On resin benzyl deprotection tests

Before reattempting the synthesis of the small library using the improved resin and coupling agent choice, it was decided to briefly explore whether benzyl deprotection could be performed on the solid phase immediately prior to cleavage. This would provide compounds for assay without the need for post solid phase reactions.

The conditions previously used to remove benzyl protection after cleavage would not be appropriate, as the heterogeneous catalyst would not be able to access the matrix of the swelled resin. Therefore attempts were made to affect benzyl ether cleavage, under homogenous conditions, using soluble Pd species, with organosilanes as the hydrogen source. Such conditions have been reported for the reductive cleavage of benzyl ethers in solution.¹⁷⁸

To test the conditions, the lysine analogue 39 was again resynthesized, using the previously described conditions, but on 2-chlorotrityl resin and with HATU as the coupling reagent. After acetylation of the indoline nitrogen, the resin was dried. Samples of the dried resin were then swelled in anhydrous DCM and degassed with a steam of N2, before

Figure 3.9 Stuctures of PyBOP, EDCI, and DIC.

140 being subjected to different deprotection conditions. As the HPLC retention time of both the benzyl protected and the free phenol form of the lysine analogue were known, the success of on resin benzyl deprotection could be assessed by HPLC analysis of the crudes after release from the solid support.

In the end only two conditions were tested, and neither was successful. In both cases only the benzyl protected product was detected by HPLC after cleavage. The conditions tested were as follows:

- Pd(OAc)2 (30 mol %), Et2SiH (25 equiv.), Et3N (25 equiv), anhydrous DCM, N2, overnight.

- Pd(PPh3)4 (25 mol %), Ph3SiH (25 equiv), anhydrous DCM, N2, overnight.

This was a far from exhaustive search, and it is possible that a method to affect on resin benzyl deprotection could be found if more time was invested. It would be a useful addition to the process, but as it is not essential, it was decided to focus efforts on analogue generation.

It is also possible that the structure of 11 could be improved by the replacement of the benzyl ether, with an alternative protecting group. For example, the use of the more acid liable para-methoxybenzyl ether, would most likely allowed simultaneous deprotection during TFA mediated cleavage of the products from the resin. This would of course preclude cleavage conditions that utilise ultralow concentrations of TFA. However, cleavage with up 47.5 % TFA has been shown to be tolerable, so it is a feasible option. It would certainly offer flexibility, allowing cleavage of the protected products in 1 % TFA, or the deprotected products at higher concentrations.

However, the para-methoxybenzyl ether protecting group would not be compatible with the current synthesis of the 11. The activating effect of the methoxy group, would likely be susceptible to iodination, by NIS. Furthermore, it would probably be cleaved during the late stage Boc-deprotection step. Although, it could conceivable be reintroduced after Fmoc-protection. In fact, if the group was to be cleaved, and then reintroduced, then proceeding iodination of the original para-methoxybenzyl ether might be acceptable.

It certainly seems that the replacement of the benzyl ether, with a para-methoxybenzyl group, would be worth exploring in the future. However, it was not within the scope of these studies, as large scale synthesis of 11, had provided a multigram quantity of the benzyl-protected building block, and it was deemed efforts were better focused on continuing to explore its incorporation in to solid phase synthesises.

141

3.8 Repeat of the solid phase synthesis of the small library of amino acid-duocarmycin conjugates.

The library of amino acid-duocarmycin analogues was resynthesized, on 2-chlorotrityl resin, using the natural enantiomer of 11, and employing HATU as the coupling reagent.

The solid phase synthesis of each analogue was conducted on a 0.038 mmol scale, starting from commercially available preloaded resins. In addition to the five original analogues a sixth β–alanine analogue was also synthesised. Commercially preloaded 2-chlorotrityl resins are supplied as the free α-amine, thus do not require initial Fmoc-deprotection. They are supplied in this manner, as 2-chlorotrityl resins loaded with an Fmoc-protected amino acid have reduced stability on storage.¹⁴⁵ This may be attributable to mechanical stress imposed by the proximity of the large aromatic Fmoc group to the trityl structure.

The increased acid sensitivity of the 2-chlorotrityl linker was exploited to further reduce the TFA concentration during cleavage. For analogues not requiring tert-butyl side chain deprotection, cleavage was affected using 1 % TFA, and 10 % TIPS in DCM, while the TFA concentration was increased to between 10 % and 20 % with extended reaction times for those that did. Considerable variability in side chain deprotection rates was observed. For example, removal of the tert-butyl carbamate of the lysine analogue was complete with 2 hours at a TFA concentration of 10 %. However, the more stable tert-butyl ether of the serine analogue, required treatment with a TFA concentration of 20 % overnight. It is not clear whether a benefit is derived by reducing the TFA concentration below 47.5 %, when extended reaction times are required at lower concentrations. It maybe that 47.5 % is the optimal compromise between TFA concentration and reaction time for such analogues.

The scavenger composition of the cleavage cocktails was also changed from the original optimised conditions, which employed 2.5 % TIPS, and 2.5 % H₂O. This change was made because it was found that H₂O no longer served as an effective scavenger when TFA concentration was reduced below 47.5 %. When the lysine analogue was first cleaved using 10 % TFA in DCM with 2.5 % TIPS, and 2.5 % H₂O, significant formation of a side product suspected to have resulted from alkylation of the indole with the tert-butyl cation, was observed. Increasing the concentration of TIPS to 10 % effectively suppressed the formation of this side product. It is likely the reduction in the effectiveness of H₂O as a scavenger results from its reduced miscibility with the larger volumes of DCM now being used. Interestingly, if 10 % H2O was also included in the cleavage cocktail, this

142 supressed side chain deprotection of the lysine. This might be because the immiscible water layer acted as a proton sink, reducing the acidity of the DCM layer. It is likely that the concentration of TIPS could be reduced by including other DCM miscible scavengers such as EDT. However, this was not explored, due to the noxious nature of this compound.

Following cleavage the crude products were subjected to benzyl deprotection by catalytic transfer hydrogenation as previously described. Isolation from the excess ammonium formate, was affected by either reverse phase preparative HPLC, or silica gel flash chromatography, depending on the polarity of the amino acid side chain. Suitable mobile phase conditions could not be found to elute polar analogues on normal phase silica gel.

In an attempt to mediate against losses during preparative HPLC the crudes were injected in a minimal volume of DMSO, and the injection method set to insert an air plug either side of the sample. This technique prevents mixing with the mobile phase, until the sample has reached the column head.

All analogues were recovered in a usable quantity, ranging from 3.3 mg to 12 mg, representing isolated yields of between 19 % and 81 % (see figure 3.10). The best yields were for those analogues purified by flash chromatography (35, 36, 40). This may not represent intrinsically better yielding reactions for these analogues, but reflect that suboptimal recovery was being experienced with the preparative HPLC instrument. The

Figure 3.10 Structure, recovery, and yield of the analogues made in this library.

143 desired structures were confirmed by a combination of accurate mass spectrometry, ¹H NMR and DEPT-edited-HSQC experiment.

3.9 Assessment of the antiproliferation activity of 35, 36, 37, 38, 39, and 40.

The antiproliferative activity of the analogues against an HL-60 cell line was assessed using a MTS assay.¹⁷⁹ MTS is a tetrazolium compound that can be reduced by incubation with metabolising cells to give a fluorescent formazan product. This signal can be measured, and is proportional to the number of viable cells. The cell permeability of MTS is poor, and it is therefore used in conjunction with an intermediary electron acceptor, in this case PES. PES is reduced in the cytoplasm by NADH, and in turn reduces MTS in the media (scheme 3.10). In non-metabolizing cells, NADH is quickly depleted, and thus MTS reduction is inhibited.

Scheme 3.10 Reduction of MTS by viable cells, mediated by PES.

144 In the antiproliferation assay, a fixed starting concentration of cells is incubated with different concentrations of the compound under investigation, for a fixed time; in this case 72 hours. The MTS/PES reagent is then added. After incubation for a further 4 hours, the formazan signal is read. Plotting this against the log of compound concentration produces a dose response curve, from which an IC₅₀ value can be calculated for the inhibition of proliferation, and this serves as an indirect measure of cytotoxcity.

HL-60 cells are a naturally immortal cell line, originally derived from leukocytes isolated from blood donated by a female patient diagnosed with acute myeloid leukemia.¹⁸⁰ Being derived from blood, HL-60 cells are naturally adapted to allow in vitro culture as single-cell suspensions. This allows HL-60 cell cultures to be conveniently passaged by dilution.

Passaging is essential to maintain the cells in a consistent growth phase, and avoid variation between assays that might arise from senescence. When appropriately cultured, HL-60 cultures have a doubling time of around 24 hours.¹⁸¹ The HL-60 cell line was chosen here for reasons of availability and ease of culturing.

The resulting IC₅₀ for each analogue is shown in table 3.1, along with that of the commercially available cyctotoxic DNA intercalating agent doxorubicin, which was also tested as a positive control.

It was expected, that all of the analogues would have similar activity to previously reported truncated duocarmycin analogues. For example the N-acetyl duocarmcyin analogue 41 (fig 3.11), possessing the C-terminal ester of the natural product, has been reported to Table 3.1 Mean IC50 values with 95 % confidence intervals returned by the MTS assay. The assay

was performed in triplicate HL-60 cell line. Detailed protocol can be found in the experimental chapter.

145 have low nM activity, with IC₅₀ values of 1 nM and 45 nM, for the natural and unnatural enantiomers respectively.¹⁸² Admittedly these values are reported in a different cell line (murine L1210 cells). However, there is no reported evidence of HL-60 cells possessing an inherent resistance to duocamycin analogues.

It is also true that the low nM IC₅₀ values are reported for the intact spirocyclised alkylation subunit. However, it is generally accepted that halide seco forms of the alkylation subunit are equipotent to their spirocyclised counterparts, and that spriocyclisation in cells is not rate limiting.⁹⁴

Therefore, it would appear that addition of a C-terminal amino acid to the N-acetyl alkylation subunit results in at least a 1000 fold decrease in cytotoxicity. The results also tentatively suggest that the structure of the side chain may not be trivial, and apparent variation in activity was observed between the tested analogues, ranging from 30 µM to greater than 300 µM. However, with many of the confidence intervals overlapping these differences have not been shown to be significant in this study.

The suspicion at this point was that the large reduction in activity most likely reflected a decrease in cell permeability. Common to all the analogues tested is the α-carboxyl group.

These carboxylic acids will be largely ionized at physiological pH, thus inhibiting passive diffusion through the hydrophobic core of the cell membrane. Differences in cell permeability might also explain some of the apparent side chain effects. For example, the most potent analogue 36 is that possessing the non-polar aromatic side chain of phenyl alanine. This could increase the lipophilicity of this analogue promoting passive diffusion.

In contrast, two of the least potent analogues 38 and 39, contain additional ionisable groups in their side chains; the negativity charged carboxylate of glutamic acid, and the positively charged amine of lysine, this could further inhibit passive diffusion.

However the correlation between hydrophilicity and reduced activity, is not completely consistent, as is highlighted by the increased activity of the more polar serine analogue

Figure 3.11 Structure of 41.

146 (37) relative to the alanine analogue (35). Furthermore, the linear β-alanine analogue (40) appears to be considerably less active than its branched alanine counterpart. Clearly if the observed differences in activity are real, more than one factor would have to be contributing. It seems likely that the different sidechains, could have both positive or negative effects on DNA binding, as well as cell permeability, and it could be the relative combination of these factors which disrupts the trend between hydrophilicity and reduced activity.

As discussed, despite the possible differences in activity observed between the analogues, they all exhibited a reduction in cytotoxicity of over a 1000 fold, when compared to 41, and this most likely represents decreased cell permeability due to ionisation of the common α-carboxyl group. Of course the pK_a of this group will not be identical for each analogue. However, they are likely to be similar, and thus small differences in the precise molar fraction of unionised acid, are unlikely to contribute significantly to differences in cell permeability. The pKa of the α-carboxyl group is around 2, for all natural amino acids.¹⁸³ This is considerably lower than most carboxylic acids (for example acetic acid has a pK_a of around 4.75).¹⁸³ The low pK_a values of the α-carboxyl group of amino acids is attributable to the presence of the α-amino group. In the case of these analogues this group is masked by the amide bond. Therefore, it is likely that the pKa of the α-carboxyl group of these analogues is higher than that of the corresponding free amino acids. The lysine analogue may be an exception, and is likely to have the lowest pK_a, considering it is still able to form a zwitterion with the amino group of its side chain. This might be contributing to the apparent inactivity of this species in our assay.

However, assuming a physiological pH of around 7.4, and that the pKa of all the α-carboxyl groups, are likely to be below 6.15, it seems likely that all the analogues would be over 95 % ionized.

It is conceivable that this negative charge could also have a disruptive effect on minor grove binding, considering the potential charge repulsion with the polyanionic backbone of DNA. However, as will be seen from later results this appears not to be the case.

147

3.10 Synthesis and antiproliferative activity of controls 42, and