4:8.9:0.1

O O 1) O2, EtiPr2N, 3- br om ofur an r os ebengal, hv 1) Ph 3PCH 2OMeCl 2) pyr idinium p- toluene nBuLi 2) Grubss 2nd sulfonate Gen cat

HO OH CHO OH O O Employment of structural frameworks O of biologically active natural products Overall yield: 14% (11 steps); as a guilding principle for library development average yield: 84% per step Waldmann et al Natural products are biologically validated starting points in structure space for compound library development: solid-phase synthesis of dysidiolide-derived phosphatase inhibitors Angew. Chem. Int. Ed. 2002, 41, 307.

Shuli Mao @ Wipf Group Page 15 of 40 4/15/2008 Solution-Phase Synthesis

P Tag S P + B (excess) + Byproduct X A + B (excess) B Tag S X

Tag Method of Phase Separation

Polymer Filtration pH adjusted LLE or Ionizable group ion-exchange SPE

Fluorous tag 3-Phase LLE (heavy) or fluorous SPE (light)

Scavenging reagents were used to form either covalent or ionic bond with excess reagents or reaction byproduct; In general terms, scavenging can be considered a ‘phase-switching” technique, wherein a chemoselective reaction Is employed to switch the phase of one product relative to another by virtue of a “tag” attached to the scavenging reagent.

Kennedy, J. P.; Williams, L.; Bridges, T. M.; Daniels, R. N.; Weaver, D.; Lindsley, C. W. Application of combinatorial science on modern drug discovery J. Com. Chem. 2008, ASAP.

Shuli Mao @ Wipf Group Page 16 of 40 4/15/2008 Solution-Phase Synthesis Using Fluorous Tag

Antitumor Insulin receptor activator

O SO Cl BP in 2 P d( PPh 3)4, M eO B r 1) 3-Iodoindole, 88% Tl 2CO 3, quant

2) PdCl2(dppf )2, N OM e C 8F17 Bs Rf HBpin, 88% 8 O O M eO Br N B sRf8 B Pin B r OMe H O N O N M e TIP S O N M eO 1) Pd(P Ph 3) 4, M eO Tl 2CO3 1) M eI, Cs2CO3, 96% OMe 2) CsF 2) M g, NH 4Cl, 95% OMe O 88% ( 2 steps) N B sRf N O 8 H

Kasahara, T.; Kondo, Y. Fluorous-tagged indolylboron for the diversity-oriented synthesis of biologically-attractive bisindole derivatives Chem. Commun. 2006, 891.

Shuli Mao @ Wipf Group Page 17 of 40 4/15/2008 Solution-Phase Synthesis Using Fluorous Tag

Solid-phase synthesis of bisindole derivatives is hard to monitor, fluorous synthesis made it easier; Pd-cat

coupling is used consecutively; New sulfonamide type tag (Rf8-Bs) was developed.

Shuli Mao @ Wipf Group Page 18 of 40 4/15/2008 Comparison of Combinatorial Library and DOS Library

• Combinatorial library: (a) Tens of thousand to millions of compounds; (b) Structures are not very complex (c) May have a specific target

• DOS library: (a) Tens to hundreds of compounds; (b) Most have cyclic architectures with many stereocenters and resemble natural product; (c) DOS are utilized as small-molecule chemical probes for understanding cellular processes and are not biased toward a specific biological target

Shuli Mao @ Wipf Group Page 19 of 40 4/15/2008 Diversity-Oriented Synthesis-1st Example

Tempest, P. A.; Armstrong, R. W. Cyclobutenedione derivatives on solid support: toward multiple core structure libraries J. Am. Chem. Soc. 1997, 119, 7607.

Shuli Mao @ Wipf Group Page 20 of 40 4/15/2008 Diversity-Oriented Synthesis

Tan, D. S.; Foley, M. A.; Shair, M. D.; Schreiber, S. L. Stereoselective synthesis of over two million compounds having structural features both reminiscent of natural products and compatible with miniaturized cell-based assays J. Am. Chem. Soc. 1998, 120, 8565.

Shuli Mao @ Wipf Group Page 21 of 40 4/15/2008 Diversity-Oriented Synthesis

DOS aims at generating natural product-like compounds that are (a) easy to access, (b) rich in dense, chiral functional groups, and (c) rich in stereochemically and three- dimentional, skeletally diverse architectures.

• Appendage diversity • Stereochemical diversity • Skeleton diversity

Shuli Mao @ Wipf Group Page 22 of 40 4/15/2008 Appendage Diversity

• Using coupling reactions to attach different appendages to a common molecular skeleton • A split-pool synthesis can be used when a molecular skeleton has multiple reactive sites with potential for orthogonal functionalization

Shuli Mao @ Wipf Group Page 23 of 40 4/15/2008 Appendage Diversity

Shuli Mao @ Wipf Group Page 24 of 40 4/15/2008 Appendage Diversity

Four substituents can be varied.

Lindsley, C. W.; Chan, L. K.; Goess, B. C.; Joseph, R.; Shair, M. D. Solid-phase biomimetic synthesis of carpanone-like molecules J. Am. Chem. Soc. 2000, 122, 422.

Shuli Mao @ Wipf Group Page 25 of 40 4/15/2008 Limitations of Appendage Diversity

Compounds having a common molecular skeleton display chemical information similarly in 3D space, thus limiting the pool of potential binding partners to only those macromolecules with a complementary 3D binding surface

Shuli Mao @ Wipf Group Page 26 of 40 4/15/2008 Stereochemical Diversity

• Increase the number of relative orientations of potential macromolecule-interacting elements in small molecules • Require powerful reagents that can override substrate bias and deliver diastereomeric products with very high selectivity

Chavez, D. E.; Jacobsen, E. N. Catalyst-controlled inverse-electron-demand hetero-Diels-Alder reactions In the enantio- and diastereoselective synthesis of iridoids natural products Org. Lett. 2003, 5, 2563.

Shuli Mao @ Wipf Group Page 27 of 40 4/15/2008 Stereochemical Diversity

allylic alco hol epoxyols 1,3-diols OMe O Me OH OH OMe OH OM e m -CPBA OH OMe n-BuLi; Me 3Al BnO B nO BnO OM e l 2 1 2 T iC r O R R OH B 1 1 C p 2 g R R uM BnO OM e i -B

1 R S harpless R OM e e OH OMe OH OM e O H OH OMe d- epoxidation M eMgCl, CuCl A l 1 BnO B nO BnO a: R = H OM e O Me OM e 1 1 O b: R = M e R R1 R 1 R 2

OR Dess -Martin Dess -Martin NaBH(O Ac) 3 sy n-1,3-diol oxidation oxidation anti-1,3-diol not shown

enones epoxyketones hydroxyketo nes OM e O Me

O O Me O OMe BnO BnO O OH OMe O 1 BnO R 1 R S mI2 OM e R 1 O OM e O OM e B nO B nO O Me OM e O R1 R1

Shang, S.; Iwadare, H.; Macks, D. E.; Ambrosini, L. M.; Tan, D. S. A unified synthetic approach to polyketides having both skeletal and stereochemical diversity Org. Lett. 2007, 9, 1895.

Shuli Mao @ Wipf Group Page 28 of 40 4/15/2008 Skeletal Diversity

• Products with many distinct molecular skeletons are particularly effective at achieving a diverse display of chemical functionality in 3D space • Differentiating processes Strategy 1: Pluripotent functional group strategy Strategy 2: Multiple group pairing strategy • Folding processes

Shuli Mao @ Wipf Group Page 29 of 40 4/15/2008 Differentiating Processes

• Using different reagents to transform a common substrate with the potential for diverse reactivity

Strategy 1: Pluripotent functional group strategy Strategy 2: Multiple group pairing strategy

Shuli Mao @ Wipf Group Page 30 of 40 4/15/2008 Pluripotent Functional Group Strategy

Wyatt, E. E.; Fergus, S.; Galloway, W.; Bender, A.; Fox, D. J.; Plowright, A. T.; Jessiman, A. S.; Welch, M.; Spring, D. R. Skeletal diversity construction via a branching synthetic strategy Chem. Commun. 2006, 3296.

Shuli Mao @ Wipf Group Page 31 of 40 4/15/2008 Pluripotent Functional Group Strategy

(a) C6H6, Rh2(O2CCF3)4, 70%; (b) RCCH, Rh2(OAc)4, [BuCCH, 57%]; (c) RNH2, NaOH then MeOH, H2SO4, [MeNH2, 35%]; (d) dienophile [DMAD, 59%]; (e) C5H6, 92%

Shuli Mao @ Wipf Group Page 32 of 40 4/15/2008 Pluripotent Functional Group Strategy

(a) Rh2(OAc)4, furan, then I2, 60% (91%); (b) DMAD, 84% (88%); (c) LDA, RCOR’, then Rh2(OAc)4; 8: 49% (90%); 9: 68% (97%); (d) PhCHO, PhNH2, then DMAD, Rh2(OAc)4, dr = 20:1, 51% (80%); (e) Guanidine carbonate 62% (96%); (f) Resorcinol, H2SO4, 74% (95%); (g) NH2OH, 77% (89%); (h) Thiophene-2-carboxaldehyde, guanidine carbonate, Then 3-formylchromone, 43% (98%) Yield and purity (in brackets)

Phenotypic screening showed that a high number of the compounds modulate the growth of pathogenic strains of methicillin resistant Staphylococcus aureus (MRSA): 100 µM (29%), 50 µM (6%), 25 µM (4%), 10 µM (2%). The most active ones have MIC 3.56 and 6.05 µg/mL.

Shuli Mao @ Wipf Group Page 33 of 40 4/15/2008 Multiple Group Pairing Strategy

Skeletal diversity was achieved by chemoselective activation of different pairs of functional groups

Obtained by Cinchona catalyzed enantioselective Michael addition

Comer, E.; Rohan, E.; Deng, L.; Porco, J. A., Jr. An approach to skeletal diversity using functional group pairing of multifunctional scaffolds Org. Lett. 2007, 9, 2123.

Shuli Mao @ Wipf Group Page 34 of 40 4/15/2008 Folding Processes

• Transform substrates having different appendages that pre-encode skeletal information (called σ elements) into products having distinct molecular skeletons using common reaction conditions

Shuli Mao @ Wipf Group Page 35 of 40 4/15/2008 Folding Processes O

R4 R1 Protic N N R3 R2 O

O MW Protic R2 OH R2 R -CHO NH -R 300 W 1 2 3 O N R4-NC 20min O R R4 NH 1

R4 Aprotic HN O R3 S N

H O H R2

Santra, S.; Andreana, P. R. A one-pot, microwave-influenced synthesis of diverse small molecules by multicomponent reaction cascades Org. Lett. 2007, 9, 5035.

Shuli Mao @ Wipf Group Page 36 of 40 4/15/2008 Mechanism

Y t-Bu H O H2N N OEt R4 N O X A O O

HO CO2Et X R4-NC OHC-t-Bu Y Acyclic Ugi Product

Pathway A Pathway B R = Bn R4 = t-Bu microwave; protic solvent 4 X = OH; Y = OMe X = OMe; Y = H Michael aza-Michael H O O H Bn t-Bu MeO N N OEt O EtO O O N O O 6-exo t-BuHN t-Bu 5-exo OMe

O O Bn t-Bu MeO N N OEt O EtO O O N O O t-BuHN t-Bu OMe

Shuli Mao @ Wipf Group Page 37 of 40 4/15/2008 Mechanism

S B nHN O CHO B nHN O H 2N m ic rowav e S S O Me O N N OM e Bn-NC aprotic s olvent O O OM e H HO CO2Et H E tO C 2 CO Et H 2

Shuli Mao @ Wipf Group Page 38 of 40 4/15/2008 Build/Couple/Pair (B/C/P) Strategy

Br R 2

N 2 OM e H R CO2M e A r O Build Couple N Couple CO2Me N A l- cat P hos phazene O R 1 Ar O H base R 1 Ar O H Al-catalyzed Asy R 1 Suga-Ibata reaction M e 3P , DB U

Pair R 1=H, R 2=N P air 1 2 Pair 1 2 P air 1 2 3 R =CH 2N 3, R =H R =H, R =CH 2N 3 R =NH 2, R =H

O Ph Ph O NH N N NH NH NH A r A r O O O N H N O Ph H Ph A r O H A r O H Al-cat

Nielsen T. E.; Schreiber, S. L Towards the optimal screening collection: a synthesis strategy Angew. Chem. Int. Ed. 2008, 47, 48. Mitchell, J. M.; Shaw, J. T. A structurally diverse library of polycyclic lactams resulting from systematic Placement of proximal functional groups Angew. Chem. Int. Ed. 2006, 45, 1722.

Shuli Mao @ Wipf Group Page 39 of 40 4/15/2008 Conclusion

TOS, focused synthesis and DOS are all important approaches to explore chemical space. They all play very important role in studying biological systems and discovering drugs.

“Although no longer in the spotlight and heralded as the savior of the drug industry, combinatorial chemistry is alive and well: actually, combinatorial science is more prevalent and widespread than ever before.” -----Craig W. Lindsley

DOS is a new and challenging field, the development of it will lead to the discovery of new chemistry as well as new entities in the chemical space; however, whether it is the most efficient and successful way or not needs to be evaluated in the future.

Shuli Mao @ Wipf Group Page 40 of 40 4/15/2008