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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
J Org Chem. Author manuscript; available in PMC Jul 20, 2013.
Published in final edited form as:
PMCID: PMC3444172
NIHMSID: NIHMS393164
O-Nucleoside, S-Nucleoside, and N-Nucleoside Probes of Lumazine Synthase and Riboflavin Synthase
Arindam Talukdar, Yujie Zhao, Wei Lv, Adelbert Bacher, Boris Illarionov, Markus Fischer, and Mark Cushman*
Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, D-20146 Hamburg, Germany
*To whom correspondence should be addressed. Tel: 765-494-1465. Fax: 765-494-6790. cushman/at/purdue.edu
Lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin, while riboflavin synthase catalyzes the last step. O-Nucleoside, S-nucleoside and N-nucleoside analogues of hypothetical lumazine biosynthetic intermediates have been synthesized in order to obtain structure and mechanism probes of these two enzymes, as well as inhibitors of potential value as antibiotics. Methods were devised for the selective cleavage of benzyl protecting groups in the presence of other easily reduced functionality by controlled hydrogenolysis over Lindlar catalyst. The deprotection reaction was performed in the presence of other reactive functionality including nitro groups, alkenes, and halogens. The target compounds were tested as inhibitors of lumazine synthase and riboflavin synthase obtained from a variety of microorganisms. In general, the S-nucleosides and N-nucleosides were more potent than the corresponding O-nucleosides as lumazine synthase and riboflavin synthase inhibitors, while the C-nucleosides were the least potent. A series of molecular dynamics simulations followed by free energy calculations using the Poisson-Boltzmann/surface area (MM-PBSA) method were carried out in order to rationalize the results of ligand binding to lumazine synthase, and the results provide insight into the dynamics of ligand binding as well as the molecular forces stabilizing the intermediates in the enzyme-catalyzed reaction.
Riboflavin, also known as vitamin B2, is the central component of the cofactors FAD and FMN, and is therefore required for a wide variety of cellular processes. It plays a key role in energy production, and is required for the metabolism of fats, carbohydrates, and proteins. Animals, including humans, obtain it from their diet, while a variety of pathogenic Gram-negative bacteria, including Escherichia coli and Salmonella typhimurium, lack an efficient riboflavin uptake system and are therefore absolutely dependent on endogenous synthesis of this vitamin.14 The riboflavin biosynthesis gene ribB has recently been shown to play an essential role in different Salmonella disease models.5,6 Since animals lack the riboflavin biosynthetic pathway, inhibitors of the pathway should be selectively toxic to the pathogen and not the host. A detailed understanding of the structure and mechanism of the enzymes involved in the biosynthesis of riboflavin is essential for the rational design of enzyme inhibitors with antibacterial activity.
Lumazine synthase and riboflavin synthase catalyze the last two steps in the biosynthesis of riboflavin (Scheme 1). The initial steps in the biosynthesis of riboflavin lead from GTP to the pyrimidinedione 1.715 Lumazine synthase catalyzes the condensation of 3,4-dihydroxy-2-butanone 4-phosphate (2)1618 with 5-amino-6-D-ribitylamino-2,4(1H,3H)pyrimidinedione (1) yielding 6,7-dimethyl-8-D-ribityllumazine (3).19,20 The four-carbon phosphate moiety 2 originates from the pentose phosphate pool by the loss of C-4. The riboflavin synthase-catalyzed dismutation of two molecules of 6,7-dimethyl-8-D-ribityllumazine (3) results in the formation of one molecule of riboflavin (4) and one molecule of the substituted pyrimidinedione 1, which can be recycled by lumazine synthase.2129 The pyrimidinedione derivative 1 is therefore both a substrate of lumazine synthase and a product of riboflavin synthase and analogues of 1 could therefore conceivably bind to and inhibit both lumazine synthase and riboflavin synthase.
The mechanism of the reaction catalyzed by lumazine synthase has not been completely elucidated. The currently proposed mechanism outlined in Scheme 2 involves initial Schiff base formation between the four-carbon carbohydrate 2 and the pyrimidinedione derivative 1, resulting in the imine 5, which eliminates phosphate to form the enol 6 (Scheme 2). Tautomerization of the enol 6 to the ketone 7, followed by the addition of the secondary amino group to the ketone, leads to the formation of the covalently hydrated lumazine 10. Elimination of water yields the 6,7-dimethyl-8-D-ribityllumazine (3). A redox disproportionation reaction of two molecules of 3, followed by a 4 + 2 cycloaddition reaction and two elimination reactions, have recently been advanced in order to explain the conversion of two molecules of the lumazine 3 to one molecule of riboflavin (4) and one molecule of the pyrimidinedione 1 (Scheme 3).30
X-ray crystallography of complexes of the purinetrione inhibitor 15 (PDB code: 1W19) and the phosphonate analogue 16 (PDB code: 1NQW) with lumazine synthase have established that the phosphate of the hypothetical Schiff base initially binds far away from the ribityl side chain as depicted roughly in chemical structure 5.31 Although the mechanism outlined in Scheme 2 is certainly very reasonable, the details of the pathway, such as the timing of phosphate elimination relative to the conformational reorganization of the side chain to allow cyclization, remain unknown.32 For example, it has been proposed that the whole phosphate side chain rotates toward a cyclic conformation 8 with assistance from the enzyme before phosphate elimination and dehydration occur to form the cis Schiff base 7 directly (Scheme 2).31 The possible initial formation of a thermodynamically less stable cis Schiff base, or, the isomerization of the trans Schiff base 17 to the cis Schiff base 7, have not been established. By a semiempirical approach, the energy barrier for the 17 to 7 isomerization was calculated to be 19.6–21 kcal/mol.33 More recently, as a result of the temperature-dependent pre-steady-state kinetic experiments of lumazine synthase from Aquifex aeolicus, it was proposed that one of the subsequent steps occurring after phosphate elimination and tautomerization is the rate-determining step.34,35
Ligand Design
In order to gain insight into the structural change of the Schiff base side chain occurring after formation of intermediate 5, metabolically stable substrate analogues are necessary that would allow Schiff base formation, but would not allow the cyclization to proceed. The crystal structure of analogue 18 (PDB Code: 1KYY) bound to B. subtilis lumazine synthase36 has revealed that the ribitylamino nitrogen has no obvious direct role in binding the ligand to the enzyme (Figure 1), suggesting that the replacement of the nitrogen with another atom might not affect binding to the enzyme.
FIGURE 1
FIGURE 1
Hydrogen bonds and distances of the substrate analogue 18 bound in the active site of B. subtilis lumazine synthase. The distances are in Å.
Replacement of the nitrogen atom of the ribitylamine side chain with oxygen, sulfur, or carbon would not be expected to produce gross changes in the orientation of ribityl chain of 18 (Figure 1), and the resulting compounds could possibly bind to both lumazine synthase and riboflavin synthase. They obviously could not complete the catalytic cycle as they cannot undergo the nucleophilic attack by the ribityl amino group to form the cyclic lumazine derivative 3. They might therefore be expected to be lumazine synthase inhibitors, and they might also provide information about the conformations of reaction intermediates if they could be crystallized with the enzyme.
Most potent lumazine synthase inhibitors contain a C3–C5 phosphate side chain and are analogues of intermediate 5 (Scheme 2).37,38 Hypothetically, mechanism probes without a phosphate side chain would be expected to be moderate lumazine synthase inhibitors compared to the more potent ones with a phosphate side chains because the phosphate binds to Arg, Thr, Ala, Gln, and Ser residues in the active sites of lumazine synthases isolated from a variety microorganisms.31,32,3943 Accordingly, intermediate 5 is likely to have a higher affinity for the enzyme than intermediates 6 or 7. Enol 6 is an intermediate from the hypothetical reaction mechanism after phosphate cleavage. In the present study, metabolically stable analogues of lumazine synthase substrate 1 and reaction intermediate 6 were designed.
The proposed intermediate 6 is a Schiff base. Schiff bases are not stable under acidic and reductive conditions. Bioisosteres 19 and 20 were therefore designed as metabolically stable analogues of the Schiff base 6. These amides have partial double bond character between the amide nitrogen and the carbonyl carbon. Compound 19 has a methacroyl side chain attached to 5-amino-6-ribitylamino-1H-pyrimidine-2,4-dione, which resembles the intermediate 6.
Compounds 2124 mimic the intermediate 1, which is a substrate of the lumazine synthase-catalyzed reaction and a product of the riboflavin synthase-catalyzed reaction. These compounds therefore have the potential to inhibit both enzymes. There are indeed many common features of riboflavin synthase and lumazine synthase, and the dual inhibitor concept has, in principle, a strong theoretical basis. In fact, the sequences and structures of riboflavin synthases of Archaea closely resemble those of 6,7-dimethyl-8-ribityllumazine synthase, as evidenced by the crystal structure of a pentameric Methanocaldococcus jannaschii riboflavin synthase in complex with a substrate analogue.44
Molecular Modeling of O- and S-Nucleosides
A 2.4 Å resolution X-ray structure is available of the substrate analogue 18 (PDB code: 1KYY)36 complexed with B. subtilis lumazine synthase (Figure 1). The structure allows the construction of hypothetical models of the binding of 2122 to lumazine synthase (Figure 2), which were produced by docking these compounds into the active site of M. tuberculosis lumazine synthase. Docking was performed with GOLD (BST, version 3.0, 2005, for details see the Experimental section). The energies of the complexes were minimized using the MMFF94s force field while allowing the ligand and the protein structure contained within a 6 Å diameter sphere surrounding the ligand to remain flexible with the remainder of the protein structure frozen. The calculated structures of 2124 bound to lumazine synthase suggest that these inhibitors bind in the active site in an almost identical fashion to 18 (Figure 2).
Figure 2
Figure 2
Calculated structures of the O- and S-nucleoside derivatives (2124) complexed with B. subtilis lumazine synthase. The amino acid residues involved in the active site are labeled and shown in stick. The black dashed lines represent the hydrogen (more ...)
Synthesis of O-Nucleosides
Since both the ribityl hydroxyl groups and the pyrimidinedione ring have the potential to be alkylated, the attachment of a side chain on the amino group at C-5 of the pyrimidinedione moiety required that the ribityl substituent and the pyrimidinedione ring be generated in protected forms. The synthesis of the protected ribitol 26 started from D-ribose as previously described.45 Treatment of chloropyrimidine 25 with the ribitol derivative 26 was carried out in the presence of the hindered base LiHMDS. The reaction was attempted in the presence of NaH and BuLi, but LiHMDS gave the best result. The reaction proceeded in 71% yield to afford the desired product 27.
The removal of the isopropylidine groups (Scheme 4) with 0.5 N HCl in THF yielded compound 28. Hydrogenolysis of 28 with Pd/C in MeOH containing 2 drops of HCl under atmospheric pressure afforded the desired O-nucleoside 29.
The next goal was to selectively remove the benzyl groups without reducing the nitro group. Lewis acid-mediated cleavage of the benzyl groups proved to be futile. However, a hydrogenolysis reaction employing Lindlar catalyst provided solely compound 22 without even a trace of the amine 21 (Scheme 4).
Initially, dimethoxypyrimidine 31 was synthesized through a nucleophilic substitution reaction of 26 with 4-iodo-5-nitro-2,6-dimethoxypyrimidine (30) (Scheme 5).46,47 The intended deprotection of the pyrimidinedione system at a relatively late stage in the synthesis under acidic or basic conditions was complicated by the fact that the ether linkage between the ribityl group and the pyrimidine ring was very labile. In most cases the reaction gave rise to a mixture of products that were difficult to isolate. This route was eventually abandoned in favor of the synthesis detailed in Scheme 4.
Compounds 36, 40, and 43 were chosen for synthesis because they are the oxygen analogues of the corresponding ribitylaminopyrimidines that were previously reported.48 In order to provide a handle for the attachment of side chains at C-5 of the pyrimidine, the reduction of the nitro group in compound 27 was carried out in the presence of sodium hydrosulfite (Scheme 6) in refluxing 1,4-dioxane and methanol to provide amine 32. The amine 32 was treated with ethyl chlorooxoacetate in the presence of Et3N to afford ester 33. Treatment of compound 33 with 0.5 N HCl in MeOH at room temperature proceeded to compounds 34 and 35 as a 1:1 mixture of methyl and ethyl esters. Compounds 34 and 35 were easily separated by flash column chromatography. Hydrogenolysis of compounds 34 in EtOH and 35 in MeOH in the presence of Pd/C provided the required products 36 and 37 in good yield. Compounds 40 and 43 were prepared by following a similar protocol. However, synthesis of 46 presented additional challenges because of the presence of the alkene in the side chain. Compound 46 is a bioisostere of an intermediate 6/17 involved in lumazine 3 biosynthesis. The amine 32 was treated with methacrolyl chloride to afford 44. The double bond present on the side chain prevented application of the general hydrogenolysis protocol using Pd/C. Use of Lindlar catalyst (Scheme 4) was attempted, but unfortunately with compound 45 this led to both deprotection of the benzyl groups as well as reduction of double bond in the side chain to provide compound 40 instead of 46. A modified protocol was devised in order to selectively remove the benzyl groups under controlled hydrogenolysis in which 1,4-cyclohexediene was used as the source of hydrogen. Addition of 1,4-cyclohexediene to a reaction mixture containing compound 45 and Lindlar catalyst gave rise to the desired pyrimidinedione 46.
Synthesis of S-Nucleosides
The synthesis of S-nucleoside 23 and the nitro derivative 24 were described earlier.49 The syntheses of additional metabolically stable sulfides that can structurally mimic the substrates, hypothetical intermediates, and products involved in 6,7-dimethyl-8-ribityllumazine (3) and riboflavin (4) biosynthesis were undertaken in order to explore the effects of sulfur incorporation. Following the standard protocol (Scheme 7), derivatization of the amine 47 with acid chlorides provided the expected amide products in very low yield. Reaction of 47 with various acids using peptide coupling synthesis methods was therefore explored. The reaction proceeded in only 10% yield in THF, but changing the solvent to pyridine increased the efficiency of the reaction so that moderate yields of 48 and 50 could be obtained. Removal of the acetonide protecting groups under acidic conditions afforded the desired sulfide derivatives 49 and 51.
Synthesis of N-Nucleosides
The N-nucleosides 56, 60, 63, 66, and 69 were synthesized as metabolically stable analogues of the hypothetical intermediates 6, 7, 9, and 10. The synthesis of 56 started with a nucleophilic aromatic substitution reaction of compound 25 with ribitylamine to yield the expected product 52 (Scheme 8). TBDMS protection of the hydroxyl groups of the ribityl side chain was employed to avoid their reaction during acylation of the primary amino group attached to the pyrimidinedione ring in intermediate 54. Compound 5350 was then reduced with sodium hydrosulfite to amine 54. The amine 54 is very unstable and therefore it was not isolated. Acylation of the amine 54 with methacrolyl chloride afforded the amide 55. Simultaneous removal of both types of protecting groups (TBDMS and methyl) was accomplished by heating intermediate 55 with HBr in aqueous methanol at 55–60 °C to afford the target compound 56.
The synthesis outlined in Scheme 8 proceeded well except for the last step. Several alternate methods were tried to cleave the methyl groups, but none of them afforded the desired product. For example, heating at reflux in HCl/MeOH, reaction with Amberlite-IR-120 (H+)/MeOH, and stirring at room temperature with BBr3/THF or TMSI/THF were all tried. The best method to cleave methyl groups in this case proved to be heating at reflux in HBr/MeOH solution. However, purification of the final product by flash chromatography (SiO2) was difficult. Eluting with EtOAc-EtOH-H2O-AcOH (67:23:9:1) was effective but leached silica gel from the column. Fortunately, the silica could be removed by passing compound 56 twice through Sephadex LH 20 columns.
In order to avoid the problems faced during removal of the methyl groups, in subsequent syntheses the protecting group was switched to benzyl. The unstable amine 57 was prepared according to the reported procedure.48 The amine 57 was reacted with 2-chloropropanoyl chloride, 2-chloroacetyl chloride, or 3,3,3-trifluoropropanoyl chloride to afford the corresponding amides 58, 61, and 64 (Scheme 9), which were deprotected with TBAF to yield 59, 62, and 65. Removal of the benzyl protecting groups by catalytic hydrogenolysis using Lindlar or Pearlman’s catalyst and 1,4-cyclohexadiene as a controlled source of hydrogen provided the desired products 60, 63, and 66. The Lindlar catalyst worked fine for the conversion to compound 60. Conversion of 62 to 63 and 65 to 66 using Lindlar catalyst was slow, but the hydrogenolysis reaction could be expedited by changing the catalyst to Pearlman’s catalyst. For the synthesis of the compound 69 with a conformationally restricted side chain resembling the hypothetical carbinolamine intermediate 10, 2-oxopropanoyl chloride was reacted with amine 57 in the presence of Et3N at room temperature to afford intermediate 67. The reagent 2-oxopropanoyl chloride was synthesized by reacting pyruvic acid with α,α-dichloromethyl methyl ether. Treatment of compound 67 with tetrabutylammonium fluoride removed the TBDMS groups and during the process the intermediate underwent cyclization to yield 68. Hydrogenolysis of 68 with Lindlar catalyst successfully provided the desired compound 69.
The structures of some previously reported lumazine synthase and riboflavin synthase inhibitors are listed in Chart 3 for the purpose of comparison with the presently reported compounds.41,42,48,51,52 The crystal structure of 75 bound to M. tuberculosis lumazine synthase (PDB code: 2C97)41 encouraged the synthesis of compound 78, which is described in Scheme 10.
Intermediate 80 was obtained by the reaction of 7952 with methacrolyl chloride. The chloride and double bond present in the intermediate 80 prevented the application of general hydrogenolysis deprotection protocol using Pd/C. By applying our Lindlar catalyst/1,4-cyclohexadiene methodology, the benzylic groups were selectively removed under controlled hydrogenolysis conditions.
Lindlar Catalyst and Pearlman’s Catalyst in Chemoselective Hydrogenolysis
The benzyl group is one of the most commonly used groups for the protection of oxygen and nitrogen functional groups in synthetic organic chemistry, as it is stable toward many reaction conditions and can be easily installed. Catalytic hydrogenolysis often offers the mildest method for removal of the benzyl ether protecting group. However, hydrogenolysis is often not compatible with the presence of other reducible functional groups, such as alkenes, nitro groups, and halogens. Several examples are provided here of the use of Lindlar catalyst, either with H2 (compounds 22 and 69) or 1,4-cyclohexadiene (compounds 46, 60, and 78), as the source of hydrogen. Pearlman’s catalyst was successful with 1,4-cyclohexadiene as the source of hydrogen in the cases of compounds 63 and 66.
Enzyme Inhibition Studies
The lumazine synthase substrate analogues and hypothetical intermediate analogues were tested as inhibitors of the recombinant lumazine synthases of Bacillus subtilis, Mycobacterium tuberculosis, and Schizosaccharomyces pombe, as well as the recombinant riboflavin synthase of Escherichia coli and Mycobacterium tuberculosis. The inhibition constants and inhibition mechanisms of these inhibitors are listed in Table 1 along with the previously reported compounds 7077, which are also included in Table 1 for comparison. All the synthesized metabolically stable oxalamic acid derivatives with S, O and NH linkages between the ribityl side chain and pyrimidinedione ring are analogues of the phosphate elimination intermediate 6 of the lumazine synthase-catalyzed reaction. Except for compound 7248, these probes without a phosphate side chain were in general found to be moderately active or inactive lumazine synthase inhibitors. However, some of the new compounds did display submicromolar Ki values vs. some of the enzyme. These include 23 vs. S. pombe lumazine synthase, 24 vs. M. tuberculosis riboflavin synthase, and 69 vs. M. tuberculosis riboflavin synthase. Compound 72 was found to be an outlier with unusually high inhibitory potency vs. E. coli riboflavin synthase (Ki 0.0013 μM).
Table 1
Table 1
Inhibition Constants vs S. pombe Lumazine Synthase, M. tuberculosis Lumazine Synthase B. subtilis Lumazine Synthase, M. tuberculosis Riboflavin Synthase, and E. coli Riboflavin Synthase.
The relative efficacies of the N-nucleoside, O-nucleoside, S-nucleoside and C-nucleoside substrate analogue inhibitors can be directly accessed by comparison of the nitro compounds 18 (Figure 1) (Ki 13 μM49), 22 (Ki 60 μM, Table 1), 24 (Ki 11 μM49), and 73 (Ki 220 μM49) vs. M. tuberculosis lumazine synthase. The S-nucleosides were generally more potent than the corresponding O-nucleosides, as exemplified by the relative activities of the S-nucleosides 49 (Ki 128 μM) and 51 (Ki 198 μM) vs. the O-nucleosides 43 (Ki >1000 μM) and 46 (Ki >1000 μM) against M. tuberculosis lumazine synthase. The S-nucleoside 2349 having an amino group at C-5 of the pyrimidinedione was found to be a relatively potent inhibitor of the lumazine synthases of S. pombe (Ki 0.16 μM), B. subtilis (Ki 2.6 μM), and M. tuberculosis (Ki 31 μM) and of the riboflavin synthases of M. tuberculosis (Ki 2.5 μM) and E. coli (Ki 47 μM), whereas the C-nucleoside analogue 7451 of the substrate 1 was shown previously to be completely inactive against B. subtilis lumazine synthase.51
Compound 7541 displayed a Kd of 0.72 μ vs. M. tuberculosis lumazine synthase. Compounds 7652, 7752 and 78 had very weak or no enzyme inhibitory activity. Although compound 75 lacks the ribityl side chain, it has a phosphate moiety that contributes positively to binding. The inhibitory activity is probably due in large part to the presence of the phosphate group that binds in the phosphate binding pocket of the enzyme.41 It also has a π-π stacking interaction of the pyrimidinedione ring with Trp27.
The N-nucleoside ethyl oxalate derivative 7248 proved to be an unusually potent inhibitor of E. coli riboflavin synthase, with a Ki of 0.0013 μM. It also had a Ki of 4.0 μM against M. tuberculosis lumazine synthase, whereas the O-nucleoside ethyl oxalate derivative 36 is completely inactive against all lumazine synthases and riboflavin synthases tested. In contrast, the methyl oxalate derivative 37 had weak activity (Ki of 868 μM) against M. tuberculosis riboflavin synthase. The potency and the structure of the compound 72 are reminiscent of the potent 6,7-dihydro-6,7-dioxo-8-ribityllumazine system 81 (Chart 4), which was previously shown to be a potent inhibitor of baker’s yeast riboflavin synthase (Ki 0.025 μM) and Ashbya gossypii riboflavin synthase (Ki 0.009 μM).53,54 It should be noted, however, that 72 (Ki 0.0013 μM) is more potent vs. E. coli riboflavin synthase than 81 (Ki 0.0062 μM) by a factor of 4.8. In this particular case, the greater flexibility of 72 vs. 81 may allow it to better fit the binding pocket of the enzyme. The previously synthesized, conformationally restricted compound 84 was also found to be a less potent inhibitor (Ki 0.61 μM) of E. coli riboflavin synthase.55 It is possible that the dioxolumazine 81 is a more potent riboflavin synthase inhibitor than 84 because it resembles the hypothetical intermediate 11 involved in the reaction catalyzed be riboflavin synthase.56 The related compound 69 is also a relatively potent inhibitor of M. tuberculosis riboflavin synthase (KI 0.74 μM), although it is not nearly as potent as the dioxo compound 81. Compound 69, which resembles intermediate 10 in the lumazine synthase-catalyzed reaction, inhibits M. tuberculosis lumazine synthase with a Ki value of 8.6 μM.
The O-nucleosides 36, 40, and 43 were synthesized as the oxygen analogues of the N-nucleoside inhibitors 72 (Ki 4 μM), 71 (Ki 42 μM), and 70 (Ki 110 μM) of M. tuberculosis lumazine synthase. In contrast to the N-nucleoside inhibitors, the O-nucleosides 36, 40, and 43 were totally inactive vs. lumazine synthase. The N-nucleoside 70 had a Ki of 110 μM vs. M. tuberculosis lumazine synthase, while the corresponding S-nucleoside 49 had a Kis of 128 μM vs. M. tuberculosis lumazine synthase. Crystallographic studies of 70 bound to M. tuberculosis lumazine synthase have revealed a water bridge between the ribitylamino NH and the side chain amino group of Lys138 (Protein Data Bank Accession Code 2VI5).48 The greater activity of the N-nucleosides may reflect the ability of the ribitylamino NH to function as a hydrogen bond donor toward the bridging water molecule, in contrast to the C-, O-, and S-nucleosides, which cannot act as hydrogen bond donors. It seems less likely that the NH of the ribitylamino group could act as a hydrogen bond acceptor because it is part of a vinylogous amide system. A related set of compounds that allows comparison is the S-nucleoside 49 (Ki 128 μM), the N-nucleoside 70 (Ki 110 μM), and the O-nucleoside 43 (inactive). The one N-nucleoside that does not fit the pattern at all is 56, which proved to be inactive vs. M. tuberculosis lumazine synthase.
With regard to the new monocyclic lumazine synthase intermediate analogues whose syntheses are outlined in Scheme 8 and Scheme 9, the activity order vs. M. tuberculosis lumazine synthase is 63 (Ki 57 μM) > 66 (Ki 100 μM) > 60 (Ki 279 μM) > 56 (Ki > 1000 μM). In the case of E. coli riboflavin synthase, the order is reversed: 56 (Ki 52 μM) > 60 (Ki 314 μM) > 66 (Ki > 1000 μM) = 63 (Ki > 1000 μM). The bicyclic compound 69 is exceptional because it is the most active of the new compounds vs. both M. tuberculosis lumazine synthase (Ki 8.6 μM) and E. coli riboflavin synthase (Ki 0.74 μM). However, none of the compounds in this series can match the potency vs. M. tuberculosis lumazine synthase displayed by compounds with phosphate side chains (e.g. 85 Ki 0.0041 μM).37
MD Simulation and Binding Energy Calculations
Although the mechanism probes 36 and 72 differ only in the heteroatom linkage between the ribityl side chain and the pyrimidinedione ring, they have a very large difference in their inhibitory activities against M. tuberculosis lumazine synthase and E. coli riboflavin synthase. In compounds 69 and 81, the C-5 side chains of 82 and 72 have been conformationally restricted through cyclization and they have shown good inhibitory activities against M. tuberculosis lumazine synthase and M. tuberculosis riboflavin synthase (Chart 4). In the case of lumazine synthase, conformational restriction of the side chain appears to increase the inhibitory activity. To understand these results, a series of molecular dynamics simulations followed by free energy calculations using the Poisson-Boltzmann/surface area (MM-PBSA) method were carried out.57 All simulations were performed using AMBER 9.0. For each ligand, the force field parameters were taken from the general Amber force field (GAFF), whereas the atomic partial charges were derived by geometry optimization using the Gaussian 03 package.58 These analyses have suggested a molecular basis for the interaction of these compounds with lumazine synthase and they have provided a practical method to predict ligand binding affinities in future applications.
MD Simulations of the M. tuberculosis Lumazine Synthase Complex with Ligand 70
The X-ray crystal structure of ligand 70 and M. tuberculosis lumazine synthase complex is available from the Protein Data Bank (PDB code: 2VI5).48 The C-5 sp2 carbon of the ligand in this structure appears distorted and deviates from its standard geometry, and therefore the starting structure was thoroughly energy minimized to ensure the right ligand conformation before MD simulation. The whole simulation time was 1000 ps, during which the ligand remained stable in the binding site and the ligand RMSD remain at about 0.7 Å (in Figure 3, black). Hydrogen bond analysis revealed that most of the hydrogen bonds and water bridges that are apparent in the crystal structure were retained during the simulation.
Figure 3
Figure 3
Time-dependent RMSD profile of the ligands in molecular dynamics simulations.
MD Simulations of the M. tuberculosis Lumazine Synthase Complex with Ligand 81
Ligand 81 binds tightly to the active site of M. tuberculosis lumazine synthase during the entire MD simulation process. As shown in Figure 3 (red), the ligand RMSD remained quite small, around 0.2–0.3 Å, during the whole simulation time. Figure 4 shows the minimized average structure of the binding site of lumazine synthase complex with ligand 81. Compared to ligand 70, the additional ring system in ligand 81 did not result in much change in the overall binding mode, and most of the hydrogen bonds to the binding site residues (including Ala59, Ile60, Glu61, Val81, and Asn114) were retained with ligand 81, as well as the two water bridges. The most remarkable difference was the formation of two hydrogen bonds with Lys138 and Gln141, which were not observed with ligand 70. As shown in Figure 5 (top), the hydrogen bond between the diketone carbonyl oxygen (O-7) and NH2 of Gln141 formed at 400 ps in the MD simulation, when the side chain of Gln141 rotated 90 degrees to approach the carbonyl group (O-7) of ligand 81. The distance between the (O-7) carbonyl oxygen on ligand 81 and the NH2 side chain hydrogen of Gln141 fluctuates around 1.95 Å during the next 600 ps of the MD simulation, indicating a tight hydrogen bond between them. The MD simulation also revealed a stable hydrogen bond between the NH2 of Lys138 and the (O-6) carbonyl oxygen of ligand 81. The three hydrogens on the protonated amino group of Lys138 are constantly rotating and form a hydrogen bond with the (O6) carbonyl oxygen of ligand 81 alternately during the entire simulation time, as shown in Figure 5 (bottom).
Figure 4
Figure 4
Molecular interactions between ligand 81 and M. tuberculosis lumazine synthase. Residues of the enzyme are labeled and shown in stick. Hydrogen bonding interactions are indicated by black dashed lines with key distance. The figure is programmed for walleyed (more ...)
Figure 5
Figure 5
Time dependence of the key distances for the complex of ligand 81 with lumazine synthase during molecular dynamics simulations.
According to Table 2, the estimated binding free energy (using MM-PBSA method) for ligand 81 is −42.93 KJ/mol, much lower than ligand 70 (−30.98 KJ/mol), which is consistent with the results of the experimental enzyme inhibition assay. The enhanced affinity of ligand 81 could be attributed to the following three factors. First, there is the addition of two hydrogen bonds with Lys138 and Gln141. Evidence comes from the analysis of the electrostatic (ΔEelec) term contribution to the binding free energy in Table 2. The electrostatic term in ligand 81 (−78.45 KJ/mol) is much lower than 70 (−63.10 KJ/mol), which dominates their difference in binding free energy. Second, because of the introduction of the additional dioxolumazine ring system, the π-π interaction with Trp27 is expected to be strengthened in ligand 81. In Table 2, the van der Waals term (ΔEvdw) of ligand 81 (−38.09 KJ/mol) is quite close to that of ligand 70 (−39.67 KJ/mol). In ligand 70, the amide side chain protrudes into a hydrophobic pocket around Phe90 and Val93, and these hydrophobic interactions are largely compensated by the enhanced π-π interaction with Trp27 in ligand 81. Third, the enhanced binding of ligand 81 in the active site of lumazine synthase can be attributed to the change in entropy. The 1,2-diketone chain is conformationally restricted in ligand 81, which would decrease the entropy loss during binding to the lumazine synthase binding site. Although the entropy loss is not explicitly estimated in this paper because of the tremendous calculation needed, it is an important factor.
Table 2
Table 2
Energy Contributions to Free Energy of Binding Calculated for Each Compound with the M. tuberculosis Lumazine Synthase Complexa
MD Simulations of the M. tuberculosis Lumazine Synthase Complex with Ligand 69
Ligand 69 is also calculated to bind tightly in the binding site. The ligand RMSD stays at 0.5 Å (Figure 3, green). Ligand 69 can also form a hydrogen bond between the carbonyl oxygen (O-6) with NH2 of Lys138, but not with Gln141. The estimated binding free energy for ligand 69 is −35.87 KJ/mol, which is a bit higher than ligand 81. The difference mostly originates from the high desolvation energy (ΔGsolv) for ligand 69 (88.74 KJ/mol, compared to 73.61 KJ/mol for ligand 81). Since a hydroxyl group is more polar than a carbonyl group and can act as a hydrogen bond donor as well as a hydrogen bond acceptor, the polar C-7 hydroxyl group makes ligand 69 more hydrophilic than ligand 81 and elevates its desolvation energy.
MD Simulations of the M. tuberculosis Lumazine Synthase Complex with Ligands 36 and 72
Ligand 36 is inactive in the experimental inhibitory activity assay. Consistent with this result, ligand 36 appears to be very unstable during the entire MD simulation. The ligand RMSD fluctuates mainly between 0.7–1.7 Å, with the highest RMSD up to 2 Å (in Figure 3, orange). The instability comes from the steric clash between the long 1,2-dicarbonyl side chain and the lumazine synthase binding pocket. As a result, the estimated binding free energy for ligand 36 is −21.41 KJ/mol, which is much higher than that of ligands 69, 72 and 81. The estimated binding free energy for ligand 36 is consistent with poor binding.
Ligands 36 and 72 differ only in the heteroatom linkage. Consequently, the dynamic behavior of ligand 72 is nearly the same as ligand 36 in the MD simulations. The ligand 72 also experiences large fluctuations during simulation. The ligand RMSD fluctuates between 0.5–1.0 Å (in Figure 3, blue). The binding free energy calculated for ligand 72 is only −25.84 KJ/mol, which is not consistent with its inhibitory activity relative to the other ligands in Table 2.
In conclusion, this article describes a comprehensive study of O-nucleoside, S-nucleoside, and N-nucleoside probes that has provided insights into the mechanistic details of lumazine synthase and riboflavin synthase catalysis. The following is a list of the main results: (1) All of the synthesized metabolically stable oxalamic acid derivative probes with S, O and NH linkages between the ribityl side chain and pyrimidinedione ring that are analogues of the phosphate elimination products of the lumazine synthase reaction intermediate 6 are moderate or inactive lumazine synthase inhibitors. However, compounds containing phosphate side chain have very strong affinity for lumazine synthase. This suggests that lumazine synthase predominantly catalyzes Schiff base formation and the phosphate elimination reaction and the subsequent intermediates have low enzyme affinity (Scheme 2). (2) Compounds 76, 77 and 78, which do not contain either the phosphate side chain or the ribityl side chain showed very weak or complete absence of any inhibitory activity. Whereas compound 7541 lacks the ribityl side chain, it has a phosphate group that binds to the phosphate binding site, resulting in strong affinity for lumazine synthase (Kd of 0.72 μM vs. M. tuberculosis lumazine synthase). This suggests that the pyrimidinedione ring alone has low binding affinity and the phosphate moiety contributes more positively to the binding of compound compared to the ribityl side chain. Previously reported work has shown that the ribityl side chain can be replaced by a styryl moiety with retention of affinity for the enzyme, indicating that the ribityl chain is not essential for binding.59 (3) Among all of the compounds synthesized, S-nucleoside 23 showed greater lumazine synthase inhibitory potency (Table 1) as compared to all the O-nucleoside, N-nucleoside and C-nucleoside derivatives. The greater inhibitory potency of the S-nucleoside 23 and its nitro precursor 24 compared with the O-nucleoside 29 and C-nucleoside 74 could possibly be due to electronics. The non-bonded electrons on sulfur would cause 23 to more closely resemble the natural substrate relative to the C-nucleoside 74. (4) All of the bicyclic compounds (69, 81 and 84) were found to exhibit stronger affinity for riboflavin synthase than lumazine synthase. (5) The molecular dynamics simulations provide a method for predicting ligand affinities to the active site of lumazine synthase. They also provide insight into the dynamic aspects of ligand binding. (6) A useful controlled hydrogenolysis methodology has been developed and applied to the selective cleavage of benzyl protecting groups in the presence of easily reducible functional groups. The information revealed in this study will be valuable for future structure-based drug design of lumazine synthase and riboflavin synthase inhibitors.
General
Melting points were determined using capillary tubes and are uncorrected. NMR spectra were determined at 300 or 500 MHz (1H) and 75 MHz or 125 MHz (13C) as specified. High-resolution mass spectra were recorded on double-focusing sector mass-spectrometer with magnetic and electrostatic mass analyzers. Silica gel flash chromatography was performed using 230–400 mesh silica gel.
2,4-Bis(benzyloxy)-5-nitro-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidine (27)
A solution of D-ribitol derivative 26 (62 mg, 0.27 mmol) in dry THF (5 mL) was cooled to −40 °C and LiHMDS (0.3 mL, 1 M solution in THF, 0.32 mmol) was added. The solution was stirred for 30 min at room temperature and cooled to −40 °C. Chloropyrimidine derivative 25 (100 mg, 0.27 mmol) dissolved in dry THF (5 mL) was introduced into the reaction mixture, which was slowly brought to room temperature over 5 h. The reaction was quenched using ammonium chloride, THF was removed under vacuum, the residue then dissolved in CHCl3 (15 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was purified by silica gel flash column chromatography, eluting with 15% ethyl acetate in hexane, to yield compound 27 (108 mg, 71%) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.33-7.24 (m, 10 H), 5.48 (s, 2 H), 5.40 (s, 2 H), 4.79 (dd, J = 3.9 Hz, 11.5 Hz, 1 H), 4.61 (dd, J = 6.2 Hz, 11.5 Hz, 1 H), 4.52-4.47 (m, 1 H), 4.16-4.01 (m, 3 H), 3.93-3.85 (m, 1 H), 1.39 (s, 3 H), 1.34 (s, 3 H), 1.32 (s, 3 H), 1.23 (s, 3 H); 13C NMR (75 MHz, CDCl3) δ 163.8, 162.0, 135.4, 135.0, 128.6, 128.3, 128.2, 127.6, 109.8, 109.4, 77.7, 75.0, 73.3, 70.3, 69.8, 68.0, 66.8, 27.6, 26.7, 25.3, 25.2. Anal. Calcd for C29H33N3O9: C 61.37; H 5.86; N 7.40. Found: C 61.44; H 5.88; N, 7.36.
(2R,3R,4S)-5-(2,6-Bis(benzyloxy)-5-nitropyrimidin-4-yloxy)pentane-1,2,3,4-tetrol (28)
0.5N HCl (2 mL) was added to a solution of compound 27 (50 mg, 0.09 mmol) in THF (2 mL) and the reaction mixture was stirred for 6 h at room temperature. THF was removed under vacuum, the residue then dissolved in ethyl acetate (10 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was purified by silica gel flash column chromatography, eluting with 60% ethyl acetate in hexane, to afford compound 28 (31 mg, 72%) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.35-7.27 (m, 10 H), 5.46 (s, 2 H), 5.38 (s, 2 H), 4.68 (dd, J = 2.9 Hz, 11.3 Hz, 1 H) 4.55 (dd, J = 6.2 Hz, 11.3 Hz, 1 H), 4.06-4.00 (m, 1 H), 3.76-3.63 (m, 4 H); 13C NMR (75 MHz, CDCl3) δ 164.0, 163.5, 161.8, 135.0, 134.7, 128.2, 128.0, 127.7, 127.2, 72.4, 71.3, 70.6, 70.1, 70.0, 69.6, 62.9; ESIMS m/z (rel intensity) 997 (2MNa+, 100), 863 (30), 510 (MNa+, 42). Anal. Calcd for C23H25N3O9: C 56.67; H 5.17; N 8.62. Found: C 56.81; H 5.21; N, 8.49.
5-Amino-6-((2R,3R,4S)-2,3,4,5-tetrahydroxypentyloxy)pyrimidine-2,4(1H,3H)-dione (29)
10% Pd/C (5 mg) was added to a solution of compound 28 (45 mg, 0.08 mmol) in MeOH-EtOAc (3 + 1 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite into a solution of MeOH containing HCl. The solution was concentrated to provide compound 29 (24 mg, 83%) as yellow amorphous solid: mp 200–204 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 4.14-4.08 (m, 1 H), 3.97 (dd, J = 4.8 Hz, 9.5 Hz, 1 H), 3.71-3.68 (m, 4 H), 3.52 (dd, J = 4.8 Hz, 12.0 Hz, 1 H); 13C NMR (75 MHz, MeOH-d4) δ 168.3, 166.0, 158.9, 108.8, 84.1, 73.8, 73.1, 72.5, 63.2; ESIMS m/z (rel intensity) 278 (MH+, 35); negative ion ESIMS m/z (rel intensity) 276 [(M – H+), 62], 171 (100). Anal. Calcd for C9H16ClN3O7: C, 34.46; H, 5.14; N, 13.40. Found: C, 34.12; H, 5.18; N, 13.52.
5-Nitro-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)pyrimidine-2,4(1H,3H)-dione (22)
Lindlar catalyst (5 mg) was added to a solution of compound 28 (45 mg, 0.08 mmol) in MeOH-EtOAc (3 + 1 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with 50% aq MeOH (5 mL). The solution was concentrated and the residue was purified via silica gel flash column chromatography, eluting with 10% methanol in ethyl acetate, to furnish compound 22 as a colorless oil. Compound 22 was washed several times with CH2Cl2 and THF. Finally, compound 22 was precipitated out by dissolving in MeOH and adding excess diethyl ether to afford pure compound 22 (22 mg, 79%) as an orange amorphous solid: mp 165–168 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 4.15–4.106 (m, 1 H), 4.03-3.94 (m, 3 H), 3.78-3.68 (m, 2 H), 3.68 (dd, J = 9.5 Hz, 14.0 Hz, 1 H); 13C NMR (75 MHz, MeOH-d4) δ 167.9, 164.2, 157.6, 123.0, 79.8, 79.6, 74.5, 68.4, 62.2; negative ion ESIMS m/z (rel intensity) 306 [(M – H+), 100], 172 (65). Anal. Calcd for C9H13N3O9: C, 35.19; H, 4.27; N, 13.68. Found: C, 34.97; H, 4.43; N, 13.90.
2,4-Dimethoxy-5-nitro-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidine (31)
A solution of D-ribitol derivative 26 (100 mg, 0.43 mmol) in dry THF (8 mL) was cooled to −40 °C and n-BuLi (0.3 mL, 2.5 M, 0.86 mmol) was added. The solution was stirred for 30 min at room temperature and cooled to −40 °C. Iodopyrimidine derivative 30 (122 mg, 0.39 mmol) dissolved in dry THF (8 mL) was introduced into the reaction mixture, which was slowly brought to room temperature by overnight stirring. The reaction was quenched using ammonium chloride, THF was removed under vacuum, the residue then dissolved in CHCl3 (15 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was column chromatography with flash silica gel eluting with 20% ethyl acetate in hexane to yield compound 31 (75 mg, 45%) as a colorless oil along with both the staring materials 30 and 26. 1H NMR (300 MHz, CDCl3) δ 4.81 (dd, J = 4.1 Hz, 1 H), 4.64 (dd, J = 6.0 Hz, 1 H), 4.50-4.47 (m, 1 H), 4.16-4.06 (m, 3 H), 4.05 (s, 3 H), 4.00 (s, 3 H), 3.92-3.86 (m, 1 H), 1.37 (s, 3 H), 1.33 (s, 3 H), 1.31 (s, 3 H), 1.23 (s, 3 H); 13C NMR (75 MHz, CDCl3) δ 164.4, 163.8, 162.7, 109.7, 109.4, 77.7, 75.1, 73.3, 68.0, 66.7, 55.6, 55.5, 27.5, 26.7, 25.2; EIMS m/z (rel intensity) 400 (M+ – CH3, 11), 256 (C9H10N3O6+, 20), 101 (C5H5O2+, 100); CIMS m/z (rel intensity) 416 (MH+, 14), 215 (M+ – C11H19O4, 100). Anal. Calcd for C17H25N3O9: C 49.15; H 6.07; N 10.12. Found: C 49.44; H 5.88; N, 10.34.
2,4-Bis(benzyloxy)-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidin-5-amine (32)
Sodium bicarbonate-sodium carbonate buffer (3 mL) (pH = 9.5, prepared by adjusting the pH value of saturated sodium carbonate aqueous solution to 9.5 with sodium carbonate and 1M NaOH) and Na2S2O4 (260 mg, 1.48 mmol) were added to a solution of compound 27 (120 mg, 0.211 mmol) in 1,4-dioxane (3 mL). Argon was bubbled for 20 min to degas the reaction mixture, which was stirred at room temperature for 6 h and subsequently at 100 °C for 3 h. The reaction mixture was cooled to room temperature and poured into ice water (5 mL) and extracted with diethyl ether (3 × 8 mL). The organic layer was combined, washed with brine, dried and solvent was distilled off. The residue was separated by flash chromatography eluting with 20% ethyl acetate in hexane, to yield compound 32 (82 mg, 72%) as light yellow oil. 1H NMR (300 MHz, CDCl3) δ 7.42-7.18 (m, 10 H), 5.33 (s, 2 H), 5.25 (s, 2 H), 4.59 (dd, J = 10.41 Hz, 3.58 Hz, 1 H), 4.48-4.38 (m, 2 H), 4.13-3.95 (m, 4 H), 3.91-3.82 (m, 1 H), 3.21 (brs, 2 H), 1.46 (s, 3 H), 1.37 (s, 3 H), 1.28 (s, 3 H), 1.22 (s, 3 H); 13C NMR (75 MHz, CDCl3) δ 158.5, 158.3, 155.0, 137.2, 136.7, 128.4, 128.3, 128.1, 128.0, 127.8, 109.7, 109.1, 107.7, 77.9, 75.6, 73.2, 68.7, 68.4, 68.0, 65.2, 27.9, 26.8, 25.5, 25.3; ESIMS m/z (rel. intensity) 560 (MNa+, 100), 538 (MH+, 50), 480 (9). Anal. Calcd for C29H35N3O7: C, 64.79; H, 6.56; N, 7.82. Found: C, 65.03; H, 6.41; N, 7.64.
Ethyl 2-(2,4-bis(benzyloxy)-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidin-5-ylamino)-2-oxoacetate (33)
Triethylamine (0.3 mL, 2.2 mmol) was added to a solution of compound 32 (30 mg, 0.055 mmol) in THF (5 mL). The solution was cooled to 0 °C and ethyl chlorooxacetate (18 μL, 0.16 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 2 h and 30 min at room temperature. The solvent was distilled off under reduced pressure and the residue was dissolved in dichloromethane (20 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was separated by silica gel flash column chromatography, eluting with 30% ethyl acetate in hexane, to afford compound 33 (36 mg, 96%) as a yellowish oil. 1H NMR (300 MHz, CDCl3) δ 8.11 (s, 1 H), 7.41-7.19 (m, 10 H), 5.37 (s, 2 H), 5.32 (s, 2 H), 4.67-4.59 (m, 1 H), 4.47-4.42 (m, 2 H), 4.32 (q, J = 7.16 Hz, 2 H), 4.06-3.96 (m, 3 H), 3.89-3.83 (m, 1 H), 1.34 (s, 3 H), 1.33 (t, J = 7.1 Hz, 3 H), 1.30 (s, 3 H), 1.25 (s, 3 H), 1.19 (s, 3 H); 13C NMR (75 MHz, CDCl3) δ 165.9, 161.6, 160.2, 154.7, 136.2, 136.1, 128.4, 128.2, 128.0, 127.7, 109.8, 109.2, 95.6, 77.7, 75.3, 73.2, 69.5, 69.0, 67.9, 66.0, 63.3, 27.7, 26.8, 25.3, 25.2, 14.0; ESIMS m/z (rel. intensity) 660 (MNa+, 100), 446 (2). Anal. Calcd for C33H39N3O10: C, 62.16; H, 6.16; N, 6.59; Found: C, 62.34; H, 6.30; N, 6.88.
Ethyl 2-(2,4-bis(benzyloxy)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)pyrimidin-5-ylamino)-2-oxoacetate (34) and Methyl 2-(2,4-bis(benzyloxy)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)pyrimidin-5-ylamino)-2-oxoacetate (35)
0.5N HCl (1 mL) was added to a solution of compound 33 (35 mg, 0.055 mmol) in MeOH (1 mL) and the reaction mixture was stirred for 12 h at room temperature. MeOH was removed under vacuum, the residue then dissolved in ethyl acetate (10 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was purified by silica gel flash column chromatography, eluting with 70% ethyl acetate in hexane, to give compounds 34 (16 mg, 53%) and 35 (11 mg, 37%) as a colorless oils. Compound 34: 1H NMR (300 MHz, acetone-d6) δ 9.36 (s, 1 H), 7.50-7.30 (m, 10 H), 5.46 (s, 2 H), 5.40 (s, 2 H), 4.74-4.69 (m, 1 H), 4.53-4.48 (m, 1 H), 4.42 (brs, 1 H), 4.31 (q, J = 7.12 Hz, 2 H), 4.14-4.03 (m, 3 H), 3.77-3.67 (m, 4 H), 1.34 (t, J = 7.12 Hz); 13C NMR (75 MHz, CDCl3) δ 165.6, 165.2, 159.9, 154.8, 136.0, 135.5, 128.6, 128.3, 128.2, 128.1, 95.6, 73.2, 71.5, 69.8, 69.3, 63.8, 63.3, 13.9; ESIMS m/z (rel intensity) 1137 (2M + Na+, 100), 580 (MNa+, 69), 559 (M2H+, 12), 558 (MH+, 47). Anal. Calcd for C27H31N3O10: C 58.16; H 5.60; N 7.54. Found: C 57.82; H 5.88; N, 7.21.
Compound 35: 1H NMR (300 MHz, acetone-d6) δ 9.42 (s, 1 H), 7.47-7.32 (m, 10 H), 5.46 (s, 2 H), 5.40 (s, 2 H), 4.75-4.68 (m, 1 H), 4.52-4.45 (m, 2 H), 4.19 (brs, 1 H), 4.10-4.08 (m, 2 H), 3.85 (s, 3 H), 3.75-3.70 (m, 3 H), 3.68-3.64 (m, 2 H), 3.58 (m, 1 H), 3.42 (m, 1 H); 13C NMR (75 MHz, acetone-d6) δ 167.4, 167.1, 161.5, 156.2, 137.7, 137.6, 129.2, 129.0, 128.8, 128.7, 128.5, 96.9, 73.7, 73.4, 71.8, 70.2, 70.0, 69.3, 64.5, 53.6; ESIMS m/z (rel intensity) 566 (MNa+, 100), 504 (8), 303 (8); negative ion ESIMS m/z (rel intensity) 542 [(M – H+), 100], 408 (59). Anal. Calcd for C26H29N3O10: C, 57.45; H, 5.38; N, 7.73. Found: C, 57.69; H, 5.18; N, 7.66.
Ethyl 2-(2,4-dioxo-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)1,2,3,4-tetrahydropyrimidin-5-ylamino)-2-oxoacetate (36)
10% Pd/C (5 mg) was added to a solution of compound 34 (30 mg, 0.054 mmol) in EtOH (4 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with EtOH (15 mL) and concentrated to provide compound 36 (14 mg, 70%) as white solid: mp 62–64 °C. 1H NMR (300 MHz, MeOH-d4) δ 4.52-4.47 (m, 1 H), 4.46-4.40 (m, 1 H), 4.34 (q, J = 7.10 Hz, 2 H), 4.02-3.98 (m, 1 H), 3.77-3.70 (m, 2 H), 3.67-3.61 (m, 2 H), 1.34 (t, J = 7.10 Hz, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 164.7, 162.4, 161.1, 159.2, 153.1, 93.2, 74.1, 74.0, 73.1, 72.5, 64.5, 64.1, 14.3; ESIMS m/z (rel. intensity) 777 (2M + Na+, 100), 400 (MNa+, 32), 378 (MH+, 16); negative ion ESIMS m/z (rel. intensity) 752 [(2M – H+), 42], 376 [(M – H+), 100], 241 (60). Anal. Calcd for C13H19N3O10·H2O: C 39.50; H 5.35; N 10.63. Found: C 39.67; H 5.17; N, 10.40.
Methyl 2-(2,4-dioxo-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)1,2,3,4-tetrahydropyrimidin-5-ylamino)-2-oxoacetate (37)
10% Pd/C (3 mg) was added to a solution of compound 35 (20 mg, 0.037 mmol) in MeOH (3 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with MeOH (15 mL) and concentrated to provide compound 37 (10 mg, 75%) as a colorless oil. 1H NMR (300 MHz, MeOH-d4) δ 4.49-4.42 (m, 2 H), 3.95-3.90 (m, 1 H), 3.88 (s, 3 H), 3.76-3.71 (m, 2 H), 3.64-3.58 (m, 2 H); 13C NMR (75 MHz, MeOH-d4) δ 168.2, 165.3, 160.7, 152.0, 91.3, 74.2, 74.1, 73.4, 72.8, 69.1, 64.5; ESIMS m/z (rel intensity) 386 (MNa+, 94), 256 (93), 179 (100); negative ion ESIMS m/z (rel intensity) 362 [(M – H+), 100], 348 (8), 231 (7). Anal. Calcd for C12H17N3O10·2H2O: C 36.10; H 5.30; N, 10.52. Found: C 36.33; H 5.43; N 10.49.
N-(2,4-Bis(benzyloxy)-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidin-5-yl)isobutyramide (38)
Triethylamine (0.3 mL, 2.2 mmol) was added to a solution of compound 32 (115 mg, 0.21 mmol) in THF (5 mL). The solution was cooled to 0 °C and isobutyryl chloride (25 μL, 0.24 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 6 h. The solvent was distilled off under reduced pressure and the residue was dissolved in dichloromethane (20 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was flash column chromatographed with flash silica gel, eluting with 35% ethyl acetate in hexane, to afford compound 38 (110 mg, 85%) as a yellowish-white solid: mp 150–153 °C. 1H NMR (300 MHz, CDCl3) δ 7.43-7.24 (m, 10 H), 6.53 (s, 1 H), 5.34 (s, 4 H), 4.68 (dd, J = 2.1, 10.5 Hz, 1 H), 4.47-4.39 (m, 2 H), 4.08-4.0 (m, 3 H), 3.92-3.89 (m, 1 H), 2.47 (m, 1 H), 1.39 (s, 3 H), 1.35 (s, 3 H), 1.30 (s, 3 H), 1.26 (s, 3 H), 1.17 (m, 6 H); 13C NMR (75 MHz, CDCl3) δ 175.6, 166.4, 166.1, 161.0, 136.3, 136.2, 128.2, 128.1, 127.9, 127.7, 127.4, 109.6, 109.0, 97.0, 77.5, 75.4, 73.1, 69.2, 68.6, 67.7, 65.7, 35.3, 27.6, 26.7, 25.2, 19.5, 19.3; ESIMS m/z (rel intensity) 608 (MH+, 100), 550 (14); HRMS m/z calcd for C33H42N3O8 (MH+) 608.2972, found 608.2981. Anal. Calcd for C33H41N3O8: C 65.22; H 6.80; N, 6.91. Found: C 65.40; H 6.53; N 7.12.
N-(2,4-Bis(benzyloxy)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)pyrimidin-5-ylamino)isobutyramide (39)
0.5N HCl (1 mL) was added to a solution of compound 38 (60 mg, 0.1 mmol) in THF (2 mL) and the reaction mixture was stirred for 12 h at room temperature. THF was removed under vacuum, and the residue then dissolved in ethyl acetate (10 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was column chromatographed with flash silica gel, eluting with 80% ethyl acetate in hexane, to produce compound 39 (43 mg, 81%) as white semisolid. 1H NMR (300 MHz, MeOH-d4) δ 7.42-7.29 (m, 10 H), 5.38 (s, 4 H), 4.61 (m, 1 H), 4.58 (dd, J = 4.5, 8.1 Hz, 1 H), 4.46 (dd, J = 6.6, 11.4 Hz, 1 H), 3.78-3.65 (m, 2 H), 3.68-3.62 (m, 2 H), 2.68-2.50 (m, 1 H), 1.17 (d, J = 1.2 Hz, 3 H), 1.15 (d, J = 1.2 Hz, 1 H); 13C NMR (75 MHz, MeOH-d4) δ 180.1, 168.4, 168.0, 162.9, 138.2, 137.9, 129.7, 129.5, 129.4, 129.1, 128.8, 128.6, 98.2, 84.1, 74.2, 73.5, 72.1, 70.5, 70.0, 64.6, 36.2, 19.9; ESIMS m/z (rel intensity) 550 (MNa+, 100), 528 (MH+, 68), 394 (36); negative ion ESIMS m/z (rel intensity) 526 [(M – H+), 28], 392 (100). Anal. Calcd for C27H33N3O8: C, 61.47; H, 6.30; N, 7.96. Found: C, 61.65; H, 6.31; N, 7.80.
N-(2,4-Dioxo)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)-1,2,3,4-tetrahydropyrimidin-5-yl)isobutyramide (40)
10% Pd/C (5 mg) was added to a solution of compound 39 (55 mg, 0.08 mmol) in MeOH-EtOAc (3 + 1 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite into a solution of MeOH containing HCl. The solution was concentrated to provide compound 40 (26 mg, 72%) as yellow amorphous solid: mp 116–119 °C. 1H NMR (300 MHz, MeOH-d4) δ 4.47-4.41 (m, 2 H), 3.97-3.90 (m, 1 H), 3.77-3.71 (m, 2 H), 3.64-3.60 (m, 2 H), 2.66-2.59 (m, 1 H), 1.19 (s, 3 H), 1.17 (s, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 180.9, 165.8, 165.26, 156.0, 93.5, 74.2, 73.2, 72.7, 72.0, 64.5, 36.2, 20.0; ESIMS m/z (rel intensity) 370 (MNa+, 100), 300 (11), 219 (16); negative ion ESIMS m/z (rel intensity) 346 [(M – H+), 100], 212 (6). Anal. Calcd for C13H21N3O8: C, 44.96; H, 6.09; N, 12.10. Found: C, 45.11; H, 5.93; N, 11.86.
N-(2,4-Bis(benzyloxy)-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidin-5-yl)propionamide (41)
Triethylamine (0.3 mL, 2.2 mmol) was added to a solution of compound 32 (80 mg, 0.15 mmol) in THF (5 mL). The solution was cooled to 0 °C and propionyl chloride (16 μL, 0.18 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 6 h. The solvent was distilled off under reduced pressure and the residue was dissolved in dichloromethane (20 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was flash column chromatographed with flash silica gel, eluting with 35% ethyl acetate in hexane, to afford compound 41 (77 mg, 87%) as a yellowish-white solid: mp 121–123 °C. 1H NMR (300 MHz, CDCl3) δ 7.38-7.25 (m, 10 H), 6.42 (s, 1 H), 5.31-5.28 (m, 4 H), 4.62 (dd, J = 2.4, 10.5 Hz, 1 H), 4.45-4.41 (m, 2 H), 4.04-3.98 (m, 3 H), 3.86-3.85 (m, 1 H), 2.25 (q, J = 7.4 Hz, 2 H), 1.34 (s, 3 H), 1.30 (s, 3 H), 1.25 (s, 3 H), 1.21 (s, 3 H), 1.14 (t, J = 7.2 Hz, 3 H); 13C NMR (125 MHz, CDCl3) δ 172.6, 166.5, 166.2, 161.1, 136.3, 136.2, 128.7, 128.5, 128.4, 128.1, 127.9, 127.6, 127.5, 109.8, 109.2, 97.1, 77.7, 75.7, 73.4, 69.3, 68.7, 67.8, 65.9, 29.7, 27.7, 26.9, 25.2; ESIMS m/z (rel intensity) 594 (MH+, 100), 554 (27), 245 (35); HRMS m/z calcd for C32H40N3O8 (MH+) 594.2815, found 594.2825. Anal. Calcd for C32H39N3O8: C 64.74; H 6.62; N 7.08. Found: C 64.88; H 6.85; N 6.81.
N-(2,4-Bis(benzyloxy)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)pyrimidin-5-ylamino)propionamide (42)
0.5N HCl (1 mL) was added to a solution of compound 41 (60 mg, 0.1 mmol) in MeOH (1 mL) and the reaction mixture was stirred for 12 h at room temperature. MeOH was removed under vacuum, the residue then dissolved in ethyl acetate (10 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was flash column chromatographed with silica gel, eluting with 80% ethyl acetate in hexane, to afford compound 42 (39 mg, 75%) as white solid: mp 110–113 °C. 1H NMR (300 MHz, MeOH-d4) δ 7.43-7.31 (m, 10 H), 5.38 (s, 4 H), 4.62-4.58 (m, 1 H), 4.46 (dd, J = 2.7, 10.8 Hz, 1 H), 4.08-4.02 (m, 1 H), 3.79-3.76 (m, 2 H), 3.69-3.61 (m, 2 H), 2.36 (q, J = 7.4 Hz, 2 H), 1.17 (t, J = 7.2 Hz, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 177.4, 168.8, 168.4, 163.3, 138.6, 138.4, 130.0, 129.5, 129.2, 98.7, 74.6, 74.0, 72.5, 71.0, 70.4, 65.0, 30.5, 11.0; ESIMS m/z (rel intensity) 536 (MNa+, 100), 514 (MH+, 10); negative ion ESIMS m/z (rel intensity) 512 [M – H+), 4], 462 (100); HRMS m/z calcd for C26H31N3O8Na (MNa+) 536.2009, found 536.2011. Anal. Calcd for C26H31N3O8: C 60.81; H 6.08; N 8.18. Found: C 60.95; H 6.31; N 8.02.
N-(2,4-Dioxo)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)-1,2,3,4-tetrahydropyrimidin-5-yl)propionamide (43)
10% Pd/C (5 mg) was added to a solution of compound 42 (55 mg, 0.08 mmol) in MeOH-EtOAc (3 + 1 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite into a solution of MeOH containing HCl. The solution was concentrated to provide compound 43 (25 mg, 70%) as yellow amorphous solid: mp 128–131 °C. 1H NMR (300 MHz, MeOH-d4) δ 4.62-4.58 (m, 1 H), 4.49-4.43 (m, 1 H), 4.06-4.02 (m, 1 H), 3.80-3.75 (m, 2 H), 3.67-3.61 (m, 2 H), 2.38 (q, J = 7.4 Hz, 2 H), 1.16 (t, J = 7.3 Hz, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 178.5, 163.7, 162.8, 156.0, 85.0, 72.4, 71.2, 70.7, 64.5, 30.1, 29.4, 10.5. Anal. Calcd for C12H19N3O8: C, 43.24; H, 5.75; N, 12.61. Found: C, 43.10; H, 5.72; N, 12.89.
N-(2,4-Bis(benzyloxy)-6-(((4R,4′R,5S)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methoxy)pyrimidin-5-yl)methacrylamide (44)
Triethylamine (0.3 mL, 2.2 mmol) was added to a solution of compound 32 (115 mg, 0.21 mmol) in THF (5 mL). The solution was cooled to 0 °C and methacrolyl chloride (25 μL, 0.24 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 6 h. The solvent was distilled off under reduced pressure and the residue was dissolved in dichloromethane (20 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was flash column chromatographed with silica gel, eluting with 35% ethyl acetate in hexane, to afford compound 44 (85 mg, 65%) as white amorphous solid: mp 118–120 °C. 1H NMR (300 MHz, CDCl3) δ 7.42-7.24 (m, 10 H), 6.81 (s, 1 H), 5.72 (s, 1 H), 5.37 (s, 2 H), 5.34 (s, 1 H), 5.33 (s, 2 H), 4.67 (dd, J = 1.8, 8.1 Hz, 1 H), 4.49-4.42 (m, 2 H), 4.15-4.00 (m, 3 H), 3.89 (dd, J = 4.8, 8.1 Hz 1 H), 1.97 (s, 3 H), 1.38 (s, 3 H), 1.34 (s, 3 H), 1.29 (s, 3 H), 1.24 (s, 3 H); 13C NMR (75 MHz, CDCl3) δ 167.2, 166.3, 166.2, 161.1, 140.1, 136.3, 128.3, 128.1, 128.0, 127.8, 127.4, 119.8, 109.6, 109.0, 97.0, 77.6, 75.4, 73.2, 69.3, 68.6, 67.8, 65.8, 27.5, 26.7, 25.2, 18.7; ESIMS m/z (rel intensity) 606 (MH+, 100), 550 (59), 538 (21); HRMS m/z calcd for C33H40N3O8 (MH+) 606.2851, found 606.2812. Anal. Calcd for C33H39N3O8: C 65.44; H 6.49; N, 6.94. Found: C 65.51; H 6.62; N 7.09.
N-(2,4-Bis(benzyloxy)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)pyrimidin-5-ylamino)methacrylamide (45)
0.5N HCl (1 mL) was added to a solution of compound 44 (60 mg, 0.1 mmol) in MeOH (1 mL) and the reaction mixture was stirred for 12 h at room temperature. MeOH was removed under vacuum, the residue was then dissolved in ethyl acetate (10 mL), and the organic layer was washed with water and brine, dried and concentrated. The residue was flash column chromatographed with silica gel, eluting with 80% ethyl acetate in hexane, to provide compound 45 (36 mg, 69%) as a colorless oil. 1H NMR (300 MHz, MeOH-d4) δ 7.40-7.27 (m, 10 H), 5.84 (s, 1 H), 5.48 (s, 1 H), 5.40 (s, 2 H), 5.38 (s, 2 H), 4.62 (dd, J = 3.0, 11.4 Hz, 1 H), 4.47 (dd, J = 6.6, 11.4 Hz, 1 H) 4.06-4.05 (m, 1 H), 3.79-3.77 (m, 2 H), 3.75-3.73 (m, 2 H), 1.99 (s, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 170.9, 168.5, 168.1, 163.0, 141.1, 138.1, 138.0, 129.5, 129.4, 129.1, 129.0, 128.6, 128.4, 121.7, 98.3, 74.1, 73.5, 72.0, 70.5, 70.0, 69.9, 64.6, 18.9; ESIMS m/z (rel intensity) 526 (MH+, 100), 494 (24), 392 (42); negative ion ESIMS m/z (rel intensity) 524 [(M – H+), 24], 391 (21), 390 (100). Anal. Calcd for C27H31N3O8: C, 61.70; H, 5.95; N, 8.00. Found: C, 61.91; H, 5.90; N, 7.88.
N-(2,4-Dioxo)-6-((2S,3R,4R)-2,3,4,5-tetrahydroxypentyloxy)-1,2,3,4-tetrahydropyrimidin-5-yl)methacrylamide (46)
Lindlar catalyst (5 mg) was added to a solution of compound 45 (50 mg, 0.095 mmol) in anhydrous ethanol (4 mL). 1,4-Cyclohexediene (52 μL, 0.95 mmol) was added and argon was bubbled through the reaction mixture for 10 min. The mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with ethanol (2 × 5 mL). The solution was concentrated and the residue was washed several times with CH2Cl2 and THF. Finally, the product was precipitated out by dissolving it in MeOH and adding excess diethyl ether to furnish pure compound 46 (24 mg, 73%) as a white amorphous solid: mp 170–172 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 5.87 (s, 1 H), 5.46 (s, 1 H), 4.50-4.41 (m, 1 H), 3.96-3.92 (m, 1 H), 3.73-3.71 (m, 3 H), 3.64-3.61 (m, 2 H), 2.01 (s, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 167.3, 160.8, 149.7, 144.2, 140.0, 119.8, 75.5, 73.2, 69.1, 68.6, 67.9, 65.7, 18.5; ESIMS m/z (rel intensity) 369 (MNa+, 100), 283 (13), 102 (27); negative ion ESIMS m/z (rel intensity) 344 [M – H+), 100], 325 (3), 210 (5); HRMS m/z calcd for C13H19N3O8Na (MNa+) 368.1070, found 368.1073. Anal. Calcd for C13H19N3O8: C, 45.22; H, 5.55; N, 12.17. Found: C, 45.41; H, 5.27; N, 12.40.
N-(2,4-Dioxo)-6-(((4S,4′R,5R)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methylthio)-1,2,3,4-tetrahydropyrimidin-5-yl)propionamide (48)
Propionic acid (13 μL, 0.18 mmol), 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (23 mg, 0.12 mmol) and N-hydroxybenzotriazole monohydrate (16 mg, 0.12 mmol) were added to a solution of compound 47 (40 mg, 0.12 mmol) dissolved in pyridine (3.0 mL). The reaction mixture was stirred at rt for 12 h. The solvent was distilled off under reduced pressure and the residue was dissolved in EtOAc (15 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was purified by flash column chromatography with silica gel, eluting with 5% MeOH in ethyl acetate in hexane, to afford compound 48 (30 mg, 65%) as a colorless oil. 1H NMR (300 MHz, MeOH-d4) δ 4.45 (q, J = 6.1 Hz, 1 H), 4.20-4.07 (m, 3 H), 3.89 (dd, J = 4.7, 8.1 Hz, 1 H), 3.37-3.30 (m, 2 H), 2.38 (q, J = 7.6 Hz, 2 H), 1.46 (s, 3 H), 1.38 (s, 3 H), 1.35 (s, 3 H), 1.32 (s, 3 H), 1.19 (t, J = 7.6 Hz, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 177.1, 162.5, 152.6, 152.0, 111.3, 110.8, 79.9, 79.1, 74.5, 68.8, 33.7, 29.8, 27.9, 27.1, 25.6, 25.4, 10.2; ESIMS m/z (rel intensity) 468 (MK+, 100), 452 (MNa+, 29), 430 (MH+, 5), 268 (13); negative ion ESIMS m/z (rel intensity) 428 [(M – H+), 100]; HRMS m/z calcd for C18H27N3O7SNa (MNa+) 452.1467, found 452.1461. Anal. Calcd for C18H27N3O7S: C 50.34; H 6.34; N 9.78; S 7.47. Found: C 50.46; H 6.49; N 9.81; S 7.61.
N-(2,4-Dioxo)-6-((2R,3R,4R)-2,3,4,5-tetrahydroxypentylthio)-1,2,3,4-tetrahydropyrimidin-5-yl)propionamide (49)
1N HCl (2 mL) was added to compound 48 (30 mg, 0.068 mmol) dissolved in MeOH (2 mL). The reaction mixture was stirred for 8 h at room temperature. The solution was concentrated and the residue was washed several times with CH2Cl2 (3 × 10 mL) and THF (3 × 10 mL). Finally, compound 49 was precipitated out by dissolving it in MeOH and adding excess diethyl ether to furnish pure compound 49 (17 mg, 70%) as a white amorphous solid: mp 137–140 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 3.97-3.88 (m, 1 H), 3.78-3.72 (m, 3 H), 3.67-3.56 (m, 3 H), 2.35 (q, J = 7.5 Hz, 2 H), 1.19 (t, J = 7.5 Hz, 3 H); 13C NMR (125 MHz, CDCl3) δ 177.1, 169.5, 162.6, 158.2, 104.8, 73.3, 63.1, 33.3, 29.4, 9.2; ESIMS m/z (rel intensity) 721 (2MNa+, 94), 372 (MNa+, 100), 350 (MH+, 5); negative ion ESIMS m/z(rel intensity) 348 [(M – H+), 100]; HRMS m/z calcd for C12H19N3O7SNa (MNa+) 372.0841, found 372.0843. Anal. Calcd for C12H19N3O7S: C 41.25; H 5.48; N 12.03; S 9.18. Found: C 41.31; H 5.48; N 12.21; S 9.31.
N-(2,4-Dioxo)-6-(((4S,4′R,5R)-2,2,2′,2′-tetramethyl-4,4′-bi(1,3-dioxolan)-5-yl)methylthio)-1,2,3,4-tetrahydropyrimidin-5-yl)methacrylamide (50)
Methacrylic acid (13 μL, 0.15 mmol), 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (20 mg, 0.10 mmol) and N-hydroxybenzotriazole monohydrate (14 mg, 0.10 mmol) were added to a solution of compound 47 (35 mg, 0.10 mmol) dissolved in pyridine (3.0 mL). The reaction mixture was stirred at room temperature for 12 h. The solvent was distilled off under reduced pressure and the residue was dissolved in EtOAc (15 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was purified by flash column chromatography with silica gel, eluting with 5% MeOH in ethyl acetate in hexane, to afford compound 50 (28 mg, 68%) as a white amorphous solid: mp 95–98 °C. 1H NMR (300 MHz, MeOH-d4) δ 5.89 (s, 1 H), 5.52 (s, 1 H), 5.48 (s, 1 H), 4.45 (q, J = 6.1 Hz, 1 H), 4.18-4.07 (m, 3 H), 3.89 (dd, J = 4.7, 8.1 Hz, 1 H), 3.38-3.34 (m, 2 H), 2.15 (s, 3 H), 1.46 (s, 3 H), 1.37 (s, 3 H), 1.35 (s, 3 H), 1.32 (s, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 170.9, 162.5, 153.1, 152.1, 140.8, 129.2, 121.9, 111.3, 110.8, 79.9, 79.0, 74.5, 68.8, 33.7, 27.9, 27.1, 25.6, 25.4, 18.8; ESIMS m/z (rel intensity) 464 (MNa+, 64), 442 (MH+, 100), 166 (26); negative ion ESIMS m/z (rel intensity) 440 [(M – H+), 100]; HRMS m/z calcd for C19H28N3O7S (MH+) 442.1648, found 442.1655. Anal. Calcd for C19H27N3O7S: C 51.69; H 6.16; N 9.52; S 7.26. Found: C 51.92; H 5.91; N 9.60; S 7.02.
N-(2,4-Dioxo)-6-((2R,3R,4R)-2,3,4,5-tetrahydroxypentylthio)-1,2,3,4-tetrahydropyrimidin-5-yl)methacrylamide (51)
1 N HCl (2 mL) was added to compound 50 (30 mg, 0.068 mmol) dissolved in MeOH (2 mL). The reaction mixture was stirred for 8 h at room temperature. The solution was concentrated and the residue was washed several times with CH2Cl2 (3 × 10 mL) and THF (3 × 10 mL). Finally, compound 51 was precipitated out by dissolving in MeOH and adding excess diethyl ether to furnish pure compound 51 (19 mg, 78%) as a white amorphous solid: mp 140–143 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 5.88 (s, 1 H), 5.49 (s, 1 H), 3.99 (q, J = 6.1 Hz, 1 H), 3.78-368 (m, 2 H), 3.65-3.59 (m, 2 H), 3.30-3.27 (m, 2 H), 2.0 (s, 3 H); 13C NMR (125 MHz, MeOH-d4) δ 171.2, 163.8, 154.1, 141.0, 129.9, 121.7, 108.6, 74.7, 74.4, 74.0, 64.7, 35.9, 19.0; ESIMS m/z (rel intensity) 745 (2MNa+, 100), 384 (MNa+, 48), 362 (MH+, 14); negative ion ESIMS m/z (rel intensity) 360 [(M – H+), 100]; HRMS m/z calcd for C13H20N3O7S (MH+) 361.1022, found 361.1025. Anal. Calcd for C13H19N3O7S: C 43.21; H 5.30; N 11.63; S 8.87. Found: C 43.01; H 5.44; N 11.49; S 9.03.
2,6-Dimethoxy-5-nitro-N-((2S,3S,4R)-2,3,4,5-tetrakis(tert-butyldimethylsilyloxy)-pentyl)pyrimidine-4-amine (53).50
Compound 52 (5.2854 g, 15.8 mmol), tert-butyldimethylsilyl chloride (16.55 g, 109.8 mmol), and imidazole (7.49 g, 109.8 mmol) were dissolved in dry DMF (115 mL) and the mixture was stirred at room temperature for 2 days. DMF was then removed under reduced pressure, and the residue was stirred in ethyl acetate (90 mL) for 2 h. The precipitated salt was filtered, and the filtrate was concentrated to form a yellow oil, which was separated by silica gel flash column chromatography, eluting with hexane-EtOAc (95:5), to afford pure 53 (6.95 g, 57%) as a light yellow oil: 1H NMR (300 MHz, CDCl3) δ 9.00 (s, 1 H), 4.10-4.09 (m, 1 H), 4.06 (s, 3 H), 3.96 (s, 3 H), 3.93-3.88 (m, 2 H), 3.83-3.80 (dd, J = 2.57 Hz, J = 5.99 Hz, 1 H), 3.72-3.67 (dd, J = 5.16 Hz, J = 10.32 Hz, 1 H), 3.56-3.51 (m, 2 H), 0.87 (s, 9 H), 0.86 (s, 9 H), 0.85 (s, 9 H), 0.84 (s, 9 H), 0.11 (s, 3 H), 0.08 (s, 3 H), 0.06 (s, 6 H), 0.04 (s, 3 H), 0.03 (s, 6 H), −0.04 (s, 3 H); ESIMS (MH+) m/z 791. Anal. Calcd for C35H74N4O8Si4: C 53.12; H 9.43; N 7.08; Si 14.20. Found: C 52.89, H 9.21; N 7.34; Si 13.93.
2,6-Dimethoxy-N4-((2S,3S,4R)-2,3,4,5-tetrakis(tert-butyldimethylsilyloxy)-pentyl)pyrimidine-4,5-diamine (54)
Compound 53 (6.9 g, 8.73 mmol) was added to a methanol (175 mL) and water (10 mL) mixture. Na2S2O4 (11.4 g, 65.4 mmol) was added to the reaction mixture. The mixture was heated at reflux and stirred for 6 h. The reaction mixture was then cooled to room temperature. The solution was filtered through celite and the filtrate was dried to afford a residue. The residue was separated by silica gel flash column chromatography with hexane-ethyl acetate 20:1 as the mobile phase to afford the product 54 as unstable yellow oil (6.24 g, 94%) that soon turned purple. 1H NMR (300 MHz, CDCl3) δ 4.03-3.98 (m, 1 H), 3.93-3.89 (m, 1 H), 3.90 (s, 3 H), 3.85 (s, 3 H), 3.84-3.80 (m, 1 H), 3.76-3.64 (m, 2 H), 3.57-3.45 (m, 2 H), 0.88-0.86 (m, 36 H), 0.10-0.00 (m, 24 H); 13C NMR (75 MHz, CDCl3) δ 161.2, 159.6, 159.1, 100.8, 75.0, 71.7, 64.7, 54.1, 53.6, 43.0, 31.6, 29.6, 26.1, 25.9, 25.3, 22.6, 18.4, 18.3, 18.2, 18.0, 14.1, −4.1, −4.3, −4.6, −4.7, −4.9, −5.3, −5.4; ESIMS (MH+) m/z 761. Anal. Calcd for C35H76N4O6Si4: C 55.21; H 10.06; N 7.36; Si 14.76. Found: C 55.58; H 10.20; N 7.14; Si 14.40.
N-(2,4-Dimethoxy-6-((2S,3S,4R)-2,3,4,5-tetrakis(tert-butyldimethylsilyloxy)-pentylamino)pyrimidine-5-yl)methacrylamide (55)
Compound 54 (3.28 g, 4.32 mmol) was mixed with THF (30 mL). Triethylamine (6.0 mL, 43.3 mmol) was added to the THF solution. The mixture was cooled to 0 °C and methacryloyl chloride (678 mg, 6.48 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 0.5 h. The reaction mixture was warmed to room temperature and stirred for 20 min. The mixture was dried in vacuo to get a residue and that was purified by silica gel flash column chromatography with hexane-ethyl acetate 20:1 as the mobile phase to afford the product 55 as a colorless oil (2.53 g, 71%). 1H NMR (300 MHz, CDCl3) δ 5.84 (s, 1 H), 5.58 (brs, 1 H), 5.45 (s, 1 H), 3.95-3.91 (m, 2 H), 3.89 (s, 3 H), 3.88 (s, 3 H), 3.78-3.68 (m, 3 H), 3.57-3.51 (m, 1 H), 3.44-3.41 (m, 1 H), 2.06 (s, 3 H), 0.87-0.83 (m, 36 H), 0.08- –0.05 (m, 24 H); 13C NMR (75 MHz, CDCl3) δ 166.8, 164.3, 162.3, 139.4, 120.9, 94.5, 74.6, 71.6, 64.6, 54.4, 54.0, 43.3, 31.9, 31.6, 29.7, 26.1, 25.9, 22.6, 18.7, 18.4, 18.3, 18.2, 18.0, 14.1, −4.0, −4.3, −4.4, −4.6, −5.2, −5.3, −5.4; ESIMS (MH+) m/z 829. Anal. Calcd for C39H80N4O7Si4: C 56.48; H 9.72; N 6.75; Si 13.54. Found: C 56.83; H 9.40; N 6.38; Si 13.21.
N-[2,4-Dioxo-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino]-1,2,3,4-tetrahydropyrimidin-5-yl)methacrylamide (56)
Compound 55 (0.7 g, 0.85 mmol) was dissolved in a solution made from 48% HBr-H2O (2:1, 30 mL) and MeOH (30 mL) and the mixture was stirred at 55–60 °C for 3 h. The solvent was removed in vacuo, the residue was dissolved in MeOH (10 mL), and ethyl ether (60 mL) was added. After 24 h in the refrigerator, the precipitate was filtered out as a light red solid, which was dissolved in water (60 mL), decolorized with active charcoal, and filtered. The solvent was removed from the filtrate and the residue was purified by silica gel flash column chromatography (EtOAc-EtOH-H2O-AcOH 67:23:9:1) twice and sephadex LH 20 column twice with MeOH to remove silica gel and other inorganic impurities and provide the product 56 (100 mg, 34%) as a white semisolid powder: 1H NMR (300 MHz, D2O) δ 5.88 (s, 1 H), 5.55 (s, 1 H), 3.87-3.47 (m, 7 H), 1.95 (s, 3 H); 13C NMR (125 MHz, D2O) δ 172.4, 162.6, 153.6, 151.3, 138.1, 123.1, 86.3, 72.2, 72.1, 70.3, 62.3, 44.1, 17.7; ESIMS m/z (rel. intensity) 389 [(M2Na+ – H+)+, 100], 367 (MNa+, 76); HRMS Calcd for C13H20N4O7Na (MNa+) 367.1230, found 367.1226. Anal. Calcd for C13H20N4O7·1.5 H2O·1 MeOH: C 41.68; H 6.75; N 13.89. Found: C 41.27; H 6.35; N 14.19.
N-(2,4-Bis(benzyloxy)-6-((2S,3S,4R)-2,3,4,5-tetrakis(tert-butyldimethylsilyloxy)pentylamino)pyrimidin-5-yl)-2-chloropropanamide (58)
Compound 57 (210 mg, 0.23 mmol) was mixed with THF (5 mL). TEA (0.3 mL, 2.1 mmol) was added to the THF solution. The mixture was cooled to 0 °C and the 2-chloropropanoyl chloride (34 μL, 44 mg, 0.34 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 0.5 h. The mixture was dried in vacuo to yield a residue and that was purified by silica gel flash column chromatography to provide the product 58 as a yellow oil (200 mg, 87%). 1H NMR (300 MHz, CDCl3) δ 7.48-7.26 (m, 10 H), 5.42-5.35 (m, 4 H), 4.08-3.65 (m, 7 H), 1.77-1.75 (d, J = 6.7 Hz, 3 H), 0.93-0.90 (m, 36 H), 0.15-0.01 (m, 24 H); 13C NMR (75 MHz, CDCl3) δ 168.9, 164.1, 162.1, 162.1, 160.3 160.2, 137.0, 136.5, 128.3, 128.2, 128.0, 127.8, 127.7, 127.6, 93.5, 93.4, 76.6, 74.5, 71.3, 68.8, 68.3, 64.5, 60.3, 55.7, 43.2, 26.0, 25.9, 22.7, 22.6, 18.4, 18.2, 18.1, 17.9, 14.1; ESIMS m/z (rel. intensity) 1005.32 [M(Cl37)H+, 64.10], 1003.34 [M(Cl35)H+, 100]; HRMS Calcd for C50H88ClN4O7Si4 (MH+) 1003.5419, found 1003.5408. Anal. Calcd for C50H87ClN4O7Si4: C 59.81; H 8.73; N 5.58; Si 11.19. Found: C 60.03; H 8.97; N 5.61; Si 11.25.
N-(2,4-Bis(benzyloxy)-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino)pyrimidin-5-yl)-2-chloropropanamide (59)
Compound 58 (144 mg, 0.14 mmol) was mixed with THF (7 mL). TBAF (1.0 M tetra-n-butylammonium fluoride in THF, 0.65 mmol, 0.65 mL) was added to the reaction mixture. The mixture was stirred at room temperature for 4 h and then dried in vacuo to afford a residue. The residue was purified by silica gel preparative TLC (solvent system: EtOAc-MeOH 20:1) to give a white solid 59 (65 mg, 83%): mp 132–134 °C. 1H NMR (300 MHz, MeOH-d4) δ 7.33-7.17 (m, 10 H), 5.24-5.21 (d, J = 8.2 Hz, 4 H), 4.53-4.46 (q, J = 6.8, 13.7 Hz, 1 H), 3.80-3.42 (m, 7 H), 1.55-1.53 (d, J = 6.9 Hz, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 172.9, 166.3, 163.8, 163.0, 138.5, 138.3, 129.4, 129.4, 129.0, 128.95, 128.9, 128.6, 94.1, 74.4, 74.2, 72.8, 70.0, 69.3, 64.6, 55.2, 44.8, 22.2; ESIMS m/z (rel. intensity) 549 [M(Cl37)H+, 34], 547 [M(Cl35)H+, 100]; HRMS Calcd for C26H32ClN4O7 (MH+) 547.1960, found 547.1959. Anal. Calcd for C26H31ClN4O7: C 57.09; H 5.71; N 10.24. Found: C 56.85; H 5.49; N 10.45.
2-Chloro-N-(2,4-dioxo-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino)1,2,3,4-tetrahydropyrimidin-5-yl)propanamide (60)
Lindlar catalyst (5 mg) was added to a solution of compound 59 (50 mg, 0.13 mmol) in anhydrous ethanol (4 mL). 1,4-Cyclohexediene (0.1 mL, 1.3 mmol) was added and argon was bubbled through the reaction mixture for 10 min. The mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with ethanol (2 × 5 mL). The solution was concentrated and the residue was washed several times with CH2Cl2 and THF. Finally, compound 60 was precipitated out by dissolving it in MeOH and adding excess diethyl ether to furnish pure compound 60 (18 mg, 66%) as a white amorphous solid: mp 208–211 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 4.51 (q, J = 7.0, 13.7 Hz, 1 H), 3.75-3.72 (m, 1 H), 3.67-3.61 (m, 2 H), 3.54-3.46 (m, 2 H), 3.23-3.19 (m, 2 H), 1.18 (t, J = 7.6 Hz, 3 H); 13C NMR (125 MHz, MeOH-d4) δ 172.1, 161.8, 153.2, 150.7, 86.2, 72.9, 72.2, 71.5, 63.0, 54.0, 44.6, 20.6; ESIMS m/z (rel. intensity) 369 [M(Cl37)H+, 32], 366 [M(Cl35)H+, 100]; HRMS m/z Calcd for C12H20ClN4O7 (MH+) 367.1021, found 367.1023.
N-(2,4-Bis(benzyloxy)-6-((2S,3S,4R)-2,3,4,5-tetrakis(tert-butyldimethylsilyloxy)pentylamino)pyrimidin-5-yl)-2-chloroacetamide (61)
Compound 57 (0.7 g, 0.77 mmol) was mixed with THF (20 mL). TEA (1 mL, 6.9 mmol) was added to the THF solution. The mixture was cooled to 0 °C and 2-chloroacetyl chloride (88 μL, 121 mg, 1.1 mmol) was added drop wise. The reaction mixture was stirred at 0 °C for 0.5 h. The mixture was dried in vacuo to afford a residue that was purified by silica gel flash chromatography to provide the product 61 as a yellow oil (0.7 mg, 92%). 1H NMR (300 MHz, CDCl3) δ 7.57 (s, 1 H), 7.45-7.26 (m, 10 H), 5.44-5.33 (m, 4 H), 4.14 (s, 2 H), 3.99-3.47 (m, 7 H), 0.92-0.88 (m, 36 H), 0.14-0.00 (m, 24 H); 13C NMR (75 MHz, CDCl3) δ 165.0, 164.0, 162.2, 160.1, 137.0, 136.6, 128.4, 128.3, 128.1, 127.9, 127.8, 127.5, 93.2, 74.5, 71.4, 68.9, 68.2, 64.4, 43.1, 42.5, 26.1, 26.1, 25.9, 18.4, 18.3, 18.2, 18.0, −4.0, −4.4, −4.4, −4.6, −5.2, −5.3, −5.4; ESIMS m/z (rel. intensity) 991 [M(Cl37)H+, 63], 989 [M(Cl35)H+, 100]; HRMS m/z Calcd for C49H86ClN4O7Si4 (MH+) 989.5262, found 989.5269. Anal. Calcd for C49H85ClN4O7Si4: C 59.45; H 8.65; N 5.66; Si 11.35. Found: C 59.69; H 8.73; N 5.47; Si 11.07.
N-(2,4-Bis(benzyloxy)-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino)pyrimidin-5-yl)-2-chloroacetamide (62)
Compound 61 (40 mg, 0.04 mmol) was mixed with THF (2 mL). TBAF (1.0 M tetra-n-butylammonium fluoride in THF, 0.2 mmol, 0.2 mL) was added to the reaction mixture. The mixture was stirred at room temperature for 4 h and then dried in vacuo to produce a residue. The residue was purified by silica gel preparative TLC (solvent system: EtOAc-MeOH 20:1) to yield a white solid 62 (17 mg, 79%): mp 130–131 °C. 1H NMR (300 MHz, MeOH-d4) δ 7.29-7.15 (m, 10 H), 5.25 (d, J = 15.0 Hz, 2 H), 5.18 (d, J = 15.2 Hz, 2 H), 4.09 (s, 2 H), 3.77-3.67 (m, 1 H), 3.66-3.40 (m, 6 H); 13C NMR (75 MHz, MeOH-d4) δ 169.9, 166.3, 163.8, 163.1, 138.5, 138.4, 129.4, 129.0, 128.8, 128.5, 94.0, 74.4, 74.2, 72.9, 70.0, 69.2, 64.6, 44.8, 43.3; ESIMS m/z (rel. intensity) 535 [M(Cl37)H+, 36], 533 [M(Cl35)H+, 100]; HRMS m/z Calcd for C25H30ClN4O7 (MH+) 533.1798, found 533.1803. Anal. Calcd for C25H29ClN4O7: C 56.34; H 5.48; N, 10.51. Found: C 56.41; H 5.61; N 10.79.
2-Chloro-N-(2,4-dioxo-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino)-1,2,3,4-tetrahydropyrimidin-5-yl)acetamide (63)
Compound 62 (40 mg, 0.08 mmol) was mixed with anhydrous ethanol (5 mL). 1, 4-Cyclohexadiene (130 mg, 1.6 mmol) and Pearlman’s catalyst (40 mg, 20% Pd(OH)2 on carbon) were added to the reaction mixture. The mixture was stirred at room temperature under argon for 18 h and then filtered. The filtrate was then dried in vacuo to yield a residue. The residue was purified by prep TLC (solvent system: EtOAc-EtOH-H2O 15:5:2) to provide a white solid 63 (17 mg, 64%): mp 173–174 °C. 1H NMR (500 MHz, D2O) δ 4.25 (s, 2 H), 3.85-3.81 (m, 1 H), 3.75-3.69 (m, 2 H), 3.65-3.44 (m, 4 H); 13C NMR (125 MHz, D2O) δ 171.3, 162.5, 155.8, 153.2, 85.8, 72.19, 72.1, 70.5, 62.3, 43.8, 42.2; ESIMS m/z (rel. intensity) 353 [(M(Cl37)-H+), 24,], 351 [(M(Cl35)-H+), 100,]; HRMS Calcd for C11H16ClN4O7 (M – H+) 351.0708, found 351.0707. Anal. Calcd for C11H17ClN4O7: C 37.46; H 4.86; N, 15.88. Found: C 37.35; H 4.61; N 16.04.
N-(2,4-Bis(benzyloxy)-6-((2S,3S,4R)-2,3,4,5-tetrakis(tert-butyldimethylsilyloxy)- pentylamino)pyrimidin-5-yl)-3,3,3-trifluoropropanamide (64)
Compound 57 (0.58 mg, 0.64 mmol) was mixed with THF (15 mL). TEA (0.9 mL, 6.9 mmol) was added to the THF solution. The mixture was cooled to 0 °C and 3,3,3-trifluoropropanoyl chloride (65 μL, 0.64 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 0.5 h. The mixture was dried in vacuo to provide a residue that was purified by silica gel flash chromatography to yield the product 64 as a yellow oil (0.49 mg, 75%). 1H NMR (300 MHz, DMSO-d6) δ 7.45-7.29 (m, 10 H), 5.78 (s, 1 H), 5.44-5.28 (m, 4 H), 4.03-4.01 (m, 1 H), 3.87-3.89 (m, 1 H), 3.76-3.69 (m, 2 H), 3.58-3.50 (m, 3 H), 3.40-3.3.37 (m, 2 H), 0.90-0.83 (m, 36 H), 0.13--0.02 (m, 24 H); 13C NMR (75 MHz, CDCl3) δ 164.11, 162.1, 161.7, 160.2, 136.9, 136.3, 128.6, 128.4, 128.2, 128.0, 127.8, 127.7, 129.3-118.3 (q, J = 275.6 Hz), 93.4, 74.7, 71.2, 69.2, 68.9, 68.4, 64.5, 43.3, 42.2-41.1 (q, J = 29.3 Hz), 26.0, 25.8, 18.3, 18.2, 18.1, 17.9, −4.1, −4.3, −4.4, −4.5, −4.7, −4.7, −5.3, −5.4, −5.5; 19F NMR (300 MHz, CDCl3) δ 16.9 ( t, J = 11.7 Hz, 3 F); HRMS Calcd for C50H86F3N4O7Si4 (MH+) 1023.5526, found 1023.5519. Anal. Calcd for C50H85F3N4O7Si4: C 58.67; H 8.37; N, 5.47; Si, 10.98. Found: C 58.83; H 8.08; N 5.40; Si, 11.15.
N-(2,4-Bis(benzyloxy)-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino)pyrimidin-5-yl)-3,3,3-trifluoropropanamide (65)
Compound 64 (131 mg, 0.13 mmol) was mixed with THF (6 mL). TBAF (1.0 M tetra-n-butylammonium fluoride in THF, 0.58 mmol, 0.58 mL) was added to the reaction mixture. The mixture was stirred at room temperature for 4 h and then dried in vacuo to afford a residue. The residue was purified by silica gel preparative TLC (solvent system: EtOAc-MeOH 20:1) to produce a white solid 65 (61 mg, 84%): mp 137–138 °C. 1H NMR (300 MHz, MeOH-d4) δ 7.32-7.17 (m, 10 H), 5.25-5.23 (m, 4 H), 3.88-3.86 (m, 1 H), 3.78-3.53 (m, 6 H), 3.37-3.30 (m, 2 H); 13C NMR (75 MHz, MeOH-d4) δ 166.3, 166.2, 163.8, 163.0, 138.5, 138.3, 129.4, 129.4, 129.0, 128.8, 128.6, 131.3-120.3 (q, J = 274.4 Hz), 94.0, 74.4, 74.2, 72.9, 70.0, 69.3, 64.6, 54.7, 44.8, 41.7-40.6 (q, J = 29.4 Hz); 19F NMR (300 MHz, CDCl3) δ 11.3 (t, J = 11.5 Hz, 3 F); HRMS Calcd for C26H29F3N4O7Na (MNa+) 589.1886, found 589.1889. Anal. Calcd for C26H29F3N4O7: C 55.12; H 5.16; N, 9.89. Found: C 54.93; H 5.23; N 10.07.
N-(2,4-Dioxo-6-((2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino)-1,2,3,4-tetrahydropyrimidin-5-yl)-3,3,3-trifluoropropanamide (66)
Compound 65 (30 mg, 0.05 mmol) was mixed with anhydrous ethanol (3 mL). 1,4-Cyclohexadiene (80 mg, 1.0 mmol) and Pearlman’s catalyst (30 mg, 20% Pd(OH)2 on carbon) were added to the reaction mixture. The mixture was stirred at room temperature under argon for 24 h and then filtered. The filtrate was then dried in vacuo to yield a residue. The residue was purified by prep TLC (solvent system: EtOAc-EtOH-H2O 15:5:2) to afford a white solid 66 (15 mg, 72%): mp 189–190 °C. 1H NMR (500 MHz, D2O) δ 3.84-3.83 (m, 1 H), 3.77-3.69 (m, 2 H), 3.61-3.54 (m, 4 H) 3.50-3.42 (m, 2 H); 13C NMR (125 MHz, D2O) δ 167.9, 162.4, 154.9, 152.5, 123.9 (q, J = 274.1 Hz), 85.9, 72.1, 70.3, 62.3, 43.8, 39.6 (q, J = 29.1 Hz); 19F NMR (300 MHz, DMSO-d6) δ 12.10 (t, J = 11. 7 Hz, 3 F); HRMS (ESI) Calcd for C12H16F3N4O7 (M – H+) 385.0971, found 385.0976. Anal. Calcd for C12H17F3N4O7: C 37.31; H 4.44; N, 14.50. Found: C 37.33; H 4.67; N 14.39.
N-(2,4-Bis(benzyloxy)-6-[(2S, 3S, 4R)-2,3,4,5-tetrakis(tert-butyldimethy-silanyloxy)-pentylamino]-pyrimidin-5-yl)-2-oxopropanamide (67)
Triethylamine (0.3 mL) was added to a solution of compound 57 (180 mg, 0.2 mmol) in THF (5 mL). The solution was cooled to 0 °C and 2-oxopropanoyl chloride (24 μL, 0.24 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 12 h. The solvent was distilled off under reduced pressure and the residue was dissolved in dichloromethane (20 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was column chromatographed with flash silica gel, eluting with 35% ethyl acetate in hexane, to afford compound 67 (135 mg, 70%) as yellowish oil. 1H NMR (300 MHz, CDCl3) δ 8.21 (brs, 1 H), 7.43-7.24 (m, 10 H), 5.75 (m, 1 H), 5.42-5.27 (m, 4 H), 4.0 (m, 2 H), 3.88 (m, 2 H), 3.79 (m, 1 H), 3.59 (m, 1 H), 3.41 (m, 1 H), 2.47 (s, 3 H), 0.94 – 0.86 (m, 36 H), 0.20-0.05 (m, 24 H); 13C NMR (75 MHz, CDCl3) δ 196.0, 163.7, 162.0, 159.2, 158.1, 137.0, 136.5, 128.5, 128.3, 128.1, 128.0, 127.7, 93.4, 74.5, 71.4, 68.9, 68.3, 64.5, 43.4, 26.14, 26.08, 25.9, 24.3, 18.4, 18.3, 18.2, 18.0, −4.0, −4.4, −4.5; ESIMS m/z (rel intensity) 983 (MH+, 100), 965 (11), 719 (16); negative ion ESIMS m/z (rel intensity) 981 [(M – H+), 100], 911 (65), 847 (35); HRMS m/z calcd for C50H86N4O8Si4 (MH+) 983.5601, found 983.5609.
2,4-Bis(benzyloxy)-7-hydroxy-7-methyl-8-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl)-7,8-dihydropteridin-6(5H)-one (68)
Compound 67 (60 mg, 0.06 mmol) was dissolved in THF (3 mL), and TBAF (0.07 mL, 0.36 mmol, 1 M solution in THF) was added. The reaction mixture was stirred at room temperature for 8 h. THF was removed under vacuum. The residue was extracted with ethyl acetate (3 × 10 mL), washed with water (2 × 10 mL), dried with anhydrous Na2SO4, and concentrated under reduced pressure. The residue was column chromatographed with flash silica gel, eluting with 5% MeOH in ethyl acetate, to afford compound 68 (22 mg, 69%) as an oil. 1H NMR (300 MHz, MeOH-d4) δ 8.21 (brs, 1 H), 7.43-7.28 (m, 10 H), 5.43 (ABq, J = 8.4, 15.6 Hz, 2 H), 5.36 (s, 2 H), 4.18-4.10 (m, 1 H), 3.92-3.80 (m, 2 H), 3.81-3.51 (m, 4 H), 1.39 (s, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 164.8, 170.0, 157.5, 150.6, 138.4, 137.9, 129.50, 129.46, 129.2, 128.94, 128.88, 126.1, 99.4, 90.8, 79.0, 74.2, 71.5, 70.1, 69.6, 64.7, 45.9, 24.5; ESIMS m/z (rel intensity) 509 (MH+ – H2O, 56), 202 (100); negative ion ESIMS m/z (rel intensity) 525 [(M – H+), 71], 507 [(M – H+ - H2O), 100]; HRMS m/z calcd for C26H30N4O8 (M – H+) 525.1985, found 525.1984.
7-Hydroxy-7-methyl-8-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl)-7,8-dihydropteridin-2,4,6(1H, 3H, 5H)-trione (69)
Lindlar catalyst (5 mg) was added to a solution of compound 68 (20 mg, 0.04 mmol) in MeOH-EtOAc (3 + 1 mL). A hydrogen balloon was attached and the mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with 50% aq MeOH (5 mL). The solution was concentrated and the residue was washed several times with CH2Cl2 (3 × 10 mL) and THF (3 × 10 mL). Finally, compound 69 was precipitated out by dissolving in MeOH and adding excess diethyl ether to furnish pure compound 69 (10 mg, 77%) as a white amorphous solid: mp 180–183 °C (dec). 1H NMR (300 MHz, MeOH-d4) δ 4.20-4.17 (m, 1 H), 4.07-4.01 (m, 1 H), 3.87-3.84 (m, 1 H), 3.77-3.74 (m, 1 H), 3.66-3.54 (m, 3 H), 1.40 (s, 3 H); 13C NMR (125 MHz, MeOH-d4) δ 164.2, 159.0, 152.5, 141.1, 95.4, 91.9, 79.8, 74.3, 71.2, 64.8, 48.2, 23.8; negative ion ESIMS m/z (rel intensity) 345 [(M – H+), 10], 327 [(M – H+ – H2O), 100]; negative ion HRMS m/z calcd for C12H17N4O8 (M – H+) 345.1046, found 345.1051. Anal. Calcd for C12H18N4O8·1.75H2O: C, 38.15; H, 5.74; N, 14.83. Found: C, 37.82; H, 5.79; N, 14.42.
N-(6-Chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methacrylamide (78)
Lindlar catalyst (5 mg) was added to a solution of compound 80 (40 mg, 0.097 mmol) in anhydrous ethanol (4 mL). 1,4-Cyclohexediene (53 μL, 0.97 mmol) was added and argon was bubbled through the reaction mixture for 10 min. The mixture was stirred at room temperature for 12 h. The reaction mixture was filtered through celite, which was then washed with ethanol (2 × 5 mL). The solution was concentrated. The residue was washed several times with CH2Cl2 and THF. Finally, compound 78 was precipitated out by dissolving it in MeOH and adding excess diethyl ether to furnish pure compound 78 (14 mg, 63%) as a white amorphous solid: mp 234–236 °C. 1H NMR (300 MHz, MeOH-d4) δ 5.89 (s, 1 H), 5.53 (s, 1 H), 1.99 (s, 3 H); 13C NMR (75 MHz, MeOH-d4) δ 170.9, 162.8, 151.3, 146.0, 140.6, 122.2, 110.4, 18.7; ESIMS m/z (rel intensity) 252 (MNa+, 100), 230 (MH+, 4); negative ion ESIMS m/z (rel intensity) 228 [(M – H+), 100], 192 (32); HRMS m/z calcd for C8H8ClN3O3Na (MNa+) 252.0152, found 252.0153. Anal. Calcd for C8H8ClN3O3·0.5 MeOH: C, 41.56; H, 4.10; N, 17.11. Found: C, 41.13; H, 4.01; N, 16.80.
N-[2,4-Bis(dibenzyloxy)-6-chloropyrimidin-5-yl)methacrylamide (80)
Triethylamine (0.3 mL, 2.2 mmol) was added to a solution of compound 79 (80 mg, 0.23 mmol) in THF (5 mL). The solution was cooled to 0 °C and methacrolyl chloride (28 μL, 0.28 mmol) was added dropwise. The reaction mixture was stirred at 0 °C for 12 h. The solvent was distilled off under reduced pressure and the residue was dissolved in dichloromethane (20 mL) and washed with water (2 × 15 mL). The organic layer was dried and solvent was distilled off. The residue was flash column chromatographed with silica gel, eluting with 35% ethyl acetate in hexane, to afford compound 80 (70 mg, 73%) as white semisolid. 1H NMR (300 MHz, CDCl3) δ 7.27-7.15 (m, 10 H), 5.63 (s, 1 H), 5.24 (s, 1 H), 5.21 (m, 4 H), 1.81 (s, 1 H); 13C NMR (75 MHz, CDCl3) δ 167.0, 166.8, 161.2, 158.6, 139.3, 135.5, 135.3, 128.3, 128.1, 127.5, 120.8, 110.4, 69.9, 69.4, 18.5; ESIMS m/z (rel intensity) 432 (MNa+, 100), 410 (MH+, 34) 268 (13); HRMS m/z Calcd for C22H21ClN3O3Na (MNa+) 432.1091, found 432.1090. Anal. Calcd for C22H20ClN3O3: C, 64.47; H, 4.92; N, 10.25. Found: C, 64.22; H, 5.03; N, 9.94.
Computational Detail
The crystal structure of M. tuberculosis lumazine synthase and ligand 70 complex was obtained from the Protein Data Bank (PDB code: 2VI5).48 To minimize the size of our simulation system, only one catalysis unit of lumazine synthase was kept, including subunit A, subunit B, inorganic phosphate, ligand 70 and all surrounding crystal water. The complex structure of M. tuberculosis lumazine synthase with other ligands (36, 69, 73 and 81) was built using 2VI5 as the template, followed by an energy minimization to optimize their geometry.
MD Simulations
All simulations were performed using AMBER 9.0. MD simulations were carried out using the parm99 force field at 300 K. An explicit solvent model TIP3P water was used, and the complexes were solvated with a truncated octahedron periodic box, extended to 8 Å from the solute atoms. Sodium ions were added as counter ions to neutralize the system. For each ligand, the force fields parameters were taken from the general Amber force field (GAFF), whereas the atomic partial charges were derived by geometry optimization using Gaussian 03 package58 at Hartree-Fock (HF)/6-31G* level and subsequent single point calculation of the electrostatic potential, to which the charges were fitted using the RESP procedure.
Prior to MD simulations, two steps of minimization were carried out; in the first stage, both protein and ligand were kept fixed with a constraint of 500 kcal/mol, and the positions of the water molecules were minimized; then in the second stage, the entire system without any constraint was minimized. The two minimization stages consisted of 3000 steps in which the first 1000 were steepest descent (SD) and the last 2000 conjugate gradient (CG). Molecular dynamics trajectories were run using the minimized structure as a starting input. The time step of the simulations was 2.0 fs with a cutoff of 10 Å for the nonbonded interaction, and SHAKE was employed to keep all bonds involving hydrogen atoms rigid. Constant volume was carried out for 100 ps, during which the temperature was raised from 0 to 300 K (using the Langevin dynamics method); then 1000 ps of constant-pressure MD were carried out at 300 K. The final structure of the complexes was obtained as the average of the last 400 ps of MD minimized with the CG method until a convergence of 0.05 kcal/mol·Å.
Energy Evaluation
To calculate the binding free energy, we extracted 100 snapshots (at time intervals of 4 ps) for each species (complex, receptor and ligand) from the last 400 ps of MD of the ligand-lumazine synthase complexes. The binding free energies were calculated using the MM-PBSA method.57 The binding affinity for a protein/ligand complex corresponds to the free energy of association in solution as shown in
equation M1
(1)
In MM-PBSA, the binding affinity in eq 1 is typically calculated using
equation M2
(2)
Where ΔEMM represents the change in molecular mechanics potential energy upon formation of the complex, calculated using all bonded and nonbonded interactions. Solvation free energy, ΔGsolv, is composed of the electrostatic component (GPB) and a nonpolar component (Gnp):
equation M3
(3)
GPB was calculated using the DelPhi program with PARSE radii. The cubic lattice had a grid spacing of 0.5 Å. Dielectric constants of 1 and 80 were used for the interior and exterior, respectively, and 1000 linear iterations were performed. The hydrophobic contribution to the solvation free energy, Gnp, was calculated using the solvent accessible surface area (SASA) from the MSMS program, where γ = 0.005 42 kcal/(mol·Å2) and β = 0.92 kcal/mol with a solvent probe radius of 1.4 Å:
equation M4
(4)
TΔSsolute represents the entropic contribution to binding affinity at temperature T. The five ligands used in our calculation are structurally very similar analogues. For a series of compounds with similar structures and binding modes, the entropy contribution can be omitted if one is only interested in relative binding affinities. Since this calculation converges slowly and can have large uncertainties, we omitted the entropic contribution in this study.
Kinetic Assay of Lumazine Synthase Inhibitors
Assay mixtures contained 100 mM Tris hydrochloride, pH 7.0, 100 mM NaCl, 2% (v/v) DMSO, 5 mM dithiothreitol, 100 μM 2, 0.3 – 2.0 μM lumazine synthase, variable concentrations of 1 (3 – 100 μM) and inhibitor (0 – 200 μM) in a volume of 0.2 mL. Assay mixtures were prepared as follows. A solution (176 μL) containing 100 mM NaCl, 5.0 mM dithiothreitol, 112 μM 2, 0.34 – 2.3 μM lumazine synthase in 100 mM Tris hydrochloride, pH 7.0, was added to 4 μL of inhibitor in 100% (v/v) DMSO in a well of a 96-well microtiter plate. The reaction was started by adding 20 μL of a solution containing 100 mM NaCl, 5.0 mM dithiothreitol, and substrate 1 (30 – 1000 μM) in 100 mM Tris hydrochloride, pH 7.0. The formation of 6,7-dimethyl-8-D-ribityllumazine (3) was measured online for a period of 30 min at 27 °C with a computer-controlled plate reader at 408 nm (εLumazine = 10,200 M−1cm−1).
Kinetic Assay of Riboflavin Synthase Inhibitors
Assay mixtures contained 100 mM Tris hydrochloride, pH 7.0, 100 mM NaCl, 2% (v/v) DMSO, 5 mM dithiothreitol, 0.2 – 1 μM riboflavin synthase, variable concentrations of 3 (3 – 60 μM) and inhibitor (0 – 200 μM) in a volume of 0.2 mL. Assay mixtures were prepared as follows. A solution (176 μL) containing 100 mM NaCl, 5.0 mM dithiothreitol, 0.23 – 1.13 μM riboflavin synthase in 100 mM Tris hydrochloride, pH 7.0, was added to 4 μL of inhibitor in 100% (v/v) DMSO in a well of a 96-well microtiter plate. The reaction was started by adding 20 μL of a solution containing 100 mM NaCl, 5.0 mM dithiothreitol, and substrate 3 (30 – 600 μM) in 100 mM Tris hydrochloride, pH 7.0. The formation of riboflavin (4) was measured online for a period of 30 min at 27 °C with a computer-controlled plate reader at 470 nm (εRiboflavin = 9,600 M−1cm−1).
Evaluation of Kinetic Data
The velocity-substrate data were fitted for all inhibitor concentrations with a non-linear regression method using the program DynaFit.60 Different inhibition models were considered for the calculation. Ki and Kis values ± standard deviations were obtained from the fit under consideration of the most likely inhibition model.
Supplementary Material
1_si_001
Acknowledgments
This research was made possible by NIH Grant Nos. GM51469 and R21 NS053634, the Fonds der Chemischen Industrie, the Hans Fischer Gesellschaft, support from Research Facilities Improvement Program Grant No. C06-14499 from the National Center for Research Resources of the National Institutes of Health.
Footnotes
Supporting Information Available: All experimental procedures and data, 1H NMR and 13C NMR spectra, and computational methods. This material is available free of charge via the Internet at http://pubs.acs.org.
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