Lowering Lipophilicity by Adding Carbon: One-Carbon Bridges of

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Cite This: J. Med. Chem. XXXX, XXX, XXX−XXX

Lowering Lipophilicity by Adding Carbon: One-Carbon Bridges of Morpholines and Piperazines Seb́ astien L. Degorce,* Michael S. Bodnarchuk, Iain A. Cumming, and James S. Scott Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom

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S Supporting Information *

ABSTRACT: In this article, we report our investigation of a phenomenon by which bridging morpholines across the ring with one-carbon tethers leads to a counterintuitive reduction in lipophilicity. This effect was also found to occur in piperazines and piperidines and lowered the measured log D7.4 of the bridged molecules by as much as −0.8 relative to their unbridged counterparts. As lowering lipophilicity without introducing additional heteroatoms can be desirable, we believe this potentially provides a useful tactic to improve the drug-like properties of molecules containing morpholine-, piperazine-, and piperidine-like motifs.

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INTRODUCTION Morpholines and their derivatives are a commonly encountered motif in drug discovery projects. They may be used as groups to enhance potency through molecular interactions with a target protein (e.g., the ether oxygen acts as a key binding motif in inhibitors of lipid kinases such as some PI3K isoforms, DNAPK, mTOR, or ATR)1 or as groups to modulate physicochemical properties as the weak basicity of morpholine (e.g., N-methyl morpholine, pKa = 7.4) is similar to the pH of blood and often brings enhancements in solubility without compromising permeability to the extent seen with stronger bases. As a result, medicinal chemists have frequently utilized morpholines as part of drug discovery programs and subsequently substituted them to further optimize molecular properties. During recent medicinal chemistry discovery projects, we observed that by bridging morpholines with a one-carbon linker (effectively the net addition of a single carbon atom), lipophilicity (measured as the distribution coefficient between octanol and buffered water, log D7.4) was counterintuitively lowered. A selected set of molecules related to a series of recently disclosed IRAK4 inhibitors2 is shown in Table 1 for illustrative purposes: the observed log D7.4 of the bridged analogues 1d and 1e was significantly lower (Δlog D7.4 = −0.7) than that of the parent morpholine 1a. This was in contrast with the monomethyl analogues 1b and 1c, which showed an increase in lipophilicity (Δlog D7.4 = +0.4) and was not well predicted by partition coefficient predictors such as clogP (ΔclogP = +0.3) or ACDlogP (ΔACDlogP = −0.1), although the latter predicted a slight decrease. As measured log D7.4 is a composite of log P and pKa (for monobases log D7.4 = log P − log[1 + 10(pKa−7.4)]), we measured the pKas of 1a and 1e and © XXXX American Chemical Society

found that bridged morpholine 1e was significantly more basic than 1a (ΔpKa = +0.6), in line with ACD predictions (ΔACDpKa = +0.7). This suggested that at least some of the lipophilicity lowering effect was attributable to an increase in basicity. Predictive programs such as ACDlogD considerably underestimated the lipophilicity for these molecules, although the magnitude of the change for addition of the methyl in 1b and 1c agreed well with experimental data (Δlog D7.4 ∼ ΔACDlogD ∼ +0.5) and the ACD program correctly predicted that the bridged molecules will be less lipophilic (ΔACDlogD = −1.0, Δlog D7.4 = −0.7), albeit to a greater extent than measured. This phenomenon caught our attention because ways to lower lipophilicity without resorting to the introduction of additional heteroatoms are useful so that other properties are not compromised. For example, lowering lipophilicity by introducing hydrogen bond donors or acceptors usually results in increased polar surface area and can adversely impact permeability (and thus absorption) beyond the amount expected based on the log D reduction alone.3 Lowering lipophilicity through increasing basicity or acidity may impact other parameters, such as permeability/absorption, and may also introduce undesired activity such as hERG inhibition in the case of strong bases or high levels of plasma protein binding in the case of acids. In the morpholine examples presented in Table 1, however, no adverse effect attributable to the increased basicity of bridged morpholines 1d−e was observed on properties like hERG, permeability, or rat Received: July 23, 2018 Published: September 6, 2018 A

DOI: 10.1021/acs.jmedchem.8b01148 J. Med. Chem. XXXX, XXX, XXX−XXX

Journal of Medicinal Chemistry

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Table 1. Examples of Morpholine Derivatives and Selected Lipophilicity-Related Properties

a ACD Lab 2015 was used to generate predictions. bDistribution coefficient measured using shake-flask methodology with a buffer/octanol volume ratio of 100:1. cMeasured pKa of the morpholine. dhERG inhibition.4 eIntrinsic permeability using Caco2 cells (10−6 cm/s).5 fHepatocyte intrinsic clearance (CLint, μL/min/106 cells).6

Figure 1. Selected literature examples of one-carbon 2,5-bridged morpholines.

hepatocytes turnover (e.g., R,R enantiomer 1d was actually found to be more metabolically stable than morpholine 1a). A number of literature examples can be found of 2,5- onecarbon bridged morpholines being used in a medicinal chemistry context, and a selection of these are presented in

Figure 1, with their reported primary and off-target activities relative to the parent morpholines. Among these molecules, we found representatives of basic aliphatic morpholines (2−4), amides, and sulfonamides (5−6) and aromatic morpholines (7−11). The one-carbon 2,5-bridged morpholine moiety of B



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the KSP inhibitors 2b,7 the MCR4 agonist 6b,8 both by Merck, and the IGF1R inhibitor 4b8 by Bristol-Myers Squibb, were equipotent with their parent morpholines, but the motif could also lead to dramatic loss of potency as in the HBV capsid inhibitors 3b9 from Roche. In the case of the mTOR inhibitors 8a−c,10 medicinal chemists from Wyeth succeeded in improving selectivity over PI3Kα with one bridged morpholine analogue, albeit at some mTOR potency cost. This strategy was also applied by Sanofi researchers to improve the selectivity of the Vps34 inhibitors 7b,11 albeit with limited success. A similar approach was also reported by Genentech to improve the margin over CYP2C9 of their NAMPT inhibitors 5b.12 The use of these one-carbon, 2,5-bridged morpholines has been shown to be beneficial across a variety of unrelated targets, but surprisingly, little has been reported about the effects of this moiety on general physicochemical properties of the corresponding molecules. Within AstraZeneca, we have reported morpholine bridging in the DNAPK inhibitor 9b13 and ATR inhibitor 10b,14 both of which resulted in less potent analogues relative to the unsubstituted morpholines. Both bridged examples, like 1d and 1e, were also found to be less lipophilic than the parent despite the net addition of a carbon atom and the fact that the morpholine N is nonbasic in these examples. In the case of the pair of EGFR inhibitors 11a−b,15 both molecules showed similar potency with lipophilicity slightly higher for the bridged analogue. An analysis of the relative frequency of bridged morpholines reported in the scientific literature is presented in Figure 2.

pattern, potentially reflecting the synthetic challenge of introducing this sterically hindered nitrogen. In the corresponding bridged analogues, the 2,6- was most prevalent (0.95%), followed by the 3,5- (0.42%), with both being more exemplified than the corresponding one-carbon systems. Only very few examples of the 2,5- substitution (0.01%) were described in the literature, potentially due to synthetic challenges associated with this motif. The low prevalence of bridged morpholines in the literature, together with the interesting lipophilicity effects observed, led us to further investigate this class of compounds using a combination of computational techniques and interrogation of examples from the AstraZeneca compound database.

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RESULTS AND DISCUSSION Computational Investigation. To investigate whether basicity was the principal contributing factor to the observations above, we decided to computationally examine NAc morpholines as examples of simple, neutral systems. First, we looked at individual contributions to the predictive model ACDlogP in order to understand how the model perceived these changes (Figure 3). On N-acetylmorpholine 12, methylene groups forming the ring all contribute by +0.56, irrespective of whether they are proximal to the nitrogen or the oxygen. Additional methyl groups in 13 and 14 are given the contribution of +0.91, again irrespective of their position but to correct for the effect on the bearing ring carbon atom that carbon is now given the lower contribution of +0.15 instead of +0.56, resulting in a net ACDlogP increase of +0.49 compared to the bridged analogues. The effect of disubstitution follows the same principles. The case of one-carbon bridged morpholines 18, 19, and 22a is interesting and identical: the additional methylene is also given the standard contribution of +0.56, but the bearing carbon atoms are corrected differently (+0.21 vs +0.15) compared to 13 and 14, presumably incorporating a correction factor for the extra ring they form. We attributed this double correction to be the source of the resulting net decrease in ACDlogP compared to 12 (−0.15). The case of the two-carbon bridged morpholines 20, 21, and 23a also follows a similar correction, but the extra bridging carbon atom now outweighs the benefit (ΔACDlogP = +0.41 compared to 12). In summary, ACDlogP predicts a small decrease in lipophilicity (ΔACDlogP = −0.15) for the one-carbon bridges (regardless of connectivity) in contrast to an increase (ΔACDlogP = +0.49) for the addition of a methyl group. For the two-carbon bridges, an increase (ΔACDlogP = +0.41) in lipophilicity is predicted, although this is lower than the addition of two methyl groups (ΔACDlogP = +0.98). Three-dimensional lowest energy conformations of N-acetyl morpholines were generated and optimized by quantum mechanics (QM) at the density functional theory level, using a 6-31G**+ basis set and the B3-LYP functional. As might be expected, the effect of nonbridging methyl groups around the morpholine results in a chairlike conformation (see Supporting Information) with the flanking methyl groups generally sitting equatorially, the exception being axial-methylation on the carbon adjacent to the N atom. Distinct differences were seen, however, when the group is used to bridge across the ring. The primary effect of bridging across the morpholine ring is that this linker changes the chair conformation the ring usually prefers to adopt and locks it into a low-energy, envelope-style conformation. Bridging across either the N (18) or O (19)

Figure 2. Prevalence of bridged morpholines in the scientific literature. Prevalence of various substitutions based on a SciFinder17 search carried out on 22nd May 2018. Substitution was blocked at all positions with the exception of the nitrogen, and no account of stereochemistry was taken apart from the dimethyl substitution which was fixed as cis.

Relative to the parent unsubstituted morpholine (>1.5 M hits), the monomethyl substituted morpholines are much less common with the 2- and 3- substitutions, each accounting for around 2% of the total. The proportion of the corresponding one-carbon bridged analogues is much smaller, with the 2,5- substitution pattern most common (0.36%, although this is potentially a consequence of the 2,5- onecarbon bridges being reported in both racemic and enantiomerically pure forms), followed by the 3,5- (0.19%) and last the 2,6- (0.14%). Notably the 2,6- systems have been described in the comprehensive review of oxetanes by Wuitschik.16 For the two-carbon substitution, the 2,6- dimethyl is much more common than the 3,5- dimethyl substitution C



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Figure 4. Three-dimensional models of various bridged Nacetylmorpholines. Bridged carbon atoms are shown in purple, with the base morpholine carbon scaffold shown in green. Nitrogen atoms are shown in blue, with oxygen atoms shown in red.

Table 2. Percentage Change Relative to Morpholine 12 in the Total Surface Area and Oxygen Accessibility for Methylated Morpholine Analogues total surface area

Figure 3. ACDlogP contributions to various substituted morpholines. a Individual carbon contributions to ACDlogP in morpholines 12−23; additional atoms and their contributions are shown in purple. For clarity, unchanged contributions compared to 12 have been omitted in substituted morpholines. bOverall ACDlogP predictions. cDifferences in ACDlogP relative to N-acetylmorpholine 12.

atoms results in a more rigid structure, with the fourmembered ring adopting a conformation which is similar to that of azetidine or oxetane respectively. This leads to a significant reduction in the total surface area of the molecule compared to the 2- or 3-methyl versions (Figure 4 and Table 2). The reduced surface area results in a molecule which is both less lipophilic and more likely to be strongly solvated compared to the monomethyl versions, consistent with the observed reductions in ACDlogP. Bridging across the 2- and 5positions of the morpholine results in both enantiomers 22b and 22c adopting a boat-like conformation, which again reduces the exposed surface area of the molecule relative to the unbridged analogues 13 and 14. The predicted structure of 22b is in excellent agreement with that of a closely related small molecule crystal structure (CCDC code EZUNUK) and that of a 2,5-bridged piperazine in the Protein Data Bank (PDB 5DKC).18 It is significant to note that the solvent accessibility of the morpholine oxygen atom increases for three of the onecarbon bridged analogues (19, 22b, 22c) compared to both the monomethyl analogues (13, 14) and morpholine itself

oxygen accessibility

entry

type

absolute (Å2)

relative to 12 (%)

absolute (Å2)

relative to 12 (%)

12 13 18 14 19 22b 22c 16 20 17 21 23b 23c

unsubstituted 3-methyl 3,5- 1C bridge 2-methyl 2,6- 1C bridge 2,5- 1C bridge 2,5- 1C bridge 3,5-dimethyl 3,5- 2C bridge 2,6-dimethyl 2,6- 2C bridge 2,5- 2C bridge 2,5- 2C bridge

146 157 153 163 153 153 152 182 165 171 164 165 164

0 +8 +5 +12 +5 +5 +4 +25 +13 +17 +12 +13 +12

18 16 17 12 23 19 18 15 12 18 18 17 16

0 −11 −5 −33 +28 +6 0 −17 −33 0 0 −5 −11

(12), consistent with the hypothesis that these molecules are more strongly solvated in water. The two-carbon bridges which go across either heteroatom (20, 21) both adopt a more familiar chairlike conformation in which the bridge sits axially. Our proposed conformation of 20 is in good agreement with a disclosed crystal structure of a two-carbon bridged piperazine containing compound (4NLD).19 The surface area of these bridges is again significantly reduced compared to that of the dimethyl analogues (16, 17). The two enantiomers of the asymmetric bridges across the 2- and 5- positions (23b, 23c) adopt a rigid conformation akin to the bicyclo[2.2.2]octanes, with the oxygen atom being significantly more solvent accessible compared to the 2,5-dimethyl analogue 15. Once again, the D



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Table 3. Effect on Measured log D7.4 Consecutive to Substitution Across Multiple Morpholine/Piperazine/Piperidine Analoguesa

a Matched molecular pair analysis based on molecules restrained to 300 ≤ MW ≤ 700 and −2 ≤ log D7.4 ≤ +5. Δlog D7.4 relative to the unsubstituted morpholine, piperazine, or piperidine derivatives are reported as averages between all matched pairs with standard deviations. For simplicity, morpholine numbering was kept throughout, i.e., with atom “X” being arbitrarily attributed position 1. Color coding:

Table 4. Effect on Measured log D7.4 Consecutive to Disubstitution Across Multiple Morpholine/Piperazine/Piperidine Analoguesa

Matched molecular pair analysis based on molecules restrained to 300 ≤ MW ≤ 700 and −2 ≤ log D7.4 ≤ +5. Δlog D7.4 relative to the unsubstituted morpholine, piperazine, or piperidine derivatives are reported as averages between all matched pairs with standard deviations. For simplicity, morpholine numbering was kept throughout, i.e., with atom “X” being arbitrarily attributed position 1. Color coding: a

both basic and neutral morpholines, we elected to apply this approach to the AstraZeneca compound collection and extended it to look at other six-membered rings (such as piperidines and piperazines). Our internal compound collection was queried using a number of the substructures (details in the Supporting Information) to produce Tables 3 and 4. The method is exemplified below for the case of morpholines and applies to other studied variants. Further substitution was prohibited except on the highlighted N atom, and molecules that contained more than one morpholine motif were excluded for simplicity. Additional constraints on molecular weight (300 ≤ MW ≤ 700) and measured log D7.4 (−2 ≤ log D7.4 ≤ +5) were used to ensure molecules were in drug-like space and, in the case of log D, within the measurement range of the assay. A customized, proprietary Pipeline Pilot protocol similar to that previously published by our group22 was used to identify the unsubstituted analogues as matched pairs. This protocol essentially proceeded in three key steps: (a) fragmentation of the substituted morpholine to extract the variable “R” group

surface area of the bridge is less than that of the unbridged version, consistent with the calculated ACDlogP. The key findings from the conformational analysis are that the increased conformational rigidity enforced by bridging leads to a more rigid, compact structure, with lower surface area and, importantly, that the morpholine O is more exposed to solvent. Crucially, the predicted conformations are in excellent agreement with crystallographic poses of these substructures and closely related analogues. When partitioned between octanol and water, bridged morpholines might therefore express a preference for water solvation. The combination of these effects is hypothesized to help lower the log D of the bridged morpholines relative to their flanked examples. Matched Molecular Pair Analysis (MMPA). MMPA, which compares the properties of two molecules that differ only by a single structural transformation,20,21 is a useful method to interrogate large data sets and extract trends and likely effects on various parameters of changing one group to another. Given the lipophilicity effects seen with bridging of E



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attached to the N atom (see exemplar structures in Table 3), (b) attachment of the resulting R group to the N atom of unsubstituted morpholine, and (c) exact match against existing molecules. Matched pairs were then later combined based on their common R group to form families of molecules for each type of X: for monomethyl morpholines, only structures of single enantiomers were included; for dimethyl morpholines, only the cis-2,6- and cis-3,5 structures were retained; in the case of the 2,5 bridges, racemic and single enantiomer structures were kept and analyzed separately because lipophilicity of diastereoisomeric mixtures can be different. The resulting list was then manually curated, and matched pairs where at least one of the results was out of range were excluded. Statistics and visualizations were generated using TIBCO Spotfire v7.9.1. The typical assay error on our log D7.4 measurements being approximately ±0.1 (based on cyclobenzaprine being used as a standard, log D7.4 = 2.8, StdDev = 0.1, N = 3824), log D visualizations are presented with horizontal lines at ±0.2 (i.e., twice the assay error, one for each member of the pair) to highlight log D differences that we considered to be outside of the expected noise of the assay. Likewise, results in Tables 3 and 4 were color-coded in bins of 0.2. The results were analyzed and are discussed below. 2- and 3-Methyl Substitution. As shown in Figure 5, the addition of a single methyl group in morpholines at either the

examples and larger standard deviations should be treated with caution. One-Carbon Bridges. In the case of 2,5- one-carbon bridged cores, the effect noted on our project examples (Table 1) proved to be a general trend across a larger number of morpholine/piperazine analogues. Figure 6 shows that 2,5-

Figure 6. One-carbon bridges. Visualization based on Table 3. Δlog D7.4 of matched molecular pairs are expressed relative to the unsubstituted core, and error bars are shown at ± StdDev.

one-carbon bridged morpholines generally display a much lower log D than the corresponding unsubstituted morpholines (Δlog D7.4 = −0.18 to −0.44), in contrast to the increase noted for 2- and 3-methyl counterparts (Δlog D7.4 = +0.32 to +0.40). When we extended our analysis, we observed similar decreases in NH (Δlog D7.4 = −0.34 to −0.53), NMe (Δlog D7.4 = −0.70 to −0.90), and NAc (Δlog D7.4 = −0.41 to −0.47) piperazines, and a few racemic piperidines (Δlog D7.4 = −0.17). The observation above led us to investigate other types of one-carbon bridges such as the 2,6- and 3,5- analogues. Unfortunately, fewer examples were available, but the bridged molecules again proved less lipophilic than the corresponding methyl analogues, although statistically significant reductions in lipophilicity relative to the unsubstituted cores were not seen. For example, there was little to no difference for 2,6- onecarbon bridged morpholines (6-oxa-3-azabicyclo[3.1.1]heptane; Δlog D7.4 = −0.04) and NH piperazines (3,6diazabicyclo[3.1.1]heptane; Δlog D7.4 = +0.09). The most notable observations were made on 2,6- one-carbon bridged NMe (6-methyl-3,6-diazabicyclo[3.1.1]heptane; Δlog D7.4 = −0.49) and NAc piperazines (1-(3,6-diazabicyclo[3.1.1]heptan-6-yl)ethenone, Δlog D7.4 = −0.27), albeit on limited examples. The trend was also confirmed in 3,5- one-carbon bridges with single NMe and NAc examples. In conclusion, one-carbon bridges generally decrease the lipophilicity of morpholines, piperazines, and piperidines, with the impact being largest for the 2,5- one-carbon bridge, where lipophilicity is lowered significantly. To understand these observations further, we also looked at two-carbon bridges across the same core structures together with their corresponding cis-dimethyl analogues with the results summarized in Table 4. 2,6-, 2,5-, and 3,5-cis-Dimethyl Substitution. In a similar way to the monomethyl analogues, all four possible cisdimethylmorpholines (trans stereoisomers were not investigated because bridging can only occur with the cis-

Figure 5. Monomethyl substitution. Visualization based on Table 3. Δlog D7.4 of matched molecular pairs are expressed relative to the unsubstituted core, and error bars are shown at ± StdDev.

2 or the 3 positions were roughly in agreement with ACDlogD predictions, with lipophilicity increasing by the expected amount (Δlog D7.4 = +0.32 to +0.40). In piperazines, depending on the group on the second nitrogen, the effect was somewhat different: NH piperazines showed the same trend as morpholines, albeit slightly more pronounced (Δlog D7.4 = +0.40 to +0.45), but NMe piperazines showed less of an effect (Δlog D7.4 = +0.19 to +0.28), whereas NAc piperazines showed an effect twice as large with methyl substitution proximal to the NAc (Δlog D7.4 = +0.50) as methyl substitution distal to the NAc (Δlog D7.4 = +0.25). We attributed this last observation to the fact that a methyl group proximal to the NAc usually sits in an axial position, maximizing the surface of the additional methyl group exposed to solvent. Interestingly, this latter trend was similar in piperidines, where the increase was even larger (Δlog D7.4 = +0.79 to +0.93 vs +0.27 to +0.42), but the small number of F



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stereoisomers) showed the expected log D increase (Δlog D7.4 = +0.65 to +0.69, Figure 7), in agreement with but lower than

the analogous one-carbon bridge, although to a much smaller extent (Δlog D7.4 = −0.37 vs −0.83, respectively). The number of identified matched pairs was higher for both 2,6- and 3,5- two-carbon bridged analogues and are believed to be statistically significant, although for some the standard deviations were larger than previously observed (Figure 9).

Figure 7. Dimethyl substitution. Visualization based on Table 4. Δlog D7.4 of matched molecular pairs are expressed relative to the unsubstituted core, and error bars are shown at ± StdDev. Figure 9. Asymmetrical two-carbon bridges. Visualization based in Table 4. Δlog D7.4 of matched molecular pairs are expressed relative to the unsubstituted core, and error bars are shown at ± StdDev.

the ACDlogP incremental addition of two methyl groups (12 to 15−17, ΔACDlogD = +0.98). A similar observation was noted with limited examples of NH piperazines. In the case of NMe piperazines, however, differences were observed in the magnitude of the increase: the difference was larger with the two enantiomeric cis 2,5-dimethyl analogues (Δlog D7.4 = +0.41 to +0.45) than with the achiral cis 2,6-dimethyl analogues (numbering as per Table 4, Δlog D7.4 = +0.23). Unfortunately, no data was available for cis 3,5-dimethyl substitution, although limited data on NAc piperazines, suggested a similar behavior. Two-Carbon Bridges. Only a handful of racemic examples of 2,5- two-carbon bridges were available in our collection for analysis (consistent with the lower prevalence of these bridges seen in Figure 2) and, although limited, data also suggested log D values that would be lower than expected and considerably lower compared to the dimethyl analogues (Figure 8). In the case of the two NMe piperazines examined, these showed a reduction in log D that was consistent with the reduction of

Interestingly, no clear lowering trend emerged, and many of the measured log D7.4s of both types of bridges seemed to be closer to those of the dimethyl analogues or at best similar to the unsubstituted cores (e.g., the case of the 2,6- two-carbon bridged morpholines was comparable to that of a cis-2,6dimethylmorpholines; Δlog D7.4 = +0.45 vs +0.65, respectively). Although a neutral effect on lipophilicity from the addition of two methylene groups was also surprising in some examples (e.g., 3,5- two-carbon bridged morpholines vs cis-3,5dimethylmorpholine; Δlog D7.4 = +0.09 vs +0.68, respectively), we rarely observed lower lipophilicity as in the analogous onecarbon bridges (one notable exception was 2,6- two-carbon bridged NMe piperazines, Δlog D7.4 = −0.16). This suggested to us that the lipophilicity lowering effect seen with the onecarbon bridges is somewhat unique in its magnitude and related to their more rigid conformation, maximizing the solvent-exposed surface area of heteroatoms (Figure 4). We hypothesized that, as the size of the bridge increases, conformations become less constrained and thus the effect is less pronounced and dominated by the lipophilic addition of two methylene groups. Potential Benefits of One-Carbon Bridges. The lower lipophilicity of the one-carbon bridges can have multiple benefits on properties affected by a high partition/distribution coefficient. As this is partly caused by an increase in basicity, we examined potential effects in piperazine examples reported by our group. Figure 10 shows the effect on properties such as hERG, hepatic intrinsic clearance and permeability in relation to the pKa difference between various one-carbon bridges and the parent piperazines. The P2X(7) receptor antagonists/interleukin-1β inhibitor 24b23 showed a pKa increase similar to that measured in morpholine 1e(ΔpKa = +0.6), but similarly to the IRAK4 inhibitor, 24b displayed no increased hERG inhibition and no adverse impact on in vitro intrinsic clearances in rat hepatocytes. In a series of tankyrase/Wnt inhibitors 25a− d,24 all one-carbon bridges increased the pKa of the NH

Figure 8. Two-carbon bridges across the 2- and 5-positions. Visualization based in Table 4. Δlog D7.4 of matched molecular pairs are expressed relative to the unsubstituted core, and error bars are shown at ± StdDev. G



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Figure 10. Physicochemical and metabolic stability properties for a selection of reported one-carbon bridged piperazines.2,23−26 Data as per Table 1 unless otherwise specified.

consideration be given to other features and the overall properties of molecules. Where permeability may be a risk, a lipophilicity-lowering change may not be desirable, but in cases where high metabolism or strong hERG inhibition are observed, one-carbon bridges may offer some design solutions.

piperazine by about +0.3, but the effect on hERG was either negligible or slightly beneficial. Even in the more basic NMe analogue 25f (pKa = 8.7), no detrimental effect on hERG was observed, and in all cases the turnover in rat hepatocytes was lowered significantly. Likewise, the large increase in basicity of NMe piperazine 26b25 (ΔpKa = +1.4) did not negatively impact rat hepatocyte turnover in this series of PAK1 inhibitors but provided a large benefit in lowering hERG inhibition by nearly 100-fold (hERG ΔpIC50 = −1.9). However, in the case of 26b, a negative impact was noted on permeability, highlighting this as a possible risk and one that is potentially sensitive to the number of hydrogen bond donors and acceptors in 26a,b. Structurally related JAK1 inhibitor 27c26 was recently reported as a metabolically more stable compound in human liver microsomes and in rat hepatocytes. Interestingly, the (R,R) enantiomer 27b was found to be less stable than even the parent, suggesting a potential molecular recognition in this series. In the series of NAc piperazine IRAK4 inhibitors 28a−c,2 the two symmetrical one-carbon bridges were found to only slightly increase basicity (ΔpKa = +0.3) and, as noted before, showed a beneficial impact on hepatic metabolism stability and hERG inhibition. However, even in these near neutral examples (28b, pKa = 7.5; 28c, pKa = 7.4) intrinsic permeability was lowered in both bridges. Overall, this suggested that the benefits of onecarbon bridges in morpholines and piperazines may not be universal but may offer a meaningful opportunity in many cases. As always, we would recommend that careful

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CONCLUSION From an unexpected observation in our data, our curiosity led us to systematically investigate the lipophilicity-lowering effect of bridging morpholines and piperazines with one- and twocarbon tethers. The one-carbon bridges seem particularly effective at decreasing the distribution coefficient (log D) in a majority of cases, by as much as −0.8, relative to their unbridged counterparts. This effect was found to be partly due to increased basicity and partly due to an increased solventexposed polar surface area resulting from conformational changes. Although not a panacea, we would recommend that medicinal chemists consider the use of one-carbon bridges as a potential strategy to modulate the physicochemical properties of morpholines and piperazines, especially in cases where issues are observed with metabolism, hERG inhibition, or other detrimental properties correlated with lipophilicity. In addition, these bridged moieties can confer some targetspecific benefits, particularly where the conformational restriction can potentially be used to improve selectivity and/or increase potency via subtly changing the shape of the moiety. H



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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jmedchem.8b01148.

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The syntheses of molecules 1a−e and 28a−c (not previously described) are detailed together with summarized data used for Figures 1 and 10 (PDF) Molecular formula strings (CSV)

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. ORCID

Sébastien L. Degorce: 0000-0002-9478-5106 James S. Scott: 0000-0002-2263-7024 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We acknowledge Johan Wernevik and the Mölndal DMPK screening group for the generation of several log Ds, which enabled us to maximize the number of matched pairs in our analysis. Eva Lenz, Rodrigo Carbajo, and Paul Davey are thanked for the characterization of previously unpublished IRAK4 inhibitors reported therein. We are also grateful to William McCoull for his help with this manuscript. Finally, we thank all the AstraZeneca chemists who made bridged morpholines and piperazines and without whom this analysis could not have been done.

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ABBREVIATIONS USED ATM, ataxia telangiectasia mutated kinase; ATR, ataxia telangiectasia mutated and RAD3-related kinase; DNAPK, DNA-dependent protein kinase; EGFR, epidermal growth factor receptor; hERG, human ether-à-go-go-related gene; IGF1R, insulin-like growth factor-receptor; IRAK4, interleukin-receptor-associated kinase 4; KSP, kinesin spindle protein; MC4R, melanocortin 4 receptor; MMPA, matched molecular pair analysis; mTOR, mammalian target of rapamycin; MW, molecular weight; NAMPT, nicotinamide phosphoribosyl transferase; PAK1, P21-activated kinase 1; P2X7, purinergic receptor P2X7; PI3K, phosphatidylinositol 3′-kinase; QM, quantum mechanics

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