The Reactivity of Calicheamicin [Gamma]1I in the Minor Groove Of

DOI: 10.1002/chem.200700504 I The Reactivity of Calicheamicin g1 in the Minor Groove of DNA: The Decisive Role of the Environment Elfi Kraka,*[a] Tell Tuttle,[b] and Dieter Cremer[a] Abstract: Triggering and Bergman cyc- minor groove in such a way that out of man cyclization at body temperature I lization of calicheamicin g1 outside and a cyclohexenone by Michael addition only if present in its E chair form (acti- inside the minor groove of the an E rather than a Z form of a cyclo- vation enthalpy 16.4 kcalmolÀ1). An in- duplex 9mer-B-DNA sequence hexanone is formed, which in turn termediate biradical is formed (docking d(CACTCCTGG)·d(CCAGGAGTG) adopts a chair rather than a twistboat energy À13.6 kcalmolÀ1), which has a were investigated by using density form. Decisive for the stereochemistry sufficient lifetime to abstract two hy- functional theory and molecular me- of the Michael addition is the orienta- drogen atoms. Hydrogen abstraction is chanics (DFT and MM) descriptions in tion of the carbamate substituent at the a two- rather than one-step process which the ligand is completely de- headgroup of calicheamicin. Triggered and involves the C5(H5ACHTUNGRE ’) atom first scribed at the DFT and the receptor at calicheamicin can undergo the Berg- and then the T22(H4ACHTUNGRE ’) atom in line the MM level. The calculated docking with experimental observations. The energy of calicheamicin g I (À12.5 kcal decisive role of using a DFT rather 1 Keywords: ab initio calculations · molÀ1) is close to the measured value than an MM description for the ligand calicheamicin · DNA damage · of À9.7 kcalmolÀ1 and the site specifici- is documented. environmental effects · reaction ty is in line with experimental observa- mechanisms tions. Calicheamicin is triggered in the Introduction Enediyne 1 comprises the aglycone calicheamicinone (see also Scheme 2, Model 4) and the sugar tail with rings A, B, The discovery and recognition of the astonishingly selective C, D, and E. Discovered in 1986 as a fermentation-derived activity of the naturally occurring enediynes has generated antitumor antibiotic that is produced by Micromonospora intense chemical, biological, and medicinal interest in these echinospora (subspecies calichensis),[4] it possesses excellent remarkable compounds.[1–4] The naturally occurring ene- potency against murine tumors P388,[4] L1210 leukemias, diynes are a family of secondary metabolites that include and solid neoplasms such as colon 26 and B16 melanoma.[4,5] neocarzinostatin, esperamicin, dynemicin, kedarcidin, and The structure of 1 was determined in a stepwise approach I the target compound of this work, (À)-calicheamicin g1 (1, that included the X-ray diffraction analysis of rings B and C Scheme 1). as a single isolated unit,[6] extensive NMR studies of ring A and its attachment to ring B, ring D, and its connection to C,[5] as well as the isolated ring E.[7] The structure and at- [a] Prof. Dr. E. Kraka, Prof. Dr. D. Cremer tachment of the aglycone was established through a combi- Department of Chemistry and Department of Physics nation of NOE experiments and X-ray crystallography on University of the Pacific [6] 3601 Pacific Avenue, Stockton, CA 95211–0110 (USA) derivatives. The original stereochemistry, which was pro- Fax : (+1)194-62-607 posed for the aglycone at the position of the attachment to E-mail: [email protected] ring A, was later revised on the basis of the structure of es- [b] Dr. T. Tuttle peramicin. The revised stereochemistry places the glycosidic Department of Pure and Applied Chemistry linkage to ring A on the same side of the enediyne plane as University of Strathclyde the methyl trisulfide,[8] thus leading to S and R absolute con- 295 Cathedral Street Glasgow, G1 1XL (UK) figurations at the stereogenic centers C1 and C8. Supporting information for this article is available on the WWW The configuration of native 1 was later confirmed by the under http://www.chemeurj.org/ or from the author. enantioselective total synthesis of (À)- or (S,R)-calicheami- 9256 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Chem. Eur. J. 2007, 13, 9256 – 9269 FULL PAPER Scheme 2. fraction analysis of the aglycone could be performed. The crystal structure is observed to have a relatively planar (slightly deformed to a twistchair) cyclohexenone ring and the carbamate group is oriented in such a way that it runs parallel to the enediyne warhead (i.e., opposite to the sulfur moiety). In its native form, 1 is inactive, only once it is triggered does it become active. The triggering involves a nucleophilic attack at the trisulfide linkage[3,4] leading to the thiol 2 (Scheme 1), which can undergo an intramolecular Michael addition to form the triggered calicheamicin 3, characterized by its tricyclic headgroup. Once triggered the molecule un- dergoes a Bergman cyclization[13,14] via TS(3–4)ACHTUNGRE to form the singlet biradical 4-S, which, if properly positioned in the minor groove, subsequently abstracts two hydrogen atoms from the DNA strands to form the stable benzene derivative Scheme 1. 5. Alternatively, 4-S can undergo a retro-Bergman reaction via TS(4–6)ACHTUNGRE yielding the open enediyne 6 (Scheme 1). Hydrogen abstraction by 4-S leads to oxidative double- cone[9] and (À)- or (S,R)-1 in their enantiomerically pure strand scission, which causes irreversible damage and cell form.[10] Syntheses of (À)-calicheamicinone through differ- death (apoptosis).[1–4,15,16] This was first demonstrated by ent synthetic routes have also been successfully undertak- Zein and co-workers[17] through the ability of 1 to cause in en,[11, 12] and in the course of the synthetic work an X-ray dif- vitro double-strand scission when in the presence of thiols. Chem. Eur. J. 2007, 13, 9256 – 9269 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim www.chemeurj.org 9257 E. Kraka et al. Furthermore, the sequence specificity of the cut site of 1 ation) to (from) DNA. This, however, exceeds the possibili- was found to be well defined.[17] Chemical footprinting stud- ties of modern QM/MM molecular dynamics (MD) simula- ies established the binding site for calicheamicin as oligopur- tions. Alternatively, one could attempt to describe the ine·oligopyrimidine tetranucleotide stretches, with the high- ligand and receptor exclusively by MM. This implies setting est specificity being identified as the (T-C-C-T)·(A-G-G-A)ACHTUNGRE up a suitable force field that is able to describe the enediyne sequence.[17–19] It was also demonstrated that 1 abstracts hy- unit and the chemical processes of this unit along the Berg- drogen atoms from DNA rather than from the surrounding man cyclization path while bound to DNA. Such a force medium (proteins, etc.) and that the carbon sites that extract field, however, is hampered by the principal problem of de- the DNA hydrogens are exactly the proradical carbons in- scribing quantitatively quantum-mechanical processes with volved in the Bergman cyclization.[20] empirical force fields. Because these basic questions have There have been numerous studies clarifying the site spe- not been solved and will not be solved in the near future cificity of hydrogen abstraction,[21–23] its dependence on the one has to revert to a simplified solution. In this work we oligosaccharide tail,[16,24–27] the interactions of the tail with extensively used DFT to describe ligand 1 as accurately as DNA, and their mutual repositioning.[28, 29] These studies possible. Once the configuration of the ligand 1 was deter- were extensively based on NMR measurements, which in mined it was kept during the docking to the receptor DNA. turn laid the basis for molecular modeling descriptions.[30, 31] The latter was described at the MM level and the docking So far, only a fewquantum chemical studies have been car- process was described with the help of empirical scoring ried out to investigate the triggering of the aglycone (model functions that were parameterized to get useful complex 4 in Scheme 2),[32] the stereochemistry of its Michael addi- free binding energies in the case of proteins. In this way, we tion,[33] or the Bergman cyclization of the headgroup.[34] A obtained a rigid docking description of a QM+ MM (rather full quantum chemical investigation of 1 or 3 utilizing either than a QM/MM) description, the usefulness of which was density functional theory (DFT) or wave function theory described in previous work.[42] has so far not been carried out. Based on previous work[40–43] and according to the argu- In this work, we present a DFT and molecular mechanics ments given in the Supporting Information, we used DFT (MM) investigation in which the ligand (1, 3 or their follow- with Poples 6–31G(d)[44] and 3–21G split-valence basis up products) is for the first time completely described at the sets[45] in connection with the hybrid functional B3LYP[46–48] DFT level and the receptor by MM. We investigate the en- to describe 1. (For calculations with larger basis sets such as ergetics and stereochemistry of the triggering and the Berg- 6–31G(d,p),ACHTUNGRE 6–31+G(d), 6–311G(d,p),ACHTUNGRE and 6–311 ++G- man reaction in dependence of the substituents sitting at the (3df,3pd)ACHTUNGRE and the use of CCSD(T), see Supporting Informa- headgroup. For the latter purpose, we stepwise simplify the tion.) At B3LYP/3–21G, the geometries of 1, 3 and all triggered molecule 3 to obtain the models 1 to 7 shown in follow-up products were fully optimized. Restricted DFT Scheme 2. Normally, it is assumed that the headgroup deter- (RDFT) calculations were carried out for the singlet states, mines the energetics of the Bergman reaction.

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