Diketopiperazines Baran Group Meeting - 2/26/18

Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

A quick literature search of “diketopiperazine” returned 4,038 entries (many 2,5-DKP) ! In spite of all this, we now know that the boat is in fact the lowest energy conformer! ! Gas-phase microwave and vibrational electron spectra and ab initio calculations agree O that the boat conformation is lower in energy by about 1.5 kcal / mol O O 2 ! This small energy difference can be provided by external forces from a crystal or 3 1 NH 2 O solution environment 4 6 3 1NH 2 NH HN 5 3 1 H H 4 6 4 6 O HN 5 HN 5 O H O O 1.3–1.7 H N H 2,3-diketopiperazine H N H 2,5-diketopiperazine 2,6-diketopiperazine kcal / mol 431 entries 53 entries H H N H 1,791 entries NH H O O …spread over many subdisciplines of chemistry including natural products JACS 2000, 122, 5856; J. Phys. Chem. 1998, 102, 7519 isolation and synthesis, medicinal chemistry, clinical research, methods How does substitution at 3,6 affect 2,5-DKP conformation? Substantially… development, materials, physical organic, etc. ! cis-3,6-disubstituted 2,5-DKPs tend to prefer boat (albeit sometimes slightly flattened) ! With few exceptions (see below), C2-symmetric cyclodipeptides adopt boat confirmation There is much to learn about these seemingly simple heterocycles! Crucial reading HO Prog. Drug. Res. 1990, 35, 249 - DKP natural products review OH H O Tetrahedron 2002, 58, 3297 - 2,3-, 2,5-, 2,6-DKP synthesis, Merck med. chem. N H O Tetrahedron 2007, 63, 9923 - Natural products biology and biosynthesis N H H N H Chem. Rev. 2012, 112, 3641 - 2,5-DKP only, written by GSK med. chem. veteran H Marine Drugs 2014, 12, 6213 - Update on recently isolated DKP marine natural products O H N H O H 2,5-Diketopiperazines Cyclo(L-Ser-L-Ser) prefers a planar structure Aromatic rings like to overlap with the DKP ring, Structure and Bonding with sidechains folded above the central ring forcing a planar conformation ! Corey solved the crystal structure of 2,5-diketopiperazine in 1938, concluding a planar solid state structure with extensive intermolecular H-bonding was operative ! trans-3,6-disubstituted 2,5-DKPs have a less predicatable conformation, but this motif is ! Solution-phase NMR later agreed with planar structure, or rapidly-exhanging, equally- far less prevalent in nature (e.g. cyclo(L-Ala-D-Ala)) populated enatiomeric boat structures ! “All possible conformations of the 2,5-DKP ring in these conformationally constrained ! DFT calculations further supported planar structure in solid and solution phase flexible molecules are found within a 6 kcal / mol range.” Chem. Rev. 2012, 112, 3641; J. Quantum Chem. 2007, 107, 745; Chem. Rev. 1994, 94, 2383; Acta Crystallogr. Sect. B 1981, 37, 625

O Nomenclature IUPAC name = 2,5-Piperazinedione 2 3 1NR Common name = 2,5-diketopiperazine (2,5-DKP) 4 6 RN 5 ! Refer to the numbering scheme on the left, beginning with piperazine N1 ! As a cyclopeptide, it is often useful and convenient to name 2,5-DKPs as: O O Ph O O O OH Bn OH NH NH NH NH NH NH HN 2 2 HN 2 2 HO Bn HO O O JACS 1938, 60, 1598; JACS 1969, 91, 962; O O Ph JCSPT II 1976, 11, 1238; J. Raman Spec. 2009, 1478 Cyclo(Gly-Gly) Cyclo(L-Phe-L-Phe) Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

A (very) small sampling O H Peptides are often a red herring in drug discovery… of biologically-active 2,5 Het -DKPs NMe Pros O O Cons N " Good efficacy, safety, tolerability O N N " Chemically and physically unstable H N " High selectivity & potency " Prone to hydrolysis and oxidation Bn O " Predicatable metabolism NH N HN H O " Tenedency to aggregate NH " Shorter time to market " Short half-life, fast elimination HN " Lower attrition rates O " Usually not orally available Me O Me Me " Standard synthetic protocols " Low membrane permeability O O Me Retosiban / Epelsiban Drug Discovery Today 2015, 20, 122 Phenylahistin Tadalafil (Cialis®) GSK oxytocin inhibitor Nippon Steel Japan Eli Lilly PDE5 inhibitor preterm labor treatment Anticancer (Microtubule) ED / BPH treatment PE treatment / IVF drug How to harness the power of peptides while avoiding their liabilities? 2,5 diketopiperazines offer an attractive solution to this paradox in medicinal chemistry… O MeO H O O " Small, conformationally constrained heterocycle N O N R3 R2 NH 3 N " Modifications at all six positions easily accessed HN " Chirality easily introduced from amino acid chiral pool, etc. HN N HN N H R1 R4 " Planarity in most pharmaceutical agents absent Tryptostatin A O " Rigid backbone mimics peptide secondary structure O XR5967 O UW / UVA collab. Me Anticancer Xenova Ltd., Plasminogen activator inhibtor Me Anticancer, Cardiovascular drug OMe Example: mimicking protein secondary structure 5 H R5 R N O O R1 Me O R1 O NH nPr O O NH O N OH Me N N O NHtBu O H NH HS N 4 N N R4 O Me Me HN H N R Ar N HN O N N 2 O Avrainvillamide R2 O R O Anticancer, O 3 Aplaviroc O R3 O R GSK CCR5 antagonist Broad-spectrum antibiotic Antiviral / HIV drug Peptide β-turn DKP = β-turn mimic O MMP Inhibitor H Affymax NO2 Eur. J. Org. Chem. 2011, 2, 217 N O HN HO Example: mimicking tetrapeptide’s bioactive conformation NH H O Maculosin O Me HN Herbicide O Me NH Asp-Phe-NH2 O N - Diverse chemotypes MeN HN HN O Alaptide - Many therapeutic indications HN nPr Nueroprotective - Vastly different biological targets O SMe O agent - One common core FR200452 Fujisawa Pharma. (Trp-Met-Asp-Phe-NH2) mimic What is so special about 2,5-DKP? Anti-inflammatory, Anti-coagulent Curr. Med. Chem. 1999, 6, 433 Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

2,5-Diketopiperazines, bitterness, and the food we eat …as a catalyst in asymmetric Strecker reaction O O O O O R R R O NH NH NH R R NH HN HN HN NH O R R R HN HN R R O O O R NH ! Using the His-based O O O O O NH NH R R HN S NH NH R O R NH O HN HN R O HN R NH cyanohydrin catalyst failed R R O R NH O S R O O O HN NH O O O O HN R R HN R O R NH NH R R O HN NH R O HN to induce asymmetry R NH NH R HN NH O R O N NH O R HN HN HN R R O R O O 2 O R HN R O R NH NH Ph O R O R O NH ! More basic guanidine O HN NH O Ph R R HN H HN NH R HN R O R O O R NH R O HN O R O HN NH side chain thought to R O HN O R O N Ph (2 mol %) HN Ph accelerate proton transfer in HCN (2 eq.), MeOH the reaction of HCN with R S CN 2,5-DKPs are found in food because: photo: J. Snoblen R H -25 or -75 ºC putative aldimine ! Contamination in stored food by DKP-producing fungi, yeast, bacteria yields > 90–97% intermediate ! Natural products produced by yeast, fungi, and bacteria as fermentation byproducts ee > 92–99% ! Degradation products of additives such as artificial sweetener (e.g. aspartame), or antibiotics used in animal feed (e.g. amoxicillin) JACS 1996, 118, 4910; Eur. JOC 2005, 8, 1497 ! Thermal processing of food degrades proteins and peptides, often forming DKPs …as a catalyst in asymmetric Michael additions O O H H H ! Several flavor descriptors are associated with 2,5-DKPs, including Me N S astringent, salty, grainy, metallic, and most commonly, bitter HO C NBn HN N ! Takahasi (1974) reported Cyclo(L-Pro-L-Leu) to be the bitter O 2 H Me HN N O Ar O component of saké R S H R ! As sidechain hydrophobicity increases, perceived bitterness S Cyclo(L-Pro-L-Leu) O O H NO2 follows + R (2 mol %) R Ar CHCl / PrOH (9:1), rt NO2 3 using D-proline instead of O syn:anti 20:1 L-proline gives the Me ee 94–98% opposite enantiomer N ! Pickenhagen (1974) reported >20 cyclic dipeptides in cocoa as HN byproducts from the roasting process Eur. JOC 2011, 20, 5599 ! They were found to potentiate bitterness in theobromine, another O N N naturally occuring bitter aromatic compound, and vice versa …as a chiral auxillary in the Mannich reaction Me O O H Theobromine H Crit. Rev. Food Sci. & Nutr. 2015, 718 OTMS ZnCl2, H NH NH Ph NH2 + Et2O N Me N Me S S Bn 2,5-DKPs as reagents… OMe S Bn then HCl, Ph …as a catalyst in asymmetric cyanohydrin formation Ph Me N O Me N O MeOH, H2O CO Me (useful for chiral α-hydroxy acids, chiral amino alcohols) 2 H Ar O 80% yield Zn2+ O H 12:1 dr Re face preferential for attack H NH TL 1997, 38, 1563 from incoming silyl ketene acetal S NH O H OH HN S H H N CN CN …as a Diels-Alder chiral auxillary H R CN N N R O R O O O H H (2 mol %) TiCl , N N 4 NH H H N PhMe + HCN (2 eq.), PhMe R + R N then N -20º, 8h Bn CO2H Bn yields > 83–97% Dual activation mechanism LiOOH O endo:exo 99:1 O ee > 92–97% via dimer proposed 76:1 dr Chem. Commun. 1981, 5, 229; ACIE 1991, 107, 5759; JOC 2009, 74, 1464 Heterocycles 2009, 78, 1171 Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

O 1. Cyclization via amide bond formation c) Dipeptide via Ugi Reaction R a) General Considerations 1 2 3 2 R O 3 R R O 3 1N R O ! The most common method to synthesize 2,5-DKPs + + + C 5 4 6 N PG N R N 5 ! Large chiral pool of available amino acid S.M. PG OH NH 4 N R 2 H R R5 N N ! Racemization can be an issue 2 R R1 O R4 H O ! Amide bond must adopt cis- conformation Comparison to amino acid strategy N1,2 ! Substituents at 3,6 positions can have dramatic effect on cyclization rate Pros Cons ! Greater diversity in available ! Isonitrile component limited in b) Dipeptide cyclization from two amino acids commercial starting materials diversity (not a big deal- see below) R2 O ! Obviates need for expensive coupling ! Cyclization onto amido C-terminus O O R2 1 reagents typically requires activation (also not OMe R RHN H N * deprotect * NH ! Allows for superior diversity in library / necessarily a problem) * 2 RHN * OMe OH N * HN * analog synthesis 1 O R2 ! Dipeptide formed in single pot R R1 H O coupling agent O C-terminus activation - “Not all isonitriles are created equally” ! Cyclization on difficult substrates can be assisted by thermal, acidic, or basic conditions Solution phase: ! Solid-phase synthesis has been employed for combinatorial library synthesis R2 R3 O R2 R3 O ! Several strategies exist for solid-phase preparation of DKPs: TFA CN N N Ugi BocN NH HN NH On-resin cyclization O R1 O R4 R1 O R4 R2 DKP AllocN [1121-57-9] H Pd(PPh ) N TL 1998, 39, 1113 EtO C N O 3 4 2 HN O H O then TMG R2 O H O OMe 2 3 2 3 O R R O R R O R1 N N Chimia 2003, 57, 248 R1 OMe BocN NH TFA HN N Ugi Cleavage, then cyclization NC R1 O R4 R1 O R4 OMe 1 R O OMe DKP Me H N NHBoc R1 O [592479-02-2] J. Comb. Chem. 2009, 11, 1078 Me N TFA KOtBu; O R2 NHBoc Further Reading: TL 1998, 39, 7227; TL 2001, 42, 2269 (Solid phase isocyanide resins) 3 MeO2C N O R NaOMe R3 …a reasonable conclusion: DKPs want to cyclize! Me MeOH 2 Me O O R O R2 But what if you want to avoid this? O N O Org. Lett. 2002, 4, 1167 R3 Bulky carboxylic acid P.G.’s, or this nifty strategy… Me N O Me Me O HN HN 1 MeHN R R = OBn Me R N Me NMe HN Me Me O O t1/2 = 30 min. MeN O O Cleavage-induced cyclization Me Me Me Me O R NHBoc O Cbz-Ile O Me NH Me Me Me O Me R DCC N (+)-CSA HOBt N R O Me O NH NH CbzHN N then Me O O Het HN Het R = NHNHBoc O O Et3N Me Me Destruxin B (35%) O TL 1997, 38, 339 O Mol. Diversity 2005, 9, 111 Acyl hydrazide converted to azide for depsipeptide formation Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

O Ugi reaction, continued… e) Aza-Wittig cyclization “UDC” strategy (Ugi / deprot. / cyclize) CO Et R CO2Et 2 2 “Carboxamide template” CO2Et Cl 3 1N K2CO3 NaN3 PPh3 3 + Cl 4 6 5 O NHR N N N 5 Boc R O CO2Et NH O (82%) R Cl (90%) R N3 R N CO H R2 NH R5 R R5 2 2 BocN TFA; N O O O O R3 NC N CONHR3 4 1 R 4 2 Et3N N OEt O N ,2 EtO2C CHO R R 4 2 R R CO2Et TL 1999, 40, 5295 O N NH N PPh3 R N N N R R “Glycinamide template-” C3 / C5 Stereocenters from acid & amine component O O O O O R2 3 2 Synlett 2010, 14, 2122 1 R O R H R N 1 R1 OH R N TFA; N CONHR3 C N R3 O NHBoc NH2 6 1 R2 BocHN Et3N HN 4 R 2. Cyclization by C –N bond formation (N-alkylation) 4O R 2 4 OHC MeO C R 3 1N MeO2C R 2 O 4 6 N 5 ! Second most common disconnection for 2,5-DKP synthesis J. Med. Chem. 1998, 41, 2194 MMP inhibitor - R ! Simple symmetrical DKPs easily accessed Tetrahedron 1997, 53, 6573 J. Med. Chem. 1999, 42, 1348 Affymax SAR study O ! N-substituents have strong effect on ring closure rates N1,6 “From commerical dipeptides” 3 R O R3 1 4 N a) Chloroacetamide cylization O R OHC R3 R 2 H NH R 4 O NaH, DMSO, 60ºC N CN R4 1 N CONHR O R = alkyl, aryl O R 1 HO NH2 HN Cl R R1 J. Chem. Res. 2007, 7, 381 2 µwave, 110º R1 N conditions N R O O O H H N O 6:1 dr N NaOH, MeCN, 82º 2 H N 1 Mol. Diversity 2003, 6, 283 R R1 Cl R R = bulky alkyl, aryl O O Bull Korean Chem. Soc. 2004, 25, 415 d) Direct amino acid condensation O O b) Ugi-4CR / intramolecular N-alkylation 2 2 R In the absense of other factors, CO2H O O OH R N Cl HN this method usually suffers from H N R1 R2 R3 R2 R3 1 NH 2 R = alkyl; 1 N poor yields and is seldom used O N KOH, EtOH N R HO R1 OHC R2 H epimerization N sonication N 3 MeOH, RT R1 Cl 1 problematic O O CN R (68–86%) (71–86%) R O O TL 2001, 42, 2727 Microwave heating with trace ionic liquid addressed this issue: PhMe, c) T.M.-catalyzed intrmolecular vinyl amidation trace ionic liquid O O H O O Et3N, OMePCl2 Me Me Me H OH H N Ionic liquid assisted Me H NH2 then 1.2 eq microwave absorption Br Pd2(dba)3 NH NH H H and effected rapid N H N K2CO3 N HO N heating O N (45%) N (81%) O O Boc Boc N O H N H NTr µwave 145º Eur. J. Org. Chem. 2008, 5418 NTr PNAS 2004, 101, 11971 Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

O Chloroacetamide cyclization to form DKP… chiral α-amino acids Diels-Alder cycloaddition R 2 O Me O Me 3 1N Me COCl O O 4 6 PhMe, H N 5 N Ph N Ph Me O R nBuLi N reflux N H Cl H THF, 0ºC O Ph NH Ph N HO OH (90%) O Me N (40%) N 1 (92%) O Me O N ,6 Me (1:1 dr) Me H H NH2 Me Cl O O Molecules 1998, 3, 80 O Me O N Ph " N-Sorbyl-L-proline tether controlled regio- and stereochemistry of [4+2] cycloaddition Me no epimerization observed " Hydrogenation of DA product followed by reductive N-O cleavage and hydrolytic Ph N OH Me in cyclization step removal of proline auxillary gave targeted amino acid NH Me O 2 J. Org. Chem. 1992, 57, 6532 O Monodehydro 2,5-DKPs Condensation / Pictet-Spengler sequence " Naturally occuring motif with a wide variety of biological R O 2 N O activity including antidepressent, microtubule depolymerization, 3 1 O R1 N4 6 R1 R3 NH radical scavenging, and anticancer 5 N 1 6 R N " N ,C disconnection logical for condensation / dehydration 2 H NMe HN R1 O H NHMe R COCO H O " Hayashi & coworkers developed general method for access to 2 1 4 BOP / THF O R2 this privlidged scaffold N ,2 / N ,3 R NH 2 O R NH R O Bn O NH N 1 Cyclization via N-α-Ketoacylamino acid amides NH R HN HCl, N When tryptamine was acylated with L- Ph Ph O 2 cat. p-TsOH Me EtOAc NMe proline, opposite diastereomer was obtained R O H R3 O PhMe, reflux N Me R2 1 N 3 NH O Tetrahedron Asymmetry 2005, 16, 975 R N R (35–96%) HN R1 NPI-2358 R O H O Vascular disrupting agent, 2 Tetrahedron 2009, 65, 3688 O R Phase II O R N " Useful disconnection for varying N-substituents Via Ugi-4CR / Aza-Michael sequence N " Pfizer employed this strategy in developing novel PDE5 inhibitors R (follow up to Viagara®): O OMe O N1,2 / N1,6 BMCL 2003, 13, 1425 OHC R1 1 1 2 H R O R R H2N 2 N CN R N O 2 CO2Me NBn R N CO2Et N H O H O/MeOH PMB Cl 2 O PMB Cl N µwave 200 ºC O CO Et NH HO CO2Et 2 N O N OL 2007, 9, 5035 N 20:1 syn:anti H then H O NBn

O H2N O O >100 examples O Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18 …continued Some reactions of 2,5-Diketopiperazines Me O 1) Reactions at C / C 3 5 PMB Me O a) Enolate alkylation Me N PMB Me N TMSCl N 1) P(OEt)3 Me O PMB F 1 Me O Me O 2) NaH, R1CHO N R O PMB Me NPMB LiHMDS; Me NPMB KHMDS; Me NPMB O 1 PMBN MeI PMBN R1X PMBN R Me Me Me O Me O Me O O O O PMB Me N PMB PMB Tetrahedron Asymmetry 1998, 9, 2795 TMS Me N Me N N or PMB Cl N N Diastereoselectivity with transient D.G. NaSPh PMB R PMB R O O O O Me O Me O Me R Me Me O allyl TMS (0.9 eq) 4 : 1 N Ph N Ph R N Ph NaSPH (0.9 eq) 4 : 1 LiHMDS; LiHMDS; PMB NaSPh (2.0 eq) 1 : Ph N Ph N Me Me N 13 Ph N R MeI RMgCl RX R N suggests SN1 process (0.9 eq) or R = allyl Me O (repeat) Me O Me O PMB OH epimerization with excess base (2.0 eq) Amino Acids 2010, 38, 829 R R Tetrahedron Asymmetry 2004, 15, 3989 b) Bicycle formation via Dieckmann cyclization d) Aldol chemistry

O 1 2 1 R O R R O R2 Me O Me O Me O 1 N N N N R CO2Me N Me NR Me NR LiHMDS; H3O Me NR tBuOK; H2 / Pd N RN R1 RN R1 R2 TMSCl O (96% O RN R1CHO MeO overall) OTMS O O O O O J. Chem. Soc. Perkin Trans. 1 1998, 7, 1275 Org. Let.. 2000, 2, 1177 Me O Me O Me O c) Halogenation and displacement H RI, AIBN N Me NR Radical halogentation Me NR nBuLi; Me NR Bu3SnH RN R O O RN (HCHO)n RN 4:1 dr NBS, Br NMe Br 6-bromo- O NMe AIBN NMe indole MeN Br O O MeN or Br2, MeN then BH -THF J. Chem. Soc. Perkin Trans. 1 2001, 24, 3281 Br 3 hν, 150 ºC (72%) dragmacidin B O JOC 1988, 53, 5785 N e) Rearrangements O H Electrophilic halogenation OH O O 1 1 Me O R tBuOK, R1 NaH, THF R R2 Me O Me O rt, 24 h NBoc NHBoc 0 ºC NHBoc PMB PMB PMB Me N LiHMDS; LiHMDS; Me N BocN then 0.1N BocN then R2X BocN Me N HCl N hexachloro- N NFSI N O O O PMB Cl ethane PMB PMB F O O O Org. Biolmol. Chem. 2008, 6, 3281 + diastereomer (2:1) Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

Some reactions of 2,5-Diketopiperazines via N-acylium ion from aldehydes 1 OMe O 2) Reactions at N / N OMe O OMe O H a) N-alkylation H H MeCHO, NH Sodium hydride most commonly employed base but there are potential issues… NAc TFA NAc N …such as regioselectivity HN N O O OMe Me O O OMe O OMe O K2CO3 NaH; Me single diastereomer NMe 1 Me2SO4 NH R X NH Curr. Org. Synth. 2009, 6, 143 MeN MeN MeN CO2Bn CO2Bn CO2Bn 1 c) N-arylation O R O O via Ullmann / Goldberg reacrion TL 2003, 44, 263 O O …and epimerization CuI, O O K CO R1 1 NBn 2 3 NBn NaH R R3 HN NH DMF; N PhBr N HO µwave Ph N 3 HO 2 R X N O (77%) R R2 O TL 2002, 43, 1101 O JOC 2000, 65, 2179 O Intramolecular Goldberg reaction b) Intramolecular cyclization O O via Bronsted acid catalysis O O H NH CuI NH H H CsOAc TFA NH HN Me N Me X NH then N 90 ºC Me (70–99%) HN Ac O, py O Me O Me HN Me 2 N H (85%) Ac O (5:1 dr) OL 2010, 12, 2162 O Tetrahedron Asymmetry 1998, 9, 967 Tetracycles! via bromination / cyclization O O O H O Br CuI H Br , NH 1 2 NR diamine 1 NH MeCN NR N HN K CO N HN Bn BocN R2 2 3 N RN (86%) N H I DMF 2 Bn O Boc R R O (81%) O O ACIE 2008, 47, 1485 (4:1 dr) OL 2008, 10, 3841 via oxidative cyclization 2 SNAr at indole C position O Me H O O O OMe H Me H N N H H NH DMDO HO N + N NaH NH N DMF N N HN N NH HN (31%) OH H H OHC (63%) O N H Me O O O OHC Me JACS 1999, 121, 11964 H Gypsetin Heterocycles 1994, 38, 273 Achievable with EWG at indole C3 and OMe at N1 Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

Some reactions of 2,5-Diketopiperazines Intramolecular Aza-Wittig 2 5 3) Reactions at carbonyl C / C Me Me Reduction to piperazine HN HN O O O O N N Bu3P Me Me HN N LAH, ! recrystallized as dipicrate salt PhMe HN N THF N ! used as a chiral ligand for O (84%) N O 67% N copper-cat. acylation of diols N Me 3 Synlett 2001, 9, 1387 O OL 2006, 8, 6139 Me

Regioselective thionation 4) Cleavage of 2,5-DKP ring…

O Me O …via nucelophilic cleavage Lawesson’s Me O Me Reagent H2 N N Raney Ni O O (0.5 eq) O N Nu, O O O BnN O O H BnN 86% BnN Et3N NBoc RNH2 HN n n N Pr Pr n Nu = BnOH, O S Tetrahedron 2001, 4359 Pr BocN Nu MeOH, N RHN NHBoc (68–92%) O BnNH2, etc. O H H Bis-lactim ethers (81–98%) O O Me O Me OEt JOC 2002, 67, 1820 J. Peptide Sci. 2009, 15, 474 ! Straighforward synthesis Et3OBF4 Me NH Me N of Schöllkopf’s auxillary …via acid hydrolysis to form amino acids ! Avoids need for phosgene, HN TL 2006, 5199 N rigorous purification Me O (92%) NH Me O CAN; 2 O OEt Me NPMB 6N HCl HO + R Me OH Access to and reactivity of 1,4-dihydropyrazines PMBN (71–87%) R O NH2 R’ O O OR NH Me O LiHMDS, R’B(OH)2 nBuLi, 2 NBoc HMPA NBoc or NBoc 2,6-tBuPhOH HO + R’SnBu R Me OH 3 BocN then CAN; BocN (OPh)2P(O)Cl BocN O Pd0 6N HCl NH2 (86%) O OR (40–80%) R’ Org. Biomol. Chem. 2007, 5, 2138

Pd(OAc)2, R’ PPh , …via base hydrolysis, unsaturated amino acids NBoc 3 HCO2H N TFA BocN O O R1 (45%) N NaH; (64–99%) 1 H R1 NAc R2CHO R NAc NaOH 3 R’ R N CO2Me N R2 MeOH N 1 N 3 R R3 R H O LDA; R2 1 O O R X NBoc Tetrahedron 2004. 64. 8059 (62–85%) BocN ITE-IBA Lett. Batteries, New Technol. Med. 2004, 5, 373 Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

…via dehydration of diacids O 2,6-Diketopiperazines O Tetrahedron 1989, 45, 2763 2 3 2 3 ! Head-to-head cyclic dipeptide 1 4 O RN 1 4 NR ! Often built from large pool of natural amino acids RN NR 6 5 HO C 1 6 5 ! Much interest as antiproliferative compounds 2 R NH2, ! > 25 examples reported ! M.O.A. suspected as DNA topoisomerase II inhibition NR CDI (2 eq) R1 N NR ! acetic anhydride usueful in O 1 O N1,2 N ,2 ! Intramolecular cyclization common ring closure method HO2C (63–99%) activation / dehydration N1,6 O Thermally-induced cyclization of an amide onto an ester J. Med. Chem. 1964, 7, 241 Esters are useful coupling partners in this strategy… O O O Tetrahedron 1991, 47, 1065 O Me Me O BnNH ; N Me 2 BnHN Δ BnN tryptamine Br MeO2C N (±)-Ala-OMe MeO2C NH (85%) NH N N Br O N 175 ºC (65%) (79%) NH Me Me EtO2C HN O 2,6-DKPs via Ugi-4CR Hetereocycles 1998, 47, 965 Fused tricycles via N1,2 / N1,6 disconnection Ph Ph O Ph TL 2000, 41, 3447 tBuOK O MeOH O MeO2C Δ EtO C HO 2 EtO2C 3–14 days NH NH 3 days N NH CHO NH2 NC Cl3CCOCl, BnN (56%) EtO2C (68%) EtO2C N + + DMAP Cl3COC N BnNH2 N EtO C O O O Me 2 (40%) (99%) Me Me N N N Me Me Me Symmetrical 2,6-DKPs via α-haloamides O O O Me O Me NHEt O Me 2 3 2 3 ! Seemingly efficient way to construct 2,6-DKP RN 1 4 NR O NaH NHEt Me RN 1 4 NR Me 6 5 6 5 Br THF EtN EtN NEt ! Minimal development of this method NEt Br ! No known ways to make unsymmetrical 2,6-DKPs with this disconnection Me Me Me O O N1,2 Me Me ! Competing 2,5-DKP formation O Me O Me 1 1 N4,5 N ,2 N ,6 N4,3 N4,5 J. Chem. Res. 1983, 10, 2237 Temperature dependence on product formation Indian J. Chem. 1968, 6, 170 Abdel-Hamide, antimicrobial candidate Ph Ph Ph Cl O O O O O O NH NH Cl N neat, 2 neat, N N NH2 Ph N Cl NH EtO2C NH2 N 175 ºC + 200 ºC O N N O O O DMF py, Δ N (97%) N N N Ph (83%) O EtO2C Cl N Ph (30%) N Ph O (25%) O

Ph (4%) J. Indian Chem. Soc. 1997, 74, 613 Ph Ph Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

O O The preferred route to 2,3-DKPs for over a century… H O 2 3 O O O N 1 4 X = Cl, NHBoc RN NR H2N NH2 X LiAlH ; 6 5 + OR, imid 4 X O HN NH N OMe Ar-NH2; O N CF3 N 1 4 N O NaBH N ,2 / N ,3 Bischoff, N. Chem. Ber. 1889, 1805 H 4 H OMe (55%, NK antagonist N-Boc-α-L-tryptophan 3 steps) 1 Weinreb Amide Combinatorial library snthesis of 2,3-DKPs using solid support Merck, JMC 1995, 38, 923 CF3 Tetrahedron 2000, 56, 3319 4 NHBoc O R1 R2 R CO2H 1 2 O H R R EDCI 4 OMe NHBoc HCl, H2N N R N N N then N NHAr Cl CO2Me MeOH product H N R3 O BH3-THF 3 H O HN 2,3-DKP R H monoprotected N O (64%, O 1,2-diamine H 2 steps) imid 3 Ar R ! >100 compounds prepared in first imid 1 R generation campaign O N N R2 ! 1,6-disubstituted and 1,4,5- O O 4 ! The C2 / N1 / C6 disconnection is effective for preparation of then HF-py R NH trisubstituted 2,3-DKPs were prepared 2 3 unsymmetrical 2,3-DKPs (cleavage) O O with extremely diverse functionalities RN 1 4 NR 6 5 ! Typically a tandem reaction

O O ! The majority of cyclization reactions to produce 2,3-DKPs are N1,2 / N1,6 Antixiolytic / Antidepressant SAR study 1 2 2 3 forged at the N /C positions CIBA-GEIGY Corp., JMC 1980, 23, 952 NMe RN 1 4 NR ! General sequence involves a monoprotected 1,2-diamine treated 6 5 O KCN O O with alkyl chlorooxoacetate and then deprotected, spontaneously p-chloroaniline EtO2C N N1,2 cyclizing to give 2,3-DKP EtO NMe Cl N NMe AcOH / H2O reflux Cl N nBu EtO (43%) NC Me R NC Me N N N NC CHO Unsymmetrical 1,4-disubst. 2,3-DKPS via “tandem reductive amination / cyclization strategy” N TL 2000, 41, 8735 O Me N O Me N Me NEt LAH Me Farnesyl transferase inhibitor “aldehyde” NEt Ph NH NEt 2 Me N then H2, Pd Merck, BMCL 2001, 537 O Na(OAc) BH O HN O CO2Et 3 92%, 2 steps (90%, 6:1 dr) Ph O BocHN nBu O H2N nBu O OMe Reactions of morpholine diones, Bowman, et al. NH2 Cl N-Boc nor- O Synth. Comm. 1983, 13, 151 Me HN N leucinal; O aldehyde O O O Me O OMe Me NaBH via ring opening Na(AcO) BH then HCl, 4 O MeNH2, and addition of Me 3 (48%, O OMe N NMe (80%, 2 steps) MeOH product H2O methyl amide to Me Me 2 steps) N (90%) 2,3-DKP (90%) OMe activated double monoprotected bond CO Me 1,2-diamine 2 CO2Me Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

2,5-Diketopiperazines - Summary of Disconnections

dipeptide O cyclization Cl Cl R3HN Aza- * OH R2 Wittig O + 1 C 4 R O N 4 PPh , R 1 OMe + 5 R CO2Et 3 R HN * N R NaN3 PG OH O NH R2 Ugi 4CR / Nitroso R3 1 O N ,2 1 3 O cyclization Diels-Alder N ,2 R + NH N 2 H R4 Me N 1 O H N1,6 N ,2 O O O O Cl R4 R1 N1,6 NHR1 Chloroacetamide 1 N R4 NHR 3 cyclization T.M.-catalyzed X R HN 3 N 2 Cl vinyl amidation N R R R3 N1,6 O O N1,6 O R2 N1,2 / C 1 O N 1 N ,6 + 1 N ,2 / Cl R O N4,3 OH Condensation / 2 3 R R + Ugi 4CR / Pictet-Spengler N O NH N-alkylation H 1 2 NR 4 4 O R CO2R H R R1 NH NH H N R R O R3 2 Cl Acylation / Cl Condesnation / O Alkylation

2,5-Diketopiperazines - Summary of reactivity

Reactivity at carbon (C3, C6) O O O ! Enolate chemistry (alkylation, Reactivity at nitrogen Reactivity at carbonyl carbons NR annulation, etc.) NR ! Reduction to form piperazine ! Halogenation / displacement ! Alkylation NR RN ! Intramolecular cyclization ! Thionation ! Oxidation RN ! Arylation RN ! Wittig / Aza-Wittig ! Aldol chemistry O ! Cross coupling ! Ring contraction / rearrangement O O ! DKP cleavage to give amino acids Tom Stratton Diketopiperazines Baran Group Meeting - 2/26/18

2,6-Diketopiperazines - 2,3-Diketopiperazines - Summary of Disconnections Summary of Disconnections

Annulative acylation of 1,2-diamines O 1 4 O 2 1 R NH HN R R R NH2 Amine / α-haloester HO 2 + X + + R cyclization X HN R2 R3 Ugi 4-CR / R3 O cyclization CHO N1,2 N1,6 Cl CO2R R4 N4,3 N4,5 Stepwise acylation / 1 + NC N ,2 / Reductive amination / deprotection / cyclization N4,3 cyclization R1 Cyclization of N1,2 α-haloamides PG R3 O 1 1 4 O O 2 4 H O R2 N ,2 / R N HN R R R N 4 H X N RO R3 N ,5 N 2 3 R1 N N R4 O 4 R1 N N R3 R1 R2 R R O CO Et R X 2 H + 1 + O 1 O O N ,2 2 3 N1,2 / N ,2 4 N R R H N R1 O R 3 4 1 1 2 X R R Cl N ,6 H2N R + H X OR N1,2 O R2 1 O Amide-ester N ,6 N1,2 / cyclization N1,6 N1,2 N1,6 R2 2 O R RO2C 1 3 RO2C R HO2C N R 4 H2N 1 3 RO N R Condensation / R NH2 + N R RO2C Diester + 4 + Imminium alkylation HO2C R cyclization + RO R3 2 R4 R Diacid 1 R NH2 dehydration CDI or Ac2O