Novel FR-900493 Analogues That Inhibit the Outgrowth of Clostridium difficile Spores.

The spectrum of antibacterial activity for the nucleoside antibiotic FR-900493 (1) can be extended by chemical modifications. We have generated a small focused library based on the structure of 1 and identified UT-17415 (9), UT-17455 (10), UT-17460 (11), and UT-17465 (12), which exhibit anti-Clostridium difficile growth inhibitory activity. These analogues also inhibit the outgrowth of C. difficile spores at 2× minimum inhibitory concentration. One of these analogues, 11, relative to 1 exhibits over 180-fold and 15-fold greater activity against the enzymes, phospho-MurNAc-pentapeptide translocase (MraY) and polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA), respectively. The phosphotransferase inhibitor 11 displays antimicrobial activity against several tested bacteria including Bacillus subtilis, Clostridium spp., and Mycobacterium smegmatis, but no growth inhibitory activity is observed against the other Gram-positive and Gram-negative bacteria. The selectivity index (Vero cell cytotoxicity/C. difficileantimicrobial activity) of 11 is approximately 17, and 11 does not induce hemolysis even at a 100 μM concentration.

Introduction

Clostridium difficile, a Gram-positive bacterium, is transmitted by the fecal-oral route. C. difficile infection (CDI) can cause illness ranging from diarrhea, colitis, and toxic inflammatory bowel disease to death. C. difficile has become one of the most common causes of health care-associated infections in U.S. hospitals.[1] Approximately 250 000 people are hospitalized in the U.S. every year from CDI.[2] The infective form of C. difficile is the spore, and its germination is the first committed step in CDI onset. C. difficile is found in abundance in the environment, and colonizes in the gut where it produces toxins that cause C. difficile-associated diarrhea (CDAD).[3−5] Frequently, treatment with broad-spectrum antibiotic(s) has the adverse effect of increasing the incidence of recurrent CDIs because of the disruption of the normal balance of gut flora.[6] A recently described highly toxic strain, BI/NAP1/027, exhibits resistance to fluoroquinolones and produces >20 times more toxins than historical strains.[7] Antibiotic treatment of CDI is difficult because of the antibiotic resistance and bacterial physiology (e.g., spore formation and protective effects of pseudomembranous colitis).[8,9] Currently, there are only a limited number of drugs available for the treatment of CDAD.[10] Metronidazole and vancomycin are the primary therapy options for CDI. Vancomycin is recommended for severe infections that do not respond to metronidazole. Vancomycin, rifaximin, and fidaxomicin are used in recurrent or persistent cases.[11] For severe recurrent CDIs, fecal microbiota transplantation, which involves instillation of stool from a healthy donor into the gastrointestinal (GI) tract of the patient, has been highlighted to restore the gut microbiome to a healthy state.[12] At therapeutic concentrations, currently available drugs for the treatment of CDI are not effective in inhibiting the germination or outgrowth of C. difficile spores. Only fidaxomicin has been reported to inhibit spore production in C. difficile.[13] To date, bile acid derivatives and a few organic molecules have been studied for their efficacy in the reduction of spore viability or inhibition of spore germination.[14−19]

In our continued efforts to identify strong inhibitors of bacterial phosphotransferases [phospho-MurNAc-pentapeptide translocase (translocase I or MraY) and polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA)] (Figure ),[20−25] we have generated a small focused library based on the structure of the known MraY inhibitor FR-900493 (1, Figure )[26] and assayed against the vegetative and spore forms of a C. difficile strain. MraY is specific for UDP-N-acetylmuramyl-pentapeptide (Park’s nucleotide) forming undecaprenyl diphosphoryl-N-acetylmuramate-pentapeptide (lipid I). WecA and its homologues (e.g., TagO or TarO) in Gram-negative bacteria are responsible for the first step of wall teichoic acid synthesis that anchors the phospho-GlcNAc moiety of UDP-GlcNAc to undecaprenyl phosphate (C55–P). MraY enzymatic activity is essential for the growth of both Gram-positive and Gram-negative bacteria, and thus is considered as a target of interest for the discovery of novel antibacterial agents. The major source of MraY inhibitors resides in the nucleoside-based antibiotic group. This group has been subdivided into four classes: tunicamycins, ribosaminouridines, uridyl peptides, and capuramycins. Analysis of the pharmacological behaviors observed with several compounds in these classes shows a broad spectrum of antibacterial activity, including relevant drug-resistant strains, and in vivo efficacy without apparent toxicity. Ribosaminouridine antibiotics, which include muraymycin, liposidomycins, caprazamycin, and FR-900493 (1), exhibit the most promising biological profiles.[27] On the other hand, essentiality of the WecA/TagO transferase subfamily is not completely understood in the growth of many bacteria.[28,29] Only a few molecules have been reported to exhibit WecA inhibitory activity.[28,29] Herein, we report a structure–activity relationship (SAR) obtained from a small focused library of FR-900493 (1) in a range of enzymes (MraY, WecA, and AglH) and bacterial growth inhibitory assays. Efficacy of these new MraY inhibitors against C. difficile spores along with in vitro toxicity assessments of the selected anti-C. difficile molecules is discussed.

Figure 1

Bacterial phosphotransferases and a human glycosyltransferase. MraY (MurX) is an established drug target for Gram-positive and Gram-negative bacterial infections. WecA is essential in the growth of Mycobacterium spp. and some Gram-positive bacteria (TagO or TarO). DPAGT1 is a human glycosyltransferase. Strong inhibition of DPAGT1 may cause cytotoxicity in mammalian cells.

Figure 2

Structures of FR-900493 (1) and representative muraymycins, muraymycin A1 (2) and D1 (3). FR-900493 has only the right half of the muraymycins (the highlighted portion in blue). The unknown stereochemistries of the 5′- and 6′-positions are determined unequivocally in this study.

Results and Discussion

Chemistry and SAR of FR-900493

Aminoribosyl-uridyl peptide antibiotics such as FR-900493 (1) and muraymycins are an important class of natural products for the development of novel antibacterial agents.[30,31] Chemical syntheses of 1 and muraymycin analogues are essential to perform exhaustive SAR studies.[32] Muraymycin A1 (2) is one of the most active members of this family against both Gram-positive and Gram-negative bacteria. The fatty acid side chain (R2) of 2 is critical for antimicrobial activity as muraymycin D1 (3) and the other related molecules lacking the R2 group are poorly active (Figure ).[25,33] Interestingly, we have demonstrated that muraymycin D1 shows strong bacteriostatic activity against Mycobacterium tuberculosis by targeting the bacterial phosphotransferases (MurX and WecA).[25] Although FR-900493 (1) possesses only one half of the structure of the muraymycins, it displays antistaphylococcal activity [minimum inhibitory concentration (MIC) 3.13 μg/mL] in vitro and in vivo. The LD50 value of 1 is over 500 mg/kg, which was determined via intravenous administrations in mice, indicating that 1 is an ideal scaffold to develop into new antibacterial agents.[26] It is interesting to note that 1 was isolated from the culture broth of Bacillus cereus (no. 2045), whereas other aminoribosyl-uridyl peptide antibiotics including muraymycins were isolated from Streptomyces spp.[31,33] Structurally, the C6′-amino group of FR-900493 is methylated, whereas O-methylation at the C2″-position is observed in muraymycin A1 and D1. Absolute stereochemistries at the C5′- and C6′-positions are speculated to be 5′S and 6′S, respectively, based on the correlations with stereochemistries of muraymycins and structurally related molecules, caprazamycins. On the basis of the proposed structure, FR-900493 was first synthesized by Hirano and co-workers who only reported physical chemistry data (e.g., NMR and optical rotation) for the synthetic molecule.[34] We have synthesized the four diastereomers of FR-900493 with respect to the C5′- and C6′-stereocenters according to the synthetic scheme developed for muraymycin D1 (3)[25] with minor modifications and compared their physical and biological data with those of the natural product. Chemical shifts and coupling constants of the 5′S,6′S-diastereomer 1 showed good agreement with those of the natural FR-900493 (see the Supporting Information).[26] The four diastereomers of FR-900493 were evaluated against the bacterial phosphotransferases MraY and WecA (Table ).[29,35]

Table 1

Inhibitory Activity of Bacterial Phosphotransferases (MraY and WecA) and C. difficile Growth by the C5′- and 6′-Diastereomers of FR-900493a

compound	WecA inhibition IC50(μM)b	MraY inhibition IC50 (μM)c	C. difficile ATCC 43596 MIC (μg/mL)d
FR-900493 (1)	5.0 ± 5.44	25.0 ± 8.67	>25.0
5′S,6′R-diastereomer (4)	>100	>100	>25.0
5′R,6′S-diastereomer (5)	>100	>100	>25.0
5′R,6′R-diastereomer (6)	>100	>100	>25.0
FR-900493-amide (7)	5.0 ± 6.34	25.0 ± 9.67	>25.0
8	>100	>100	>25.0
tunicamycin	0.15 ± 7.80	3.38 ± 7.32	>25.0

WecA and MraY assays (see the Supporting Information).

E. coli WecA-containing membrane was used.

Hydrogenivirga spp. MraY was used.

A microdilution broth method was used.

Surprisingly, 1 exhibited a weak MraY inhibitory activity (IC50 25.0 μM) but a moderate WecA inhibitory activity (IC50 5.0 μM). All unnatural diastereomers (4, 5, and 6) did not display either MraY or WecA inhibitory activity, even at a 100 μM concentration. The results of these enzymatic assays unequivocally determined the absolute stereochemistry of FR-900493 to be 5′S and 6′S configurations. We have observed that amidation of the C6′-carboxylic group in muraymycin D1 (3) does not decrease the MraY/WecA activity.[25] Similarly, FR-900493-amide (7) exhibited an MraY/WecA inhibitory activity equal to that of 1. The N-methyl group of 1 is essential to inhibit the MraY and WecA enzymes; the de-N-methyl analogue 8 completely lost the MraY/WecA inhibitory activities. FR-900493 and its analogues shown in Table were not effective in killing C. difficile (ATCC 43596) at 25.0 μg/mL or lower concentrations. As exemplified in the antibacterial activity of the muraymycin family molecules,[30] the hydrophobic residues appended on the 3-aminopropylamine portion play a key role in selectivity and susceptibility against bacteria (Figure ). We have generated a small forced library based on the core structures of 7 and 8, and the generated molecules were assayed against C. difficile (ATCC 43596) at a single concentration of 50.0 μg/mL. Four molecules (9, 10, 11, and 12) displayed anti-C. difficile activity (Table ), and sufficient amounts of these molecules were resynthesized for thorough in vitro profiling.

Table 2

Inhibitory Activity of Bacterial Phosphotransferases (MraY and WecA) and C. difficile Growth by 9–12a

compound	WecA inhibition IC50 (μM)b	MraY inhibition IC50 (μM)c	C. difficile ATCC 43596 MIC (μg/mL)d
FR-900493 (1)	5.0 ± 5.44	25 ± 8.67	>50.0
UT-17415 (9)	0.85 ± 7.50	0.69 ± 7.32	25.0 ± 7.64
UT-17455 (10)	12.5 ± 6.01	0.25 ± 5.80	12.5 ± 5.93
UT-17460 (11)	0.32 ± 4.09	0.08 ± 4.33	3.25 ± 4.40
UT-17465 (12)	12.3 ± 5.75	7.70 ± 5.47	50.0 ± 5.81
UT-01320	0.035 ± 9.14	>100	>50.0
tunicamycin	0.15 ± 7.80	3.38 ± 7.32	>50.0
vancomycin	>50.0	>50.0	2.5 ± 7.25

WecA and MraY assays (see the Supporting Information).

E. coli WecA-containing membrane was used.

Hydrogenivirga spp. MraY was used.

A microdilution broth method was used.

Syntheses of FR-900493 Analogues, 9, 10, 11, and 12

In our synthesis of muraymycin D1 (3), β-ribosylation of the C2-ether-protected ribose donor (R1 = Me in 15) and Strecker reaction with mono-protected 1,3-diaminopropane to form secondary amine were performed stereoselectively.[25] Our revised synthetic routes for FR-900493 analogues (9–12) are illustrated in Schemes and 2. The monomethoxytetrachlorodiphenylmethoxymethyl (MTPM)-protected uridine 13 was prepared according to the previously reported procedure.[36] The primary alcohol of 13 was oxidized by a modified Swern condition to provide the corresponding aldehyde in a quantitative yield, which was then subjected to Carreira’s asymmetric alkynylation reaction using (−)-N-methylephedrine,[37] furnishing the (S)-propargyl alcohol 14 in 80% yield with a selectivity of >98:2. The stereochemistry of the secondary alcohol of 14 generated via Carreira’s alkynylation was determined by the advanced Mosher’s method (see the Supporting Information).[38] The newly devised glycosyl donor 15 was designed to provide β-riboside whose protecting groups can be deprotected under mild acidic conditions. N-Iodosuccinimide (NIS)–AgBF4-promoted ribosylation of (S)-propargyl alcohol 14 with 15 furnished the β-riboside 16 exclusively in 95% yield.[23,25,39] The azido group of 16 was reduced with Zn metal in the presence of aq NH4Cl, and the generated free-amine was protected with (Boc)2O to furnish 17 in 90–92% overall yield. The alkyne moiety of 17 was subjected to a three-step procedure (partial reduction with a Lindlar catalyst, osmylation, and oxidative cleavage with Pb(OAc)4), providing the crude aldehyde 18. In a systematic screening of catalysts for Strecker reaction of 18 with the 4-aminobutanamide derivatives 19 (Scheme ) or 20 (Scheme ), it was realized that (BnO)2P(O)CH2P(O)(OBn)OH provided a ∼4:1 mixture of the 6′S- and 6′R-diastereomers (21 and 21) in greater than 80% yield. The desired diastereomer 21 was subjected to hydration reaction with HgCl2-acetaldoxime to furnish the amide 22 in 95% overall yield. N-methylation of 22 was performed via reductive amination with paraformaldehyde and NaB(CN)H3 to afford 23 in 95% yield. Global deprotection of 22 and 23 to form the desired products 9 and 10, respectively, was performed in a one-pot two-step reaction using 30% trifluoroacetic acid (TFA) followed by 80% TFA at 40 °C; the crude products were purified by C18 reverse-phase high-performance liquid chromatography (HPLC) (MeOH/H2O = 75:25) to yield 9 and 10 in 85–90% yield. The stereochemistry of the C6′-stereocenter for 21 generated via Strecker reaction was unequivocally determined via its conformational analyses (see the Supporting Information). Similarly, the analogues 11 and 12 were synthesized with the primary amine 20 via the synthetic scheme developed for 9 and 10 (Scheme ).

Scheme 1

Syntheses of Anti-C. difficile FR-900493 Analogues 9 and 10

Scheme 2

Syntheses of Anti-C. difficile FR-900493 Analogues 11 and 12

Enzyme and Bacterial Growth Inhibitory Activities of 9, 10, 11, and 12

Despite the extensive efforts to obtain membrane fractions from C. difficile (ATCC 43596), we could not obtain sufficient amounts of active C. difficile membrane containing MraY and WecA homolog. In this study, for assays, we used purified MraY from the thermophilic bacterium Hydrogenivirga (HyMraY) and the active membrane fraction (P-60) from Escherichia coli. Protein sequence alignment via BLAST[40] of HyMraY and EcWecA against C. difficile (strain F501) revealed that MraY between Hydrogenivirga spp. and C. difficile showed 57% similarity/38% identity and WecA/putative WecA homolog between E. coli and C. difficile showed 47% similarity/28% identity. We previously confirmed that the activities of inhibitor molecules against MraY and WecA are similar across various species: Mycobacterium smegmatis, M. tuberculosis, E. coli, and Hydrogenivirga spp.[21,29,35] The synthetic molecules (9, 10, 11, and 12) were evaluated against the phosphotransferases (MraY and WecA) and C. difficile strain (ATCC 43596) (Table ). The N-methyl analogues, 9 and 12, exhibited weak anti-C. difficile growth inhibitory activity, although their MraY inhibitory activities were over 30- and 3-fold, respectively, more potent than that of FR-900493 (1). In sharp contrast, the de-N-methyl analogues, 10 and 11, were over 100 and 300-times more potent in the MraY inhibitory activity than 1. The WecA inhibitory activity of 11 was ∼15-fold more than that of 1. Therefore, the anti-C. difficile activity of 11 is likely attributed to the inhibition of the MraY enzyme. This hypothesis was further supported by the fact that a selective WecA inhibitor, UT-01320,[20] did not inhibit growth of C. difficile at >50.0 μg/mL concentrations. The analogue 11 was identified to be a strong MraY/WecA inhibitor, whose activity was significantly better than that of a known MraY/WecA inhibitor, tunicamycin.[28,29,35] The anti-C. difficile activity is correlated with the enzyme inhibitory activity of MraY; 10 and 11 displayed MIC values of 12.5 and 3.25 μg/mL, respectively, against C. difficile (e.g., an MIC of 2.50 μg/mL for vancomycin).

Effect of 9, 10, and 11 on C. difficile Spores

The effect of 9, 10, and 11 on C. difficile spores was determined by counting colony-forming units (CFUs) of the spore germination on taurocholate-containing agar plates after the treatment of the C. difficile spores with these analogues (2× MIC) for 24 h. C. difficile spores show resistance to most known anti-C. difficile agents.[19] Indeed, in these studies, vancomycin, metronidazole, and linezolid did not inhibit the spore outgrowth, even at 5× MIC. On the contrary, the new MraY inhibitors 9, 10, and 11 prevented the outgrowth of the C. difficile spores into colonies at 2× MIC (Figure ).

Figure 3

Viability of C. difficile (ATCC 43596) spores treated with the MraY inhibitors, 9, 10, and 11, and representative anti-C. difficile drugs. The spores treated with molecules (2× or 5× MIC) in a BHI medium or saline (24 h) were plated on a BHI agar plate containing sodium taurocholate and incubated anaerobically for 48 h. Vancomycin, metronidazole, and linezolid were treated with 5× MIC, and 9, 10, and 11 were treated with 2× MIC. Germinated spores were counted (CFUs) (p ≤ 0.05).

Physicochemical Properties and in Vitro Toxicity of 11

UT-17460 (11) exhibited pharmacological characteristics superior to those of UT-17455 (10); (1) water solubility of 11 (22.0 mg/mL) is 200 times greater than that of 10 (0.11 mg/mL), (2) 11 is approximately 8 times less cytotoxic than 10 against Vero cells (African green monkey kidney epithelial cells, IC50 65.0 μM for 10), and (3) 11 showed relatively low induction of hemolysis (IC50 205.6 μM), whereas 10 lysed blood cells at a much lower concentration (IC50 70.0 μM) than 11 (Table ). Thus, we selected 11 for further in vitro pharmacological evaluation. WecA enzyme inhibitors have the potential to interfere with a human homologue, dolichyl-phosphate GlcNAc-1-phosphotransferase 1 (DPAGT1), which catalyzes the first step of the protein N-glycosylation process in humans (Figure ). Thus, strong inhibition of DPAGT1 may cause cytotoxicity in vitro and in vivo.[41] We have established a counterselection assay using a thermophilic dolichyl-phosphate GlcNAc-1-phosphotransferase (AglH from Methanocaldococcus jannaschii) to assess the toxicity level of antibacterial phosphotransferase inhibitors (Table ). Interestingly, 11 exhibited a relatively stronger AglH inhibitory activity (IC50 3.61 μM) than 10 and tunicamycin; however, the IC50 level of 11 against Vero cells was much higher than those of 10 and tunicamycin. The FR-900493 analogue 11 exhibited low permeability across Caco-2 epithelial monolayers (Papp rate coefficient < 1 × 10–6 cm/s) with moderate efflux (an efflux ratio of 5.5), predicting that 11 is poorly absorbed from the GI tract.

Table 3

Counterselection Assays Based on Prenyl phosphate-GlcNAc-1-phosphotransferases (WecA vs AglH) and in Vitro Cytotoxicities

	WecA inhibition IC50 (μM)a
compound	E. coli WecA	M. smegmatis WecA	AglH inhibition IC50 (μM)aM. jannaschii AglH	Vero cells IC50 (μM)a	hemolysis IC50 (μM) sheep blooda
UT-17455 (10)	12.5 ± 6.01	12.5 ± 5.42	12.5 ± 5.18	7.08 ± 5.67	70 ± 5.71
UT-17460 (11)	0.32±4.09	0.25±4.84	3.61±4.43	65±4.65	205.8±4.33
tunicamycin	0.15 ± 7.80	0.15 ± 7.22	13.27 ± 8.10	0.12 ± 7.78	15 ± 7.83

All assay procedures are described in the Supporting Information.

Spectrum of Antibacterial Activity of 11

As summarized in Figure , UT-17460 (11) exhibited a very narrow spectrum of antibacterial activity; 11 also killed the other Clostridium spp., Clostridium perfringens (MIC 3.1 μg/mL), Bacillus subtilis (MIC 1.6 μg/mL), and M. smegmatis (MIC 0.2 μg/mL) but did not inhibit the growth of Lactobacillus spp., Staphylococcus aureus, Staphylococcus pneumoniae, and all Gram-negative bacteria tested at 25.0 μg/mL or higher concentrations.

Figure 4

Antibacterial activity of UT-17460 (11, line in red).

Conclusions

FR-900493 (1) has long been known as an MraY inhibitor for which we have firmly established the stereochemistry. In our thorough enzyme inhibitory assays of the phosphotransferases, we concluded that the antibacterial activity of 1 is attributed to a combination of WecA and MraY inhibitory activities, but 1 is a weak MraY inhibitor (IC50 25.0 μM). Because WecA is not essential in the growth of many bacteria except for a few pathogens (e.g., Mycobacterium spp.),[28,42] improving MraY inhibitory activity of 1 should be a beneficial direction to identify effective antibacterial agents. Stereochemistry of the C5′- and C6′-positions of 1 is required to be the natural configuration (5′S and 6′S) to exhibit bacterial growth and MraY/WecA enzyme inhibitory activities. The C6′-CO2H group of 1 can be masked as its primary amide without decreasing MraY/WecA activity; however, the N-methyl group is essential for 1 to display phosphotransferase inhibitory activities. Muraymycins lack the N-methyl group but exhibit a strong MraY enzyme inhibitory activity. Importantly, only the muraymycin analogues having a hydrophobic side chain [e.g., muraymycin A1 (2)] exhibit a strong antimicrobial activity. We have generated a small focused library based on the structures of 7 and 8 and screened against the vegetative form of C. difficile strain (ATCC 43596) under anaerobic conditions. We identified four anti-C. difficile FR-900493 analogues, 9, 10, 11, and 12. These analogues were resynthesized via the synthetic procedures reported previously with modifications of selective ribosylation (14 → 16) and Strecker reactions (18 → 21 and 24) (Schemes and 2). The resynthesized analogues were characterized by C. difficile growth and the bacterial phosphotransferase inhibitory assays. The analogue 11 exhibited strong MraY/WecA inhibitory activity (IC50 0.08 and 0.30 μM, respectively) and killed the vegetative state of C. difficile with an MIC value of 3.25 μg/mL. In vitro cytotoxicity level of 11 was much lower than those of tunicamycin and 10; although 11 inhibited AglH at low concentrations. Toxicity of tunicamycin and 10 in mammalian cells may be largely due to the membrane disruption as demonstrated by the hemolysis assay. On the other hand, the hemolytic activity of 11 is attenuated by the pharmacologically benign hydrophobic group.[43] Interestingly, the MraY inhibitors 9, 10, and 11 inhibited the outgrowth of the C. difficile spores (endospores) at 2× MIC concentrations (Figure ). The inhibitory mechanism of outgrowth of the spores by the MraY inhibitors is far from completely understood. Recently, a strong lipid II-binding antibacterial peptide, nisin, was reported to inhibit the viability of the C. difficile spores at high concentrations.[44] The effect of fidaxomicin was also observed in the inhibition of the C. difficile spore outgrowth at high concentrations (4.0–14 μg/mL, MIC90 0.5 μg/mL against vegetative C. difficile).[45]C. difficile spores are metabolically dormant and are known to exhibit impermeability to a wide range of organic molecules.[46] Thus, organic molecules with a high molecular mass (e.g., Mw = 881.3 for 11) are not likely to permeate the spore walls and directly inhibit the viability of the spores. Certain peptides or nucleoside derivatives are recognized by the Bacillus anthracis germination machinery, increasing their susceptibility to geminated spores or outgrowing spores.[47,48] On the other hand, germination machineries of C. difficile spores remain less well-understood because of the significantly lower levels of homologues of the spore coat proteins than those of other well-studied bacteria (e.g., B. subtilis and B. anthracis).[48] Recent studies demonstrated that C. difficile uses subtilisin-like serine proteases (Csp) that regulate spore germination.[49] In C. difficile, CspC is likely to transmit the bile acid signal to CspB, which activates the spore cortex lytic enzyme (i.e., SleC) by cleavage of pro-SlecC. SlecC alters the structure of the spore cortex and induces Ca-dipicolinate release, which triggers the outgrowth of C. difficile spores.[50] Our MraY inhibitors may be involved in the induction from the spore forms to the germinating state. The germinated or outgrowing spores require MraY, which will be inhibited by the new inhibitors 9–12. We are currently evaluating the effectiveness of structurally distinct MraY inhibitors against the C. difficile spores. Correlation of nucleoside-based MraY inhibitor and ability of the C. difficile spore germination are being investigated. In preliminary bacterial growth inhibitory assays against a series of bacteria, 11 displayed a very narrow-spectrum antibiotic activity (Figure ), which is advantageous in the development of selective anti-C. difficile agents that do not disrupt the gut microbiota in humans. In addition, in vitro pharmacokinetic data obtained via the Caco-2 permeability assay may indicate that 11 is poorly absorbed from the GI tract, which may reduce the toxicity of 11 when given orally. Pharmacokinetics and oral bioavailability, susceptibility to clinically isolated C. difficile and in vivo efficacy of 11 (using preclinical animal models), and selectivity of antibacterial activity of 11 at higher concentrations (1000 μg/mL) are the object of future studies.

Experimental Section

Chemistry: General Information

All chemicals were purchased from commercial sources and used without further purification unless otherwise noted. Tetrahydrofuran (THF), CH2Cl2, and N,N-dimethylformamide were purified via an Innovative Technology’s Pure-Solve System. All reactions were performed under an argon atmosphere. All stirring procedures were performed with an internal magnetic stirrer. Reactions were monitored by thin-layer chromatography (TLC) using 0.25 mm coated commercial silica gel plates (EMD, silica gel 60F254). TLC spots were visualized by UV light at 254 nm or developed with ceric ammonium molybdate or anisaldehyde or copper sulfate or ninhydrin solutions by heating on a hot plate. Reactions were also monitored by using Shimadzu LCMS-2020 with the following solvents: A: 0.1% formic acid in water and B: acetonitrile. Flash chromatography was performed with SiliCycle silica gel (Purasil 60 Å, 230–400 mesh). Proton magnetic resonance (1H NMR) spectral data were recorded on 400 and 500 MHz instruments. Carbon magnetic resonance (13C NMR) spectral data were recorded on 100 and 125 MHz instruments. For all NMR spectra, chemical shifts (δH, δC) were quoted in parts per million (ppm) and J values were quoted in Hz. 1H and 13C NMR spectra were calibrated with a residual undeuterated solvent (CDCl3: δH = 7.26 ppm, δC = 77.16 ppm; CD3CN: δH = 1.94 ppm, δC = 1.32 ppm; CD3OD: δH = 3.31 ppm, δC = 49.00 ppm; DMSO-d6: δH = 2.50 ppm, δC = 39.52 ppm; D2O: δH = 4.79 ppm) as an internal reference. The following abbreviations were used to designate the multiplicities: s = singlet, d = doublet, dd = double doublets, t = triplet, q = quartet, quin = quintet, hept = heptet, m = multiplet, and br = broad. Infrared (IR) spectra were recorded on a PerkinElmer FT1600 spectrometer. HPLC analyses were performed with a Shimadzu LC-20AD HPLC system. All compounds were purified by reverse HPLC to be ≥95% purity. High-resolution mass spectrometry (HRMS) data were obtained from a Waters SYNAPT G2-Si (ion mobility mass spectrometer with nano-electrospray ionization).

FR-900493 (1)

1H NMR (400 MHz, D2O) δ: 7.79 (d, J = 7.9 Hz, 1H), 5.83 (d, J = 7.8 Hz, 1H), 5.75 (d, J = 2.3 Hz, 1H), 5.20 (s, 1H), 4.33 (dd, J = 2.3, 5.1 Hz, 1H), 4.28 (dd, J = 2.3, 8.4 Hz, 1H), 4.23–4.19 (m, 2H), 4.16 (dd, J = 2.8, 6.1 Hz, 1H), 4.13–4.07 (m, 2H), 3.49 (d, J = 8.3 Hz, 1H), 3.18 (dd, J = 3.6, 13.7 Hz, 1H), 3.05–3.00 (m, 3H), 2.88–2.83 (m, 1H), 2.64–2.61 (m, 1H), 2.41 (s, 3H), 1.94–1.88 (m, 1H), 1.82–1.78 (m, 1H); 13C NMR (101 MHz, D2O) δ: 175.72, 171.35, 155.21, 141.90, 110.08, 102.46, 91.42, 83.74, 80.76, 78.53, 75.41, 74.20, 71.41, 71.34, 69.98, 52.35, 41.81, 39.02, 38.65, 24.99; HRMS (ESI+) m/z: calcd for C20H34N5O11 [M + H], 520.2255; found, 520.2262.

FR-900493-5′S, 6′R-Diastereomer (4)

1H NMR (400 MHz, D2O) δ: 7.83 (d, J = 8.0 Hz, 1H), 5.90 (d, J = 8.3 Hz, 1H), 5.73 (d, J = 2.1 Hz, 1H), 5.25 (s, 1H), 4.36 (d, J = 7.7 Hz, 1H), 4.28–4.19 (m, 2H), 4.18 (d, J = 10.4 Hz, 1H), 4.12–4.06 (m, 2H), 3.45 (d, J = 10.4 Hz, 1H), 3.32 (dd, J = 14.1, 3.7 Hz, 1H), 3.15 (dd, J = 13.9, 5.6 Hz, 1H), 3.10–3.03 (m, 3H), 2.97–2.87 (m, 1H), 2.59–2.51 (m, 1H), 2.43 (s, 3H), 1.99–1.93 (m, 1H), 1.87–1.77 (m, 1H); 13C NMR (101 MHz, D2O) δ: 175.72, 171.35, 155.21, 141.90, 110.08, 102.46, 91.42, 83.74, 80.76, 78.53, 75.41, 74.20, 71.41, 71.34, 69.98, 52.35, 41.81, 39.02, 38.65, 24.99; HRMS (ESI+) m/z: calcd for C20H34N5O11 [M + H], 520.2255; found, 520.2272.

FR-900493-5′R,6′S-Diastereomer (5)

1H NMR (400 MHz, D2O) δ: 7.68 (d, J = 8.2 Hz, 1H), 5.93 (d, J = 8.1 Hz, 1H), 5.77 (d, J = 4.3 Hz, 1H), 5.33 (s, 1H), 4.50–4.44 (m, 3H), 4.20–4.11 (m, 3H), 4.06 (dd, J = 5.2, 4.7 Hz, 1H), 3.61 (d, J = 6.9 Hz, 1H), 3.37 (d, J = 13.2 Hz, 1H), 3.13 (dd, J = 13.2, 8.7 Hz, 1H), 3.06 (t, J = 7.3 Hz, 2H), 2.84 (dt, J = 13.5, 6.6 Hz, 1H), 2.74 (dt, J = 12.8, 6.7 Hz, 1H), 2.44 (s, 3H), 1.89 (dq, J = 13.8, 6.6 Hz, 2H); 13C NMR (101 MHz, D2O) δ: 175.72, 171.35, 155.21, 141.90, 110.08, 102.46, 91.42, 83.74, 80.76, 78.53, 75.41, 74.20, 71.41, 71.34, 69.98, 52.35, 41.81, 39.02, 38.65, 24.99; HRMS (ESI+) m/z: calcd for C20H34N5O11 [M + H], 520.2255; found, 520.2251.

FR-900493-5′R, 6′R-Diastereomer (6)

1H NMR (400 MHz, D2O) δ: 7.67 (d, J = 8.0 Hz, 1H), 5.91 (d, J = 8.0 Hz, 1H), 5.78 (d, J = 5.2 Hz, 1H), 5.31 (s, 1H), 4.49–4.44 (m, 1H), 4.43 (t, J = 5.3 Hz, 2H), 4.16–4.07 (m, 3H), 4.05 (t, J = 5.3 Hz, 1H), 3.54 (d, J = 7.3 Hz, 1H), 3.23 (dd, J = 13.3, 3.0 Hz, 1H), 3.10–2.98 (m, 3H), 2.80 (dt, J = 13.3, 6.7 Hz, 1H), 2.67 (dt, J = 13.3, 6.9 Hz, 1H), 2.38 (s, 3H), 1.86 (dq, J = 13.9, 7.1 Hz, 2H); HRMS (ESI+) m/z: calcd for C20H34N5O11 [M + H], 520.2255; found, 520.2247.

FR-900493-Amide (7)

1H NMR (400 MHz, D2O) δ: 7.83 (d, J = 8.1 Hz, 1H), 5.91 (d, J = 8.0 Hz, 1H), 5.72 (s, 1H), 5.27 (s, 1H), 4.44–4.37 (m, 1H), 4.32–4.25 (m, 2H), 4.23 (t, J = 6.5 Hz, 1H), 4.20–4.14 (m, 1H), 4.11 (d, J = 8.2 Hz, 1H), 3.68 (dd, J = 16.3, 8.1 Hz, 1H), 3.43 (d, J = 14.0 Hz, 1H), 3.26 (dd, J = 13.6, 5.2 Hz, 2H), 3.07 (t, J = 7.3 Hz, 2H), 3.03–2.95 (m, 1H), 2.64–2.56 (m, 1H), 2.50 (s, 3H), 2.04–1.94 (m, 1H), 1.88–1.79 (m, 1H); 13C NMR (101 MHz, D2O) δ: 175.72, 171.35, 155.21, 141.90, 110.08, 102.46, 91.42, 83.74, 80.76, 78.53, 75.41, 74.20, 71.41, 71.34, 69.98, 52.35, 41.81, 39.02, 38.65, 24.99; HRMS (ESI+) m/z: calcd for C20H35N6O10 [M + H], 519.2415; found, 519.2432.

De N-Methyl FR-900493 (8)

1H NMR (400 MHz, D2O) δ: 7.78 (d, J = 8.1 Hz, 1H), 5.89 (d, J = 7.8 Hz, 1H), 5.78 (d, J = 3.1 Hz, 1H), 5.22 (s, 1H), 4.40 (dd, J = 5.5, 3.2 Hz, 1H), 4.29 (t, J = 6.3 Hz, 1H), 4.22 (dd, J = 6.8, 5.1 Hz, 1H), 4.18 (t, J = 4.5 Hz, 1H), 4.16–4.08 (m, 3H), 3.59 (d, J = 3.8 Hz, 1H), 3.28 (d, J = 12.6 Hz, 1H), 3.11–3.02 (m, 3H), 2.77 (dt, J = 12.8, 6.8 Hz, 1H), 2.64 (dt, J = 12.7, 7.0 Hz, 1H), 1.83 (quin, J = 7.1 Hz, 2H); 13C NMR (101 MHz, D2O) δ: 175.72, 171.35, 155.21, 141.90, 110.08, 102.46, 91.42, 83.74, 80.76, 78.53, 75.41, 74.20, 71.41, 71.34, 69.98, 52.35, 39.02, 38.65, 24.99; HRMS (ESI+) m/z: calcd for C19H33N6O10 [M + H], 505.2258; found, 505.2277.

Synthesis of UT-17415 (9)

To a stirred solution of 22 (2.9 mg, 1.6 μmol) in CH2Cl2 (0.70 mL) was added TFA (0.30 mL). The reaction mixture was stirred for 2 h at room temperature (rt), and all volatiles were evaporated in vacuo. To a stirred solution of the crude mixture in H2O (0.2 mL) was added TFA (0.8 mL). The reaction mixture was stirred for 4 h at 40 °C, and all volatiles were evaporated in vacuo. The crude mixture was purified by silica gel column chromatography (CHCl3/MeOH 80:20 to CHCl3/MeOH/H2O/50% aq ammonia 56:42:7:3) to afford UT-17415 (9) (1.2 mg, 1.6 μmol, 100%): TLC (n-butanol/ethanol/CHCl3/28% aq ammonia 4:7:2:7) Rf = 0.55; HPLC condition, column: Phenomenex Kinetex 1.7 μ XB-C18 100 Å 150 × 2.10 mm column, solvents: 80:20 MeOH/0.05 M NH4HCO3 in water, UV: 254 nm; [α]D20 +0.038 (c = 0.12, methanol); IR (thin film) νmax: 3333 (br), 2955, 2926, 2855, 1676, 1541, 1515, 1467, 1413, 1273, 1204, 1135, 1063, 1010, 840, 801, 722 cm–1; 1H NMR (400 MHz, CD3OD) δ: 7.82 (d, J = 8.1 Hz, 1H), 7.44 (d, J = 8.0 Hz, 2H), 7.12 (d, J = 8.1 Hz, 2H), 5.76 (d, J = 8.0 Hz, 1H), 5.70 (s, 1H), 5.18 (s, 1H), 4.58 (s, 1H), 4.28 (d, J = 9.3 Hz, 1H), 4.21–4.16 (m, 3H), 4.14–4.07 (m, 3H), 3.61 (d, J = 9.4 Hz, 1H), 3.21 (dd, J = 13.6, 3.4 Hz, 1H), 2.83 (td, J = 12.1, 11.7, 5.0 Hz, 1H), 2.57 (t, J = 7.6 Hz, 2H), 2.46 (s, 3H), 2.46–2.40 (m, 2H), 2.00–1.89 (m, 1H), 1.79 (d, J = 12.4 Hz, 1H), 1.63–1.55 (m, 2H), 1.37–1.23 (m, 10H), 0.91–0.87 (m, 3H); 13C NMR (101 MHz, CD3OD) δ: 173.86, 172.29, 142.40, 140.18, 137.30, 129.69 (2C), 121.48 (2C), 112.07, 102.41, 92.48, 84.18, 80.50, 78.40, 76.43, 75.35, 71.95, 70.75, 68.52, 54.47, 39.45, 36.33, 35.02, 33.01, 32.78, 30.29, 30.26, 24.30, 23.70, 14.42; HRMS (ESI+) m/z: calcd for C34H53N6O11 [M + H], 721.3772; found, 721.3761.

Synthesis of UT-17455 (10)

To a stirred solution of 21 (7.9 mg, 4.5 μmol) in CH2Cl2 (0.70 mL) was added TFA (0.30 mL). The reaction mixture was stirred for 1 h at rt, and all volatiles were evaporated in vacuo. To a stirred solution of the crude mixture in H2O (0.2 mL) was added TFA (0.8 mL). The reaction mixture was stirred for 2 h at 40 °C, and all volatiles were evaporated in vacuo. The crude mixture was purified by silica gel column chromatography (CHCl3/MeOH 80:20 to CHCl3/MeOH/H2O/50% aq ammonia 56:42:7:3) to afford UT-17455 (10) (2.4 mg, 3.4 μmol, 76%): TLC (n-butanol/ethanol/CHCl3/28% aq ammonia 4:7:2:7) Rf = 0.50; HPLC condition: column: Phenomenex Kinetex 1.7 μ XB-C18 100 Å 150 × 2.10 mm column, solvents: 80:20 MeOH/0.05 M NH4HCO3 in water, UV: 254 nm; [α]D21 +0.538 (c = 0.24, methanol); IR (thin film) νmax: 3302 (br), 2955, 2926, 2855, 1672, 1605, 1542, 1515, 1466, 1412, 1271, 1203, 1185, 1131, 1111, 1062, 1010, 819, 721 cm–1; 1H NMR (400 MHz, CD3OD) δ: 7.77 (d, J = 8.1 Hz, 1H), 7.43 (d, J = 8.1 Hz, 2H), 7.12 (d, J = 8.0 Hz, 2H), 5.74 (s, 1H), 5.73 (d, J = 12.6 Hz, 1H), 5.14 (s, 1H), 4.21 (dd, J = 4.7, 4.2 Hz, 1H), 4.19–4.13 (m, 2H), 4.11 (t, J = 4.7 Hz, 1H), 4.08 (s, 2H), 4.02–3.99 (m, 1H), 3.50 (d, J = 8.9 Hz, 1H), 3.24 (d, J = 13.0 Hz, 1H), 3.16–3.09 (m, 1H), 2.73–2.60 (m, 2H), 2.57 (t, J = 7.7 Hz, 2H), 2.43 (dd, J = 7.4, 4.0 Hz, 2H), 1.86 (quin, J = 7.2 Hz, 2H), 1.59 (quin, J = 6.4, 5.7 Hz, 2H), 1.35–1.26 (m, 8H), 0.92–0.87 (m, 3H); 13C NMR (101 MHz, CD3OD) δ: 177.20, 174.18, 166.14, 152.10, 142.63, 140.13, 137.35, 129.68 (2C), 121.45 (2C), 110.58, 102.67, 92.49, 85.22, 80.48, 76.41, 75.02, 72.97, 71.23, 64.28, 43.15, 36.34, 35.45, 33.01, 32.78, 30.29, 26.60, 23.70, 14.42; HRMS (ESI+) m/z: calcd for C33H51N6O11 [M + H], 707.3616; found, 707.3624.

Synthesis of UT-17460 (11)

To a stirred solution of 23 (5.3 mg, 2.7 μmol) in CH2Cl2 (0.70 mL) was added TFA (0.30 mL). The reaction mixture was stirred for 1 h at rt, and all volatiles were evaporated in vacuo. To a stirred solution of the crude mixture in H2O (0.2 mL) was added TFA (0.8 mL). The reaction mixture was stirred for 2 h at 40 °C, and all volatiles were evaporated in vacuo. The crude mixture was purified by silica gel column chromatography (CHCl3/MeOH 80:20 to CHCl3/MeOH/H2O/50% aq ammonia 56:42:7:3) to afford UT-17460 (11) (2.2 mg, 2.5 μmol, 91%): TLC (n-butanol/ethanol/CHCl3/28% aq ammonia 4:7:2:7) Rf = 0.50; HPLC condition: column, Phenomenex Kinetex 1.7 μ XB-C18 100 Å 150 × 2.10 mm column, solvents: 75:25 MeOH/0.05 M NH4HCO3 in water, UV: 254 nm; [α]D21 +0.375 (c = 0.30, methanol); IR (thin film) νmax: 3352 (br), 2932, 1677, 1505, 1270, 1243, 1201, 1136, 1060, 840, 801, 722 cm–1; 1H NMR (400 MHz, CD3OD) δ: 7.78 (d, J = 8.1 Hz, 1H), 7.18 (dd, J = 9.0, 3.5 Hz, 4H), 7.00 (dd, J = 16.0, 8.6 Hz, 4H), 5.77 (d, J = 2.9 Hz, 1H), 5.73 (d, J = 8.1 Hz, 1H), 5.14 (s, 1H), 4.57–4.50 (m, 1H), 4.28 (s, 2H), 4.22–4.13 (m, 3H), 4.10 (dd, J = 8.6, 4.4 Hz, 1H), 4.07–3.98 (m, 2H), 3.52–3.46 (m, 3H), 3.44 (d, J = 8.8 Hz, 1H), 3.17 (d, J = 13.0 Hz, 1H), 3.14–3.02 (m, 3H), 2.60 (ddq, J = 18.4, 11.8, 6.9 Hz, 2H), 2.29 (td, J = 7.3, 2.8 Hz, 2H), 2.12 (dd, J = 14.5, 5.6 Hz, 2H), 1.93–1.73 (m, 4H), 1.39–1.25 (m, 2H); 13C NMR (101 MHz, CD3OD) δ: 175.58, 166.16, 157.62, 152.01, 142.55, 131.22, 129.62 (2C), 123.56 (2C), 118.11 (2C), 118.07 (2C), 110.51, 102.67, 92.31, 85.27, 81.41, 80.43, 76.47, 75.08, 74.07 (2C), 73.01, 71.26, 64.44, 43.72, 43.62, 34.66, 31.48, 26.89; HRMS (ESI+) m/z: calcd for C39H51F3N7O13 [M + H], 882.3497; found, 882.3512.

UT-17465 (12)

To a stirred solution of 24 (4.7 mg, 2.4 μmol) in CH2Cl2 (0.70 mL) was added TFA (0.30 mL). The reaction mixture was stirred for 2 h at rt, and all volatiles were evaporated in vacuo. To a stirred solution of the crude mixture in H2O (0.2 mL) was added TFA (0.8 mL). The reaction mixture was stirred for 4 h at 40 °C, and all volatiles were evaporated in vacuo. The crude mixture was purified by silica gel column chromatography (CHCl3/MeOH 80:20 to CHCl3/MeOH/H2O/50% aq ammonia 56:42:7:3) to afford UT-17465 (12) (2.0 mg, 2.2 μmol, 92%): TLC (n-butanol/ethanol/CHCl3/28% aq ammonia 4:7:2:7) Rf = 0.55; HPLC condition: column: Phenomenex Kinetex 1.7 μ XB-C18 100 Å 150 × 2.10 mm column, solvents: 70:30 MeOH/0.05 M NH4HCO3 in water, UV: 254 nm; [α]D20 +0.246 (c = 0.24, methanol); IR (thin film) νmax: 3276 (br), 2933, 1675, 1505, 1465, 1424, 1271, 1243, 1199, 1111 cm–1; 1H NMR (400 MHz, CD3OD) δ: 7.84 (d, J = 7.7 Hz, 1H), 7.19 (dd, J = 8.5, 3.3 Hz, 4H), 7.01 (dd, J = 13.1, 8.6 Hz, 4H), 5.86 (d, J = 7.8 Hz, 1H), 5.73 (d, J = 2.4 Hz, 1H), 5.16 (s, 1H), 4.54 (tt, J = 7.3, 3.1 Hz, 1H), 4.30–4.25 (m, 3H), 4.26 (d, J = 9.2 Hz, 1H), 4.22–4.05 (m, 6H), 3.70 (d, J = 9.2 Hz, 1H), 3.52–3.44 (m, 2H), 3.09 (ddt, J = 12.3, 8.6, 4.3 Hz, 2H), 2.91–2.82 (m, 1H), 2.58–2.53 (m, 1H), 2.50 (s, 3H), 2.30 (q, J = 6.9 Hz, 2H), 2.15–2.08 (m, 2H), 1.96–1.82 (m, 3H), 1.81–1.71 (m, 1H), 1.39–1.25 (m, 2H); 13C NMR (101 MHz, CD3OD) δ: 175.34, 172.18, 157.63, 151.97, 142.38, 131.33, 129.66 (2C), 123.55 (2C), 118.12 (2C), 118.08 (2C), 111.86, 92.05, 84.35, 80.28, 78.36, 76.42, 75.37, 74.08 (2C), 71.54, 70.80, 68.28, 43.73, 39.72, 34.50, 31.48 (2C), 24.52; HRMS (ESI+) m/z: calcd for C40H53F3N7O13 [M + H], 896.3653; found, 896.3640.

MTPM-Protected Uridine 13

The MTPM-protected uridine 13 was synthesized according to the reported procedure.[24,34] TLC (hexane/EtOAc 33:67) Rf = 0.50; [α]D22 −2.315 (c = 8.98, CHCl3); IR (thin film) νmax: 3478 (br), 3057, 2986, 2940, 1715, 1663, 1598, 1556, 1455, 1374, 1265, 1212, 1066, 1039, 853, 808, 787, 732, 702 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.51 (ddd, J = 17.3, 8.5, 0.7 Hz, 1H), 7.33–7.27 (m, 2H), 7.18 (ddd, J = 8.8, 6.9, 2.1 Hz, 1H), 6.85 (d, J = 5.1 Hz, 2H), 6.51 (d, J = 3.7 Hz, 1H), 5.72 (dd, J = 8.1, 4.0 Hz, 1H), 5.60–5.51 (m, 2H), 5.48 (dd, J = 12.6, 2.1 Hz, 1H), 4.95–4.93 (m, 1H), 4.92 (t, J = 2.4 Hz, 1H), 4.30–4.25 (m, 1H), 3.89 (ddd, J = 11.7, 9.1, 2.6 Hz, 1H), 3.82–3.73 (m, 4H), 1.57 (s, 3H), 1.36 (d, J = 2.4 Hz, 3H); 13C NMR (101 MHz, CDCl3) δ: 162.10, 162.05, 159.51, 150.97, 150.91, 141.55, 141.31, 136.88, 135.28, 135.22, 134.02, 134.00, 133.84, 133.71, 131.17, 129.38, 126.22, 126.18, 125.44, 125.40, 115.33, 114.29, 114.26, 102.05, 102.01, 97.16, 96.82, 87.15, 87.06, 83.76, 83.65, 80.29, 69.50, 62.76, 62.72, 55.69, 27.25, 25.25; HRMS (ESI+) m/z: calcd for C27H26N2O8NaCl4 [M + Na], 669.0341; found, 669.0324.

Propargyl Alcohol 14

To a stirred solution of 13 (1.54 g, 2.37 mmol) and dichloroacetic acid (0.29 mL, 3.56 mmol) in CH2Cl2 (11.9 mL) and DMSO (2.37 mL) was added N,N′-diisopropylcarbodiimide (0.56 mL, 3.56 mmol) at 0 °C, and the reaction mixture was warmed to rt. After 8 h, the reaction was quenched with saturated aq NaHCO3 and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The precipitates were filtered, and the crude mixture was used for the next reaction without purification. To a suspension of Zn(OTf)2 (3.45 g, 9.48 mmol) and (+)-N-methylephedrine (1.70 g, 9.48 mmol) in toluene (7.1 mL) was added Et3N (1.32 mL, 9.48 mmol) at rt. After 3 h, 4-phenyl-1-butyne (1.33 mL, 9.48 mmol) was added. After 4 h, a solution of the crude aldehyde in toluene (5 mL) was added. The reaction mixture was stirred for 15 h, quenched with saturated aq NaHCO3, and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude mixture was purified by silica gel column chromatography (hexane/EtOAc 60:40 to 50:50) to afford 14 (1.48 g, 1.90 mmol, 80% for 2 steps): TLC (hexane/EtOAc 50:50) Rf = 0.30; [α]D22 −0.116 (c = 2.17, CHCl3); IR (thin film) νmax: 3387 (br), 3087, 2981, 2937, 1716, 1664, 1597, 1556, 1454, 1374, 1276, 1211, 1156, 1065, 1039, 916, 856, 807, 786, 733, 698 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.53 (ddd, J = 20.4, 8.5, 0.7 Hz, 1H), 7.35–7.27 (m, 4H), 7.24–7.15 (m, 4H), 6.85 (d, J = 5.1 Hz, 2H), 6.51 (d, J = 5.4 Hz, 1H), 5.68 (dd, J = 8.1, 4.1 Hz, 1H), 5.60–5.50 (m, 3H), 4.89–4.78 (m, 2H), 4.57 (ddt, J = 12.0, 4.3, 2.0 Hz, 1H), 4.24 (dd, J = 4.4, 3.1 Hz, 1H), 3.78 (d, J = 3.3 Hz, 3H), 2.83 (t, J = 7.5 Hz, 2H), 2.53 (td, J = 7.4, 2.0 Hz, 2H), 1.57 (s, 3H), 1.36 (s, 3H); 13C NMR (101 MHz, CDCl3) δ: 162.11, 162.08, 159.50, 150.87, 150.85, 141.07, 140.84, 140.30, 140.27, 136.90, 135.36, 135.29, 133.99, 133.95, 133.79, 133.64, 131.21, 129.37, 129.34, 128.41, 128.39, 126.40, 126.21, 126.18, 125.49, 125.44, 115.34, 115.32, 114.28, 114.24, 101.79, 101.74, 96.69, 96.37, 89.23, 89.19, 86.83, 86.73, 84.09, 83.93, 80.91, 69.46, 63.02, 62.99, 55.68, 34.72, 34.70, 27.16, 25.29, 20.87, 20.85; HRMS (ESI+) m/z: calcd for C37H34N2O8NaCl4 [M + Na], 797.0967; found, 797.0994.

Ribosylation of 14

To a stirred suspension of 14 (227 mg, 0.292 mmol), 15 (497 mg, 0.584 mmol), MS3Å (900 mg), and SrCO3 (431 mg, 2.920 mmol) in CH2Cl2 (12.0 mL) were added AgBF4 (28.5 mg, 0.146 mmol) and NIS (131 mg, 0.584 mmol) at 0 °C. After 24 h, the reaction mixture was added to Et3N (2 mL) and passed through a silica gel pad (hexane/EtOAc 1:1). The combined organic phase was concentrated in vacuo. The crude mixture was purified by silica gel column chromatography (hexane/EtOAc 90:10 to 80:20 to 70:30) to afford 16 (416 mg, 0.277 mmol, 95%): TLC (hexane/EtOAc 67:33) Rf = 0.70; [α]D21 +0.100 (c = 2.09, CHCl3); IR (thin film) νmax: 2942, 2892, 2866, 2102, 1743, 1724, 1675, 1600, 1556, 1456, 1382, 1371, 1278, 1218, 1099, 1070, 1049, 1013, 999, 882, 807, 772, 745, 681 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.54 (dd, J = 23.1, 8.5 Hz, 1H), 7.32–7.27 (m, 4H), 7.24–7.16 (m, 4H), 6.84 (d, J = 7.3 Hz, 2H), 6.51 (d, J = 3.7 Hz, 1H), 5.71–5.64 (m, 2H), 5.60–5.49 (m, 2H), 5.20–5.16 (m, 3H), 4.79 (ddd, J = 7.5, 6.5, 3.1 Hz, 1H), 4.64 (td, J = 5.9, 2.6 Hz, 1H), 4.57 (ddt, J = 11.4, 6.3, 1.9 Hz, 1H), 4.28 (dt, J = 6.2, 2.8 Hz, 1H), 4.19 (tt, J = 6.1, 3.0 Hz, 1H), 3.79–3.72 (m, 7H), 3.50 (ddd, J = 13.0, 7.6, 3.3 Hz, 1H), 3.35 (dd, J = 13.0, 3.4 Hz, 1H), 2.83 (t, J = 7.4 Hz, 2H), 2.55 (td, J = 7.4, 1.8 Hz, 2H), 2.29 (t, J = 1.6 Hz, 2H), 2.24 (dd, J = 5.1, 2.1 Hz, 2H), 1.62–1.55 (m, 7H), 1.36 (d, J = 2.0 Hz, 3H), 1.08–1.00 (m, 54H); 13C NMR (101 MHz, CDCl3) δ: 175.61, 170.98, 170.88, 170.71, 170.70, 170.64, 162.17, 162.14, 159.45, 150.75, 150.72, 140.39, 140.19, 140.15, 140.13, 136.92, 136.91, 135.43, 135.29, 133.94, 133.80, 133.65, 131.24, 129.36, 129.31, 128.46 (2C), 128.40 (2C), 126.46, 126.44, 126.19, 126.10, 125.56, 125.45, 115.29, 115.25, 114.23, 114.22, 104.61, 104.55, 101.83, 101.82, 88.84, 88.20, 84.44, 84.35, 83.93, 81.43, 81.33, 80.57, 79.88, 76.49, 75.86, 75.83, 74.12, 71.78, 71.73, 71.40, 70.73, 69.60, 69.47, 68.85, 68.78, 59.97, 59.96, 55.67, 46.15, 45.97, 44.72, 44.58, 34.65, 34.51, 34.49, 32.67, 32.61, 32.57, 28.00, 27.38, 27.35, 27.30, 27.07, 25.34, 25.27, 20.89, 18.05 (12C), 11.91 (6C); HRMS (ESI+) m/z: calcd for C74H106Cl4N5O15Si2 [M + H], 1500.5978; found, 1500.5992.

Synthesis of 17

A suspension of 16 (286 mg, 0.19 mmol), NH4Cl (305 mg, 5.70 mmol), and Zn (373 mg, 5.70 mmol) in EtOH/H2O (9:1, 9.5 mL) was stirred at 80 °C for 12 h and cooled to rt. The precipitates were filtered, and the combined organic solution was concentrated in vacuo. The crude mixture was used for the next reaction without purification. To a stirred solution of the crude amide in THF (9.5 mL) were added saturated aq NaHCO3 (9.5 mL) and Boc2O (124 mg, 0.57 mmol). The reaction mixture was stirred for 6 h at rt, and the aqueous layer was extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude mixture was purified by silica gel column chromatography (hexane/EtOAc 85:15 to 80:20 to 67:33) to afford 17 (258 mg, 0.16 mmol, 86% for 2 steps): TLC (hexane/EtOAc 70:30) Rf = 0.30; [α]D21 +0.012 (c = 0.90, CHCl3); IR (thin film) νmax: 3387 (br), 3090, 2941, 2866, 1742, 1720, 1676, 1600, 1556, 1505, 1456, 1366, 1278, 1219, 1161, 1100, 1070, 1049, 1013, 998, 882, 806, 772, 745, 681 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.54 (dd, J = 19.9, 8.5 Hz, 1H), 7.33–7.27 (m, 4H), 7.24–7.16 (m, 4H), 6.85 (d, J = 7.3 Hz, 2H), 6.51 (d, J = 4.8 Hz, 1H), 5.72–5.64 (m, 2H), 5.60–5.48 (m, 2H), 5.26 (d, J = 6.0 Hz, 1H), 5.17 (d, J = 8.6 Hz, 2H), 5.13–5.08 (m, 1H), 4.82–4.76 (m, 1H), 4.65 (t, J = 7.0 Hz, 1H), 4.51 (dd, J = 13.8, 6.0 Hz, 1H), 4.31–4.26 (m, 1H), 4.23–4.17 (m, 1H), 3.78 (d, J = 2.7 Hz, 3H), 3.74 (d, J = 6.9 Hz, 4H), 3.48–3.40 (m, 1H), 3.36–3.26 (m, 1H), 2.83 (t, J = 7.4 Hz, 2H), 2.56 (t, J = 7.5 Hz, 2H), 2.27 (t, J = 2.6 Hz, 2H), 2.23 (t, J = 3.0 Hz, 2H), 1.62–1.55 (m, 7H), 1.42 (s, 9H), 1.37 (d, J = 2.6 Hz, 3H), 1.11–0.99 (m, 54H); 13C NMR (101 MHz, CDCl3) δ: 159.46, 150.79, 136.91, 131.26, 129.33, 128.48 (2C), 128.37 (2C), 126.48, 126.11, 125.44, 115.30, 115.26, 79.95, 59.98, 55.68, 46.42, 46.16, 45.95, 44.83, 44.78, 42.49, 34.51, 34.49, 32.60, 32.55, 31.91, 29.69, 28.71, 28.40, 28.34, 27.37, 27.33, 27.29, 27.26, 27.09, 27.05, 25.36, 22.68, 22.63, 20.87, 18.06 (6C), 17.90 (6C), 14.12, 11.92 (3C), 11.78 (3C); HRMS (ESI+) m/z: calcd for C79H116Cl4N3O17Si2 [M + H], 1574.6597; found, 1574.6609.

Synthesis of 21

To a stirred solution of 17 (258 mg, 0.16 mmol) and quinoline (38.7 μL, 0.33 mmol) in EtOAc (50 mL) and MeOH (50 mL) was added Lindlar catalyst (300 mg). H2 gas was introduced, and the reaction mixture was stirred under a H2 atmosphere (600 psi) at rt. The reaction mixture was stirred for 11 h under a H2 atmosphere (600 psi) at rt. The reaction mixture was filtered through Celite, and the filtrate was washed with 1 N HCl. The combined organic solution was dried over Na2SO4 and concentrated in vacuo. The crude mixture was used for the next reaction without purification. To a stirred solution of the crude mixture in t-BuOH/acetone (1:1, 2.1 mL) were added NMO (192 mg, 1.64 mmol) and OsO4 (4% in water, 1.04 mL, 0.16 mmol) at rt. After 2 h, the reaction solution was diluted with EtOAc and quenched with saturated aq NaHCO3/saturated aq Na2SO3 (2:1). The heterogeneous mixture was stirred for 30 min and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude mixture was passed through a silica gel pad (hexane/EtOAc 33:67) to afford the diols as a diastereomeric mixture. This mixture was used for the next reaction without further purification. To a stirred solution of the diols (22.1 mg, 0.014 mmol) and NaHCO3 (11.5 mg, 0.14 mmol) in CH2Cl2 (0.7 mL) was added Pb(OAc)4 (12.1 mg, 0.027 mmol) at 0 °C. The reaction mixture was stirred for 2 h at 0 °C, quenched with saturated aq NaHCO3, and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude aldehyde 18 was used for the next reaction without purification. To a stirred solution of (BnO)2P(O)–CH2–P(O)(OBn)OH (30.6 mg, 0.069 mmol) in CH2Cl2 (0.4 mL) was added a CH2Cl2 (0.3 mL) solution of 18 and 19. To the reaction mixture was added TMSCN (17.1 μL, 0.14 mmol) and stirred for 9 h at rt. After completion, the reaction mixture was quenched with saturated aq NaHCO3 and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (hexane/EtOAc 80:20 to 60:40) to afford the Strecker products. To a stirred solution of the desired Strecker product (8.8 mg, 5.0 μmol) in EtOH/H2O (9:1, 0.5 mL) were added HgCl2 (2.7 mg, 0.010 mmol) and acetaldoxime (3.0 μL, 0.050 mmol) at rt. After being stirred for 6 h at rt, the reaction mixture was concentrated under reduced pressure. The residue was quenched with saturated aq NaHCO3 and extracted with CHCl3. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (hexane/EtOAc 80:20 to 60:40) to afford 21 (16.7 mg, 9.49 μmol, 69% for two steps) and 21 (4.1 mg, 2.34 μmol, 17% for two steps): 21: TLC (hexane/EtOAc 60:40) Rf = 0.40; [α]D21 +0.075 (c = 0.73, CHCl3); IR (thin film) νmax: 3317 (br), 2930, 2865, 1719, 1675, 1600, 1462, 1102, 1071, 882, 772, 683 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.68 (s, 1H), 7.49 (dd, J = 11.4, 8.8 Hz, 1H), 7.39 (d, J = 7.9 Hz, 2H), 7.32 (s, 1H), 7.19 (d, J = 8.5 Hz, 2H), 7.11 (d, J = 8.0 Hz, 2H), 6.86 (d, J = 9.3 Hz, 2H), 6.50 (d, J = 15.4 Hz, 1H), 5.73 (dd, J = 23.0, 8.0 Hz, 1H), 5.59 (d, J = 5.9 Hz, 1H), 5.54 (d, J = 9.4 Hz, 2H), 5.42 (t, J = 10.1 Hz, 1H), 5.25 (s, 1H), 5.08–5.00 (m, 2H), 4.96–4.82 (m, 2H), 4.50–4.45 (m, 1H), 4.25–4.19 (m, 1H), 4.15–4.06 (m, 1H), 3.94–3.83 (m, 1H), 3.80–3.63 (m, 10H), 3.49–3.41 (m, 1H), 3.39–3.31 (m, 1H), 3.03 (dt, J = 12.0, 6.1 Hz, 1H), 2.71–2.61 (m, 1H), 2.54 (t, J = 7.3 Hz, 2H), 2.51–2.45 (m, 1H), 2.29–2.17 (m, 4H), 1.67–1.51 (m, 10H), 1.41 (s, 9H), 1.28 (dd, J = 15.7, 8.1 Hz, 10H), 1.05 (s, 42H), 1.01 (s, 6H), 0.95 (s, 6H), 0.87 (t, J = 6.4 Hz, 3H); 13C NMR (101 MHz, CDCl3) δ: 170.9, 159.5, 136.9, 136.8, 131.3, 131.2, 129.42, 129.36, 128.84 (2C), 128.82 (2C), 128.80 (2C), 126.4, 126.2, 125.1, 120.09, 120.05, 115.4, 115.31, 115.30, 114.84, 114.81, 84.90, 84.87, 80.84, 80.78, 80.2, 79.8, 79.4, 78.2, 76.1, 74.3, 60.0, 59.9, 55.8, 55.7, 52.0, 46.2, 46.0, 44.83, 44.77, 35.4, 32.56, 32.55, 31.8, 31.5, 29.7, 29.19, 29.16, 28.4, 28.3, 27.3, 27.2, 22.7, 18.1 (12C), 14.1, 11.9 (6C); HRMS (ESI+) m/z: calcd for C88H135Cl4N6O18Si2 [M + H], 1759.8126; found, 1759.8135.

21R

TLC (hexane/EtOAc 60:40) Rf = 0.30; 1H NMR (400 MHz, CDCl3) δ: 7.74 (dd, J = 16.8, 11.4 Hz, 1H), 7.51 (dd, J = 11.7, 8.5 Hz, 1H), 7.47–7.29 (m, 3H), 7.23–7.15 (m, 2H), 7.10 (t, J = 9.5 Hz, 2H), 6.85 (d, J = 8.8 Hz, 2H), 6.49 (d, J = 4.6 Hz, 1H), 5.76 (dd, J = 21.1, 8.1 Hz, 1H), 5.65 (d, J = 23.4 Hz, 1H), 5.56 (d, J = 9.2 Hz, 1H), 5.52 (d, J = 3.9 Hz, 1H), 5.46 (t, J = 10.8 Hz, 1H), 5.40–5.23 (m, 2H), 5.23–5.16 (m, 1H), 5.10–5.05 (m, 1H), 5.02 (s, 1H), 4.90–4.78 (m, 1H), 4.26 (t, J = 6.3 Hz, 1H), 4.21 (d, J = 8.9 Hz, 1H), 3.96–3.89 (m, 1H), 3.80–3.71 (m, 10H), 3.68–3.63 (m, 1H), 3.48–3.39 (m, 1H), 3.04–2.95 (m, 1H), 2.75–2.66 (m, 1H), 2.53 (t, J = 7.7 Hz, 2H), 2.44 (d, J = 12.1 Hz, 1H), 2.37–2.27 (m, 2H), 2.23 (d, J = 14.7 Hz, 2H), 1.65–1.51 (m, 10H), 1.42 (s, 9H), 1.36–1.23 (m, 10H), 1.08–1.01 (m, 42H), 0.97 (s, 6H), 0.90–0.85 (m, 9H); HRMS (ESI+) m/z: calcd for C88H135Cl4N6O18Si2 [M + H], 1759.8126; found, 1759.8113.

Synthesis of 22

To a stirred solution of 21 (8.8 mg, 5.0 μmol) in EtOH/H2O (9:1, 0.5 mL) were added HgCl2 (2.7 mg, 0.010 mmol) and acetaldoxime (3.0 μL, 0.050 mmol) at rt. After being stirred for 6 h at rt, the reaction mixture was concentrated under reduced pressure. The residue was quenched with saturated aq NaHCO3 and extracted with CHCl3. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (CHCl3/MeOH 99.5:0.5 to 99.2:0.8 to 98.8:1.2) to afford 22 (7.9 mg, 4.5 μmol, 89%): TLC (CHCl3/MeOH 95:5) Rf = 0.40; IR (thin film) νmax: 3335 (br), 2927, 2865, 1668, 1601, 1460, 1099, 1071, 882, 681 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.59 (dd, J = 19.5, 8.5 Hz, 1H), 7.40 (d, J = 8.0 Hz, 2H), 7.30 (t, J = 2.6 Hz, 1H), 7.24–7.18 (m, 1H), 7.11 (d, J = 8.0 Hz, 2H), 6.84 (d, J = 7.2 Hz, 2H), 6.50 (s, 1H), 5.84 (br s, 1H), 5.59–5.47 (m, 3H), 5.26–5.14 (m, 2H), 5.06–4.97 (m, 1H), 4.96–4.87 (m, 1H), 4.84–4.73 (m, 1H), 4.55 (t, J = 5.0 Hz, 1H), 4.28–4.14 (m, 2H), 3.80–3.70 (m, 7H), 3.59–3.46 (m, 1H), 3.41 (brs, 2H), 2.83 (brs, 2H), 2.54 (t, J = 7.7 Hz, 3H), 2.50–2.43 (m, 1H), 2.29–2.21 (m, 4H), 1.99 (brs, 2H), 1.65–1.53 (m, 10H), 1.43 (s, 9H), 1.35 (d, J = 5.2 Hz, 3H), 1.32–1.24 (m, 10H), 1.05 (d, J = 3.2 Hz, 48H), 1.00–0.97 (m, 6H), 0.87 (t, J = 6.8 Hz, 3H); 13C NMR (101 MHz, CDCl3) δ: 159.6, 159.5, 136.87, 136.85, 136.4, 135.2, 134.0, 133.64, 133.59, 131.3, 129.42, 129.40, 128.9 (2C), 126.2, 125.3, 120.2, 120.1, 115.4 (2C), 74.5, 60.0, 59.9, 55.73, 55.72, 46.2, 46.1, 46.0, 44.8, 35.4, 32.7, 32.6, 31.8, 31.5, 29.69, 29.67, 29.6, 29.5, 29.4, 29.3, 29.24, 29.16, 29.09, 28.51, 28.49, 28.48, 28.45, 28.43, 28.42, 28.36, 28.33, 28.31, 28.28, 27.33, 27.30, 27.25, 27.2, 25.3, 22.7, 18.1 (12C), 14.1, 11.9 (6C); HRMS (ESI+) m/z: calcd for C88H137Cl4N6O19Si2 [M + H], 1777.8231; found, 1777.8219.

Synthesis of 23

To a stirred solution of 22 (5.8 mg, 3.3 μmol) and paraformaldehyde (2.9 mg, 0.098 mmol) in CH3CN (0.5 mL) was added NaB(CN)H3 (6.2 mg, 0.098 mmol). After being stirred for 4 h at rt, the reaction mixture was quenched with saturated aq NaHCO3 and extracted with CHCl3. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (hexane/EtOAc 40:60) to afford 23 (5.5 mg, 3.1 μmol, 95%): TLC (hexane/EtOAc 33:67) Rf = 0.60; [α]D21 +0.022 (c = 0.28, CHCl3); IR (thin film) νmax: 2932, 2866, 1718, 1672, 1601, 1463, 1101, 1071, 884 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.75 (d, J = 17.0 Hz, 1H), 7.56 (d, J = 8.6 Hz, 1H), 7.43 (d, J = 8.1 Hz, 2H), 7.34 (d, J = 8.1 Hz, 1H), 7.30 (s, 2H), 7.20 (dt, J = 8.5, 2.0 Hz, 1H), 7.10 (d, J = 8.1 Hz, 2H), 6.85 (s, 2H), 6.51 (d, J = 7.9 Hz, 1H), 6.28 (brs, 1H), 5.95 (d, J = 21.6 Hz, 1H), 5.84–5.78 (m, 1H), 5.74 (d, J = 23.3 Hz, 1H), 5.54 (s, 2H), 5.49 (d, J = 9.6 Hz, 1H), 5.18 (brs, 1H), 5.11 (s, 2H), 5.02 (brs, 1H), 4.88–4.83 (m, 1H), 4.80–4.74 (m, 1H), 4.39–4.31 (m, 2H), 4.24–4.18 (m, 1H), 3.92 (t, J = 5.8 Hz, 1H), 3.78 (s, 3H), 3.74 (q, J = 6.6 Hz, 4H), 3.68–3.63 (m, 1H), 3.50–3.40 (m, 2H), 3.37–3.30 (m, 1H), 2.83–2.74 (m, 1H), 2.68–2.59 (m, 1H), 2.54 (t, J = 7.8 Hz, 2H), 2.49 (s, 3H), 2.37 (q, J = 8.0, 7.6 Hz, 2H), 2.29–2.20 (m, 4H), 1.98–1.88 (m, 2H), 1.62–1.52 (m, 6H), 1.40 (s, 9H), 1.36 (brs, 3H), 1.33–1.23 (m, 6H), 1.09–1.01 (m, 48H), 0.98 (s, 6H), 0.87 (t, J = 6.4 Hz, 3H); 13C NMR (101 MHz, CDCl3) δ: 171.0, 162.0, 159.5, 157.1, 136.9, 131.3, 129.4, 128.7 (2C), 119.9 (2C), 115.3, 115.1, 114.2, 70.6, 70.1, 69.9, 67.1, 60.4, 60.1, 59.96, 59.95, 58.9, 55.8, 55.7, 54.4, 54.1, 46.22, 46.16, 46.1, 45.3, 44.9, 44.8, 44.7, 42.3, 41.2, 39.93, 39.86, 39.6, 39.04, 38.97, 35.4, 32.7, 32.64, 32.63, 32.62, 32.58, 31.9, 31.8, 31.7, 31.6, 31.53, 31.48, 29.69, 29.67, 29.6, 29.4, 29.22, 29.17, 28.50, 28.49, 28.4, 27.29, 27.28, 27.21, 27.17, 25.23, 25.20, 22.68, 22.66, 18.1 (12C), 14.1, 11.9 (6C); HRMS (ESI+) m/z: calcd for C89H139Cl4N6O19Si2 [M + H], 1791.8388; found, 1791.8404.

Synthesis of 24

To a stirred solution of the diols (32.5 mg, 0.020 mmol) synthesized for 21 and NaHCO3 (16.9 mg, 0.20 mmol) in CH2Cl2 (1.0 mL) was added Pb(OAc)4 (17.9 mg, 0.040 mmol) at 0 °C. The reaction mixture was stirred for 2 h at 0 °C, quenched with saturated aq NaHCO3, and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude aldehyde 18 was used for the next reaction without purification. To a stirred solution of (BnO)2P(O)–CH2–P(O)(OBn)OH (45.0 mg, 0.10 mmol) in CH2Cl2 (0.5 mL) was added a CH2Cl2 (0.5 mL) solution of 18 and 20. After 6 h, to the reaction mixture was added TMSCN (25.2 μL, 0.20 mmol) and stirred for 12 h at rt. After completion, the reaction mixture was quenched with saturated aq NaHCO3 and extracted with EtOAc. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (hexane/EtOAc 80:20 to 60:40) to afford 24 (23.9 mg, 12.0 μmol, 61% for two steps) and 24 (5.1 mg, 2.6 μmol, 13% for two steps). 24: TLC (hexane/EtOAc 50:50) Rf = 0.40; [α]D21 +0.102 (c = 0.75, CHCl3); IR (thin film) νmax: 3342 (br), 2941, 2866, 1718, 1675, 1505, 1464, 1243, 1164, 1101, 1071, 883, 772, 688 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.49 (dd, J = 8.5, 4.3 Hz, 1H), 7.32 (d, J = 2.0 Hz, 1H), 7.22–7.11 (m, 7H), 6.94–6.88 (m, 5H), 6.86 (d, J = 6.5 Hz, 2H), 6.50 (d, J = 8.6 Hz, 1H), 6.25–6.16 (m, 1H), 5.73 (dd, J = 22.2, 8.0 Hz, 1H), 5.60 (t, J = 8.8 Hz, 1H), 5.56–5.41 (m, 3H), 5.21 (d, J = 4.4 Hz, 1H), 5.05–4.98 (m, 2H), 4.94–4.77 (m, 2H), 4.53–4.37 (m, 3H), 4.25–4.16 (m, 2H), 4.05–3.98 (m, 1H), 3.80–3.69 (m, 6H), 3.68–3.63 (m, 1H), 3.56 (dd, J = 17.3, 3.4 Hz, 1H), 3.48 (ddt, J = 11.6, 7.2, 4.0 Hz, 2H), 3.44–3.29 (m, 1H), 3.08 (dq, J = 9.5, 5.3, 4.8 Hz, 2H), 2.95 (dt, J = 11.4, 5.5 Hz, 1H), 2.47 (td, J = 12.0, 11.4, 5.7 Hz, 1H), 2.36–2.14 (m, 5H), 2.13–2.05 (m, 2H), 1.97–1.85 (m, 3H), 1.84–1.75 (m, 1H), 1.58 (t, J = 6.9 Hz, 2H), 1.55–1.50 (m, 4H), 1.40 (s, 9H), 1.33 (d, J = 4.8 Hz, 3H), 1.28–1.23 (m, 3H), 1.08–1.02 (m, 42H), 1.01 (s, 6H), 0.94 (d, J = 2.1 Hz, 6H); 13C NMR (101 MHz, CDCl3) δ: 172.4, 171.0, 170.9, 159.5, 155.8, 150.9, 150.7, 142.8, 136.9, 136.8, 135.3, 135.1, 134.13, 134.05, 133.86, 133.85, 133.78, 131.2, 131.1, 129.42, 129.37, 129.0, 126.4, 126.2, 125.5, 125.2, 122.5 (2C), 121.8, 119.3, 118.4, 116.8 (2C), 116.6 (2C), 115.4, 115.3, 114.71, 114.66, 106.4, 102.3, 102.2, 84.8, 80.7, 80.6, 79.9, 79.8, 79.3, 76.2, 74.32, 74.30, 72.9, 60.38, 60.35, 60.0, 59.9, 55.72, 55.71, 52.0, 46.6, 46.2, 45.9, 44.84, 44.77, 42.99, 42.96, 42.4, 41.2, 33.53, 33.49, 32.6, 32.5, 30.3, 28.4, 27.3 (2C), 27.17, 27.16, 27.1, 25.4, 18.1 (12C), 14.2, 14.1, 11.91 (3C), 11.90 (3C); HRMS (ESI+) m/z: calcd for C94H135Cl4F3N7O20Si2 [M + H], 1934.8007; found, 1934.8021. 24: TLC (hexane/EtOAc 60:40) Rf = 0.30; 1H NMR (400 MHz, chloroform-d) δ: 7.53 (d, J = 8.7 Hz, 1H), 7.33–7.29 (m, 1H), 7.21–7.07 (m, 7H), 6.94–6.88 (m, 5H), 6.85 (d, J = 6.8 Hz, 2H), 6.54 (s, 1H), 5.71 (d, J = 7.9 Hz, 1H), 5.58–5.49 (m, 3H), 5.46 (t, J = 8.9 Hz, 1H), 5.24–5.20 (m, 1H), 5.15–5.08 (m, 1H), 5.08–5.00 (m, 1H), 4.92 (dd, J = 11.5, 5.6 Hz, 1H), 4.85–4.78 (m, 1H), 4.49–4.39 (m, 2H), 4.39–4.18 (m, 3H), 3.98 (dd, J = 11.1, 5.4 Hz, 1H), 3.81–3.70 (m, 6H), 3.69–3.61 (m, 2H), 3.52–3.43 (m, 2H), 3.37–3.32 (m, 1H), 3.08 (ddd, J = 12.4, 8.5, 3.8 Hz, 2H), 2.99–2.91 (m, 1H), 2.65 (dd, J = 12.8, 6.5 Hz, 1H), 2.31–2.18 (m, 5H), 2.13–2.04 (m, 2H), 1.96–1.85 (m, 4H), 1.67–1.52 (m, 6H), 1.40 (s, 9H), 1.38–1.29 (m, 3H), 1.25 (s, 6H), 1.10–0.98 (m, 42H), 0.97 (s, 6H), 0.88 (t, J = 6.7 Hz, 3H); HRMS (ESI+) m/z: calcd for C94H135Cl4F3N7O20Si2 [M + H], 1934.8007; found, 1934.8000.

Synthesis of 25

To a stirred solution of 24 (15.4 mg, 8.0 μmol) in EtOH/H2O (9:1, 0.5 mL) were added HgCl2 (4.3 mg, 0.016 mmol) and acetaldoxime (4.9 μL, 0.080 mmol) at rt. After being stirred for 6 h at rt, the reaction mixture was concentrated under reduced pressure. The residue was quenched with saturated aq NaHCO3 and extracted with CHCl3. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (CHCl3/MeOH 99.5:0.5 to 99.2:0.8 to 98.8:1.2) to afford 25 (15.3 mg, 7.8 μmol, 98%): TLC (CHCl3/MeOH 95:5) Rf = 0.30; [α]D21 +0.144 (c = 0.53, CHCl3); IR (thin film) νmax: 3335 (br), 2940, 2866, 1719, 1676, 1505, 1464, 1367, 1242, 1162, 1101, 1070, 882, 681 cm–1; 1H NMR (400 MHz, CDCl3) δ: 7.53 (dd, J = 8.6, 5.1 Hz, 1H), 7.30 (s, 1H), 7.28–7.22 (m, 2H), 7.21–7.12 (m, 6H), 6.91 (d, J = 8.5 Hz, 4H), 6.86 (d, J = 2.6 Hz, 2H), 6.51 (d, J = 8.7 Hz, 1H), 5.94 (brs, 1H), 5.79–5.67 (m, 3H), 5.56–5.47 (m, 2H), 5.17 (brs, 1H), 5.06 (s, 1H), 4.96 (brs, 1H), 4.82–4.73 (m, 2H), 4.43 (tt, J = 7.8, 3.8 Hz, 1H), 4.39–4.28 (m, 3H), 4.21 (brs, 1H), 4.13 (brs, 1H), 3.78 (s, 3H), 3.73 (q, J = 7.4 Hz, 5H), 3.67 (brs, 1H), 3.48 (ddd, J = 11.7, 7.2, 3.7 Hz, 2H), 3.41–3.28 (m, 1H), 3.17 (s, 1H), 3.09 (ddd, J = 12.2, 8.2, 3.3 Hz, 2H), 2.80–2.60 (m, 2H), 2.38–2.15 (m, 7H), 2.13–2.05 (m, 2H), 1.93 (ddd, J = 12.8, 8.0, 3.7 Hz, 2H), 1.85–1.79 (m, 2H), 1.54 (s, 3H), 1.42 (s, 9H), 1.34 (s, 3H), 1.04 (d, J = 2.8 Hz, 42H), 1.01 (s, 6H), 0.96 (s, 6H); 13C NMR (101 MHz, CDCl3) δ: 162.1, 162.0, 159.6, 159.5, 156.2, 155.8, 150.9, 150.4, 142.80, 142.78, 136.88, 136.86, 135.23, 135.21, 133.9, 133.6, 131.33, 131.30, 131.29, 129.40, 129.37, 129.2, 129.1, 129.02, 128.98, 126.24, 126.22, 126.21, 125.40, 125.36, 124.5, 124.4, 123.20, 123.19, 122.5 (2C), 121.8, 120.1, 119.3, 116.8 (2C), 115.4, 80.4, 80.02, 79.99, 79.96, 79.95, 79.92, 79.87, 79.85, 79.83, 74.51, 74.50, 72.7, 70.4, 70.3, 69.5, 60.0, 59.9, 55.73, 55.72, 46.7, 46.19, 46.15, 46.13, 46.11, 46.10, 46.07, 46.0, 44.8, 34.7, 34.5, 32.61, 32.58, 30.2, 29.7, 29.64, 29.60, 28.50, 28.45, 28.42, 28.38, 28.34, 27.25 (2C), 27.19, 27.16, 25.31, 25.29, 25.27, 18.1 (12C), 14.1, 12.2, 11.9 (6C); HRMS (ESI+) m/z: calcd for C94H137Cl4F3N7O21Si2 [M + H], 1952.8112; found, 1952.8098.

Synthesis of 26

To a stirred solution of 25 (7.8 mg, 4.0 μmol) and paraformaldehyde (3.6 mg, 0.12 mmol) in CH3CN (0.5 mL) was added NaB(CN)H3 (7.5 mg, 0.12 mmol). After being stirred for 17 h at rt, the reaction mixture was quenched with saturated aq NaHCO3 and extracted with CHCl3. The combined organic extracts were dried over Na2SO4 and concentrated in vacuo. The crude product was purified by silica gel column chromatography (hexane/EtOAc 33:67) to afford 26 (4.7 mg, 2.4 μmol, 59%): TLC (hexane/EtOAc 20:80) Rf = 0.50; 1H NMR (400 MHz, chloroform-d) δ: 7.57 (d, J = 8.8 Hz, 1H), 7.38 (dd, J = 19.7, 7.9 Hz, 1H), 7.29 (s, 1H), 7.22–7.10 (m, 5H), 6.90 (d, J = 9.1 Hz, 4H), 6.85 (d, J = 3.6 Hz, 2H), 6.51 (d, J = 5.1 Hz, 1H), 6.25 (d, J = 27.7 Hz, 1H), 5.84 (dd, J = 13.4, 8.0 Hz, 1H), 5.55 (s, 1H), 5.48 (brs, 1H), 5.13 (brs, 1H), 5.09 (s, 1H), 4.99 (brs, 1H), 4.86 (d, J = 6.3 Hz, 1H), 4.74 (d, J = 7.0 Hz, 1H), 4.43 (tt, J = 7.5, 3.6 Hz, 1H), 4.36–4.28 (m, 4H), 4.20 (dd, J = 8.6, 3.5 Hz, 1H), 3.77 (s, 3H), 3.74 (t, J = 6.5 Hz, 4H), 3.69–3.63 (m, 2H), 3.51–3.42 (m, 4H), 3.29 (d, J = 14.5 Hz, 1H), 3.08 (ddd, J = 12.2, 8.4, 3.4 Hz, 2H), 2.76–2.68 (m, 1H), 2.61–2.51 (m, 1H), 2.45 (s, 3H), 2.29–2.14 (m, 5H), 2.12–2.05 (m, 2H), 1.96–1.83 (m, 4H), 1.55 (s, 3H), 1.39 (s, 9H), 1.37 (s, 3H), 1.26 (s, 3H), 1.04 (d, J = 4.6 Hz, 42H), 1.01 (s, 6H), 0.99 (s, 6H); 13C NMR (101 MHz, CDCl3) δ: 173.0, 172.3, 171.22, 171.15, 162.0, 159.5, 157.5, 155.8, 150.6, 142.83, 142.81, 136.9, 135.4, 131.3, 129.36, 129.35, 129.31, 129.30, 129.03, 128.99, 128.95, 128.93, 126.1, 122.5 (2C), 116.8 (2C), 116.6, 115.33, 115.29, 107.3, 106.9, 84.1, 79.30, 79.28, 79.26, 79.24, 79.23, 74.88, 74.87, 73.6, 72.83, 72.80, 70.61, 70.56, 69.8, 67.3, 60.39, 60.36, 60.0, 59.9, 55.70 (2C), 54.2, 46.6 (2C), 46.1, 46.0, 45.0, 44.9, 44.7, 43.1, 41.2, 32.61, 32.59, 30.33 (2C), 30.27, 30.25, 29.69, 29.67, 29.65, 29.60, 28.52, 28.45, 27.31, 27.28, 27.24, 27.23, 27.22, 27.15, 25.14, 25.11, 22.7, 18.1 (12C), 14.2, 14.1, 11.9 (6C); HRMS (ESI+) m/z: calcd for C95H139Cl4F3N7O21Si2 [M + H], 1966.8269; found, 1966.8288.

MIC Assays

M. smegmatis (ATCC 607), Klebsiella pneumoniae (ATCC 8047), Pseudomonas aeruginosa (ATCC 27853), Acinetobacter baumannii (ATCC 19606), S. aureus (BAA-1683), C. difficile (ATCC 43596), Enterococcus faecium (ATCC 349), Fusobacterium periodontium ATCC 33693), Bacteroides fragilis (ATCC 25285), Streptococcus pneumoniae (ATCC 6301), Bacillus subtilis (ATCC 6051), C. perfringens (ATCC 13124), Lactobacillus casei (ATCC 393), Lactobacillus acidophilus (ATCC 4356), and E. coli (ATCC 10798) were obtained from American Type Culture Collection (ATCC). A single colony of M. smegmatis was obtained on Difco Middlebrook 7H10 nutrient agar enriched with albumin, dextrose, and catalase. Single colonies of P. aeruginosa, K. pneumoniae, A. baumannii, S. aureus, E. faecium, and E. coli were grown on tryptic soy agar for 24 h at 37 °C in a static incubator and cultured in tryptic soy broth until log phase to be an optical density (OD) of 0.2–0.5. The OD was monitored at 600 nm using a 96-well microplate reader. A single colony of C. difficile was obtained on a brain–heart infusion (BHI) agar plate and incubated at 37 °C under anaerobic conditions for 48 h. Seed cultures and larger cultures were obtained using a BHI broth. The flasks were incubated anaerobically for 48 h at 37 °C and cultured to mid-log phase (OD600 0.4). The other bacteria were cultured in the recommended conditions by ATCC.[48] The inhibitors were dissolved in polyethylene glycol 300–H2O (1/1, a final concentration of 1 mg per 100 μL). This concentration was used as the stock solution for all studies. Bacterial cultures were treated with serial dilutions of inhibitors and incubated at 37 °C for 48 h. The MIC was determined by a 96-well plate reader (BioTek Synergy XT, Winooski, VT, USA) at 570 and 600 nm. If necessary, viable bacteria in each well (96-well plate) were measured via CFUs on a BHI agar plate. The absorbance measurements were also performed using a BioTek Synergy XT (Winooski, VT, USA) 96-well plate reader at 570 and 600 nm.

Cytotoxicity Assays

Cytotoxicity assays were performed using Vero monkey kidney (ATCC CCL-81) and HepG2 human hepatoblastoma cell (ATCC HB-8065) lines. Vero or HepG2 cells were cultured in 75 cm2 flasks and transferred to 96-well cell culture plates using ATCC-formulated Eagle’s minimum essential medium containing 10% fetal bovine serum and penicillin–streptomycin. Serially diluted aliquots of each test compound at concentrations ranging from 0.78 to 200 μg/mL were added to the cells. Control compounds with known toxicity, such as tunicamycin, colistin, or tobramycin, were included on each plate. The plates were incubated, and cytotoxic effects were determined via the MTT assay.

Spore Preparation

C. difficile (ATCC 43596) was inoculated on a BHI agar plate and incubated at 37 °C under anaerobic conditions for 14 days. The spores were collected from the agar using sterile distilled water and purified according to the procedures described in the literature.[17] The vegetative forms of C. difficile were killed upon heating at 50 °C for 30 min. The prepared spores were suspended in sterile distilled water at 4 °C.

Spore Viability Testing

A solution of test compound was added to a suspension containing C. difficile spores (2 × 105 mL–1), and the mixture was incubated at 37 °C for 24 h. The spore suspension treated with the test compound was centrifuged (4700g), and the pellet was washed with sterile distilled water, plated on a BHI agar containing 0.1% sodium taurocholate (a germination agent), incubated at 37 °C for 48 h under anaerobic conations. The resulting colonies were counted.

MraY (MurX), WecA, and AglH Assays

Preparations of the membrane fractions from E. coli, M. smegmatis, and Hydrogenivirga spp. were performed according to the procedures previously described.[27,33] Procedures for the purification of MraY and AglH and inhibitory assays using these phosphotransferases are described in the Supporting Information.