Synthesis and evaluation of cyclic secondary amine substituted phenyl and benzyl nitrofuranyl amides as novel antituberculosis agents

Abstract

In an ongoing effort to develop new and potent antituberculosis agents, a second generation series of nitrofuranyl amides was synthesized based on the lead compound 5-nitro-furan-2-carboxylic acid 3,4-dimethoxy-benzylamide. The primary design consideration was to improve the solubility and consequently bioavailability of the series by the addition hydrophilic rings to the benzyl and phenyl B ring core. The synthesis of 27 cyclic, secondary amine substituted phenyl and benzyl nitrofuranyl amides is described and their activity against M. tuberculosis reported. The series showed a strong structure-activity relationship as the benzyl nitrofuranyl amides were significantly more active than similarly substituted phenyl nitrofuranyl amides. Para-substituted benzyl piperazines showed the most antituberculosis activity. Compounds in the series were subsequently selected for bioavailability and in vivo testing. This study lead to the successful discovery of novel compounds with increased antituberculosis activity in vitro and a better understanding of the requisite pharmacological properties to advance this class.

Introduction

Someone in the world is newly infected with TB bacilli every second. Overall one third of the world’s population is currently infected with tuberculosis and it has been estimated that 5 – 10% of those people are expected to become sick or infectious at some point their lifetime.¹ According to World Health Organization, in 2003 8.8 million new TB cases arose and an estimated 1.7 million deaths resulted from TB.² The major challenges for tuberculosis control are the development of multidrug-resistant tuberculosis (MDRTB) strains and the increasing numbers of immunocompromised individuals with HIV infections who are highly susceptible to the disease.³ Consequently, there is an urgent need to develop new, potent, fast-acting antituberculosis drugs with low toxicity profiles that can be used in conjunction with drugs used to treat HIV infections.

Recently, we described a novel set of nitrofuranyl amides with potent antituberculosis activity.⁴ Compounds in this series were easily synthesized, and exhibited good therapeutic indices. They are members of an emerging new class of nitroaromatic antibiotics that are currently being intensively investigated as new antituberculosis drugs.⁵ Most importantly, one of the compounds 5-nitro-furan-2-carboxylic acid 3,4-dimethoxy-benzylamide (1) (fig. 1), has demonstrated significant oral activity in a mouse model of tuberculosis infection. However, formulation of these compounds for oral administration and in vivo experimentation was problematic due to their poor solubility. This suggested that poor bioavailability may have hindered the activity of several compounds tested in vivo. Such problems have previously been encountered in the development of other synthetic antimicrobial agents and most notably in the development of the fluoroquinolone class of antibiotics. The addition of a piperazine ring to the quinolone core of the first generation quinolones lead to a significant improvement in oral activity and tissue penetration found in second generation fluoroquinolone Norfloxacin.⁶ This strategy also proved fruitful in the development of the orally bioavailable Ansamycin anitibiotics such as the highly potent antituberculosis drug Rifampin, which was developed from RifamycinSV by formylation and addition of a piperazinyl hydrazine side chain.⁷

Figure 1.

Target lead compounds and target phenyl and benzyl nitrofuranyl amides.

Accordingly, we chose to explore this strategy in the development of the nitrofuranyl amide series. During exploratory experiments, the methoxy group in the lead compound 1 (MIC = 0.2 μg/mL) was substituted with a dimethyl amino group 2 (Fig. 1). Compound 2 retained good MIC activity (0.1 μg/mL) suggesting that substitution of cyclic secondary amines such as piperazine derivatives would be tolerated within the structure activity relationship of this series and that these compounds might have increased the biological activity and pharmacological properties.

In this paper we describe the synthesis and evaluation of several classes of cyclic secondary amine substituted phenyl and benzyl nitrofuranyl amides as novel anti-tuberculosis agents.

Chemistry and in vitro SAR

Synthesis of compound 2 was carried out by a simple acid chloride amide forming reaction. The 5-nitro-furan-2-carbonyl chloride (11) was treated with (4-aminomethyl-phenyl)-dimethyl-amine in presence of Et₃N to give the desired amide 2 in 89% yield.

Synthesis and evaluation of substituted phenyl nitrofuranyl amides

Synthesis of the substituted phenyl amides (3a–j) involved a three reaction sequence of nucleophilic aromatic substitution, nitro reduction and acylation with the nitrofuranoic acid chloride (Scheme 1). The fluorine of 3 or 4-fluoro nitrobenzene (6 and 7) was first substituted by conventional aromatic nucleophilic displacement with secondary amides morpholine, 1-methyl-piperazine, 1-benzyl piperazine, 4-benzyl piperadine and 1-(2-pyridyl) piperazine to give corresponding substituted nitrobenzenes 12a–j with yields ranging 78%–95%.⁸ It was noted that the substitution of p-fluoro nitrobenzene was faster than m-fluoro nitrobenzene, 8 hrs compared with 24 hrs, respectively. The nitro functional group of compounds 12a–j, except compounds 12c and 12h, was reduced by catalytic hydrogenation to give the corresponding anilines 13a–j in quantitative yields. Due to sensitivity of the benzyl substituted piperazines to hydrogenation, the amines 12c and 12h were reduced to their corresponding amides 13c and 13h (both in 82% yields) using SnCl₂.2H₂O. Finally, all the amines, 13a–j, were treated with 5-nitro-furan-2-carbonyl chloride (11) to give the desired phenyl amides 3a-j in 82–90% yields.

Scheme 1.

Reagents: Reagents: a) K₂CO₃, DMSO, 90 °C, 8 h for 6 and 24 h for 7; b₁) H₂, pd/c, EtOAc-MeOH, room temp., 8 h; b₂) For 12c and 12h; SnCl₂.2H₂O, EtOAc, refluxm 2 h.; c) 11, CH₂Cl₂, Et₃N, room temp.

The antituberculosis activities of 3a–j (Table 1) showed overall lower activity than initial leads 1 and 2. Pyridinyl and benzyl subsitituted piperazines 3e and 3c showed the greatest activity when placed in the para-position. The same substitution to the meta-position, 3j and 3h, led to a significant decrease in activity. It was interesting to note that for the smaller ring systems in 3a and 3b vs 3f and 3g no difference in activity with the placement of rings meta or para was observed.

Table 1.

Cyclic secondary amine substituted phenyl nitrofuranyl amides and their anti-tuberculosis activity

No.	Compound	M. tb H37Rv MIC90 (μg/mL)
3a		3.13
3b		12.5
3c		0.8
3d		3.13
3e		0.4
3f		3.13
3g		12.5
3h		12.5
3i		12.5
3j		3.13

Synthesis and evaluation of substituted benzyl nitrofuranyl amides

The benzyl amide series was prepared using a similar synthetic pattern of nucleophilic aromatic substitution: reduction followed by acylation (Scheme 2). In this case, a cyano group was used as an electron-withdrawing group to facilitate the nucleophilic aromatic substitution. Accordingly, the fluorine of the 3-or 4-fluoro benzonitrile (8 or 9 respectively) was substituted with corresponding cyclic secondary amines in DMSO at 90° C in the presence of potassium carbonate to give compounds 14a–h in 83% to 96% yields.⁹ The substituted benzonitriles were subjected to reduction using Red-Al reagent to afford corresponding crude amines,¹⁰ which were further reacted immediately with 5-nitro-furan-2-carbonyl chloride to give benzyl amides 4a–h in yields ranging from 69% to 96%.

Scheme 2.

Reagents: a) K₂CO₃, DMSO, 90 °C, 8 h; b) Red-Al, 0 °C, dry THF, 3 h.; c) 11, CH₂Cl₂, Et₃N, room temp.

Compounds 4a–h were made from commercially available piperazine and morpholine starting materials. In order to expand the diversity of substitution, a method to synthesize novel piperazine derivatives was developed from the starting material 4-piperazin-1-yl-benzonitrile (15), which upon alkylation with different alkyl halides provided alternative piperazine substitutions. Accordingly, alkylation of 15 with bromomethyl-cyclopropane gave the nitrile 16 (93% yield),¹¹ which on reduction with Red-Al followed by treatment with acid chloride 11 in presence of base gave the desired amide 4k in 82% overall yield (Scheme 3).

Scheme 3.

Reagents: a) K₂CO₃, DMF, room temp., 7 h; b) Red-Al, 0 °C-room temp., dry THF, 3 h.; c) 11, CH₂Cl₂, Et₃N, room temp.

Further fuctionalization of the sulfur group in the thiomorpholine ring of amide 4h was performed to create compounds with lower potential serum binding.¹² This was achieved by stepwise oxidation of 4h with m-chloroperbenzoic acid to give the sulfoxide 4i and the sulfone 4j derivatives in 15% and 20% yields respectively (Scheme 4).¹

Scheme 4.

Reagents: a) m-CPBA, NaHCO₃, CH₂Cl₂, room temp., 30 min.

To further explore the SAR of these compounds, the piperazine group was separated from the phenyl ring with a hydrazone link creating a similar substitution to the modification found in the derivatization of rifampin from rifamycin. Amine 17 was reacted with acid chloride 11 to give amide 18 in 65% yield. The benzyl alcohol group of 18 was oxidized to give the corresponding aldehyde,¹⁴ which was further treated with 4-methyl-piperazin-1-yl-amine in ethanol to give the hydrazone derivative 4l in 74% yield (Scheme 5).¹⁵

Scheme 5.

Reagents: a) 11, NEt₃, CH₂Cl₂, room temp., 14 h; b) Dess-Martin periodinane, pyridine, CH₂Cl₂, room temp., 2 h; c) 4-methyl-piperazin-1-yl-amine, ethanol, 1 h reflux, 14 h room temp.

The antituberculosis activity of 4a–l (Table 2) showed interesting SAR. Compounds 4c and 4k had significantly increased activity over the initial leads 1 and 2. In this series para-substitution was again favored over meta (4c vs 4f, 4b vs 4e, 4d vs 4g). The thiomorpholine analogue 4h (0.1 μg/mL) had slightly better activity than the morpholine analogue 4a (0.2 μg/mL). However, further derivatization of 4a to its oxides 4i and 4j, reduced the MIC activity. Replacing the benzyl group on the piperazine in 4c with a simple cyclopropyl methyl substitution (4k) maintained good activity at 0.05 μg/mL. The rifampin side chain hydrazone derivative 4l showed moderate activity with increased hydrophilicity.

Table 2.

Cyclic secondary amine substituted benzyl nitrofuranyl amides and their anti-tuberculosis activity

No.	Compound	M. tb H37Rv MIC90 (μg/mL)
4a		0.2
4b		0.2
4c		0.0125
4d		0.8
4e		3.125
4f		0.1
4g		1.56
4h		0.1
4i		3.13
4j		12.25
4k		0.05
4l		0.4

Synthesis and evaluation of fluorine substituted benzyl amides

After synthesis of amides 4a–l it was proposed to explore the addition of more functionality on the phenyl ring of the benzyl amine moiety. This was achieved by starting from a di-substituted benzonitrile such as 3,4-difluorobenzonitrile (10).¹⁶ The reaction of nitrile 10 with cyclic secondary amines, in presence of a base, substituted the fluorine group in the para-position, which generated the corresponding tertiary amines 19a–e in 75% to 88% yields. Subsequently, the nitrile group in 19a–e was reduced with Red-Al to give corresponding benzylamines, which were then treated with 5-nitro-furan-2-carbonyl chloride to give the final targeted amides 5a–e in 77% to 89% yields (Scheme 6).

Scheme 6.

Reagents: a) K₂CO₃, DMSO, 90 °C, 8 h; b) Red-Al, 0 °C-room temp., dry THF, 3 h.; c) 11, CH₂Cl₂, Et₃N, room temp.

The antituberculosis activity of 5a–e, with a fluorine substitution at the meta-position (Table 3), demonstrated a similar SAR to the benzyl series with only slightly lower MIC values in general. The benzyl piperazine analog 5a exhibited the best activity.

Table 3.

Fluorine substituted benzyl nitrofuanyl amides and their anti-tuberculosis activity

No.	Compound	M. tb H37Rv MIC90 (μg/mL)
5a		0.025
5b		0.8
5c		0.8
5d		0.4
5e		0.2

Oral bioavailability and in vivo efficacy studies

The MIC values of compounds in these series are good and compare favorably with other known antituberculosis agents. Preliminary in vitro MIC testing in presence of protein was performed to evaluate whether protein binding might affect the antituberculosis activity of the compounds. In vitro MIC₅₀ values were established with and without the presence of 10% mouse serum for M. tuberculosis H37Rv, according to NCCLS guidelines (Table 4).¹⁷ Serial drug dilutions were performed 1:3, and therefore a 3-fold decrease in MIC in this assay was not considered significant. The results showed that only compound 4g had potential protein binding issues. Since in vivo testing of novel compounds occurs primarily via the oral route, the ability of the compounds to cross the intestinal tract needed to be assessed. Therefore, compounds were selected for advancement into animal studies based on bioavailability assays that determined which compounds achieved sufficient serum levels able to eradicate the disease. Where possible the selected compounds were formulated as hydrochloride salts to maximize dissolution and bioavailability. The compounds were orally dosed to mice and subsequently the mice were bled at set intervals. The serum collected from these mice was then serially diluted and tested for anti-tuberculosis activity in a bioassay using M. tuberculosis.¹⁸ The results from the bioassay reflect approximate concentrations of unbound bioactive product in the serum rather than providing total drug levels. It was clear that compounds 2 and 4g had the best absorption (Cmax) and compounds 4c and 4g had the best combination of low MIC and Cmax values. A further subset of compounds was advanced for in vivo testing in a mouse model of tuberculosis infection (Table 5).^19–21

Table 4.

Results of the in vivo biological activity and basic bioavailability assay

Comp	MIC50 H37Rv (μg/ml)		Results from serum Assay		Tmax (hours)	Half-life (hours)3	Bioavailability4
	No serum	+10% serum	Dilution factor1	Cmax (μg/mL) Approximate drug concentration in mouse serum2
INH	0.041	0.12	>1:320	>38.4	ND	ND	High
2.HCl	0.041	0.12	1:40–1:80	7.2	0.5	4.9	Medium
4a	0.041	0.2	1:10–1:20	3	ND	ND	Medium
4b.HCl	0.041	0.12	1:10–1:40	2.4	0.5	3.5	Low
4c.HCl	0.014	0.014	1:80–1:160	2.24	0.5	1.1	High
4f.HCl	0.014	0.041	1:40	1.64	0.5	1.3	Medium
4g	0.041	0.2	1:20–1:40	6	ND	ND	High
4h	0.014	0.041	1:20–1:40	0.82	ND	ND	Low
4k.HCl	0.041	0.041	1:40–1:80	3.28	0.5	1.3	Medium
5a	0.014	0.041	1:40	1.64	ND	ND	Medium
5b.HCl	0.37	0.37	1:10–1:80	7.4	0.5	3.5	Low

¹The dilution factor represents the last dilution step of the serum samples in which drug activity was still observed in the bioassay

²Drug levels in the mouse serum are estimated by multiplying the dilution factor by the MIC value of the drug in the presence of 10% serum;

³Estimated based on graph of concentration vs. time curve;

⁴Bioavailability factor (BF) = Cmax/MIC in presence of serum; Bioavailability: Low = BF 1–20; Medium = BF 21–80; High = BF >80 30

Table 5.

Viable number of M. tuberculosis bacilli in the lungs of infected mice after 9 days of drug treatment (SEM= standard error).

Compound	Lungs (Log10CFU +/−SEM)	Log10 reduction untreated	CPU versus controls
2	7.46 +/− 0.25	1.04
4c	7.92 +/− 0.27	0.58
4h	7.53 +/− 0.14	0.97
5a	7.65 +/− 0.11	0.85
INH	3.88 +/− 0.36	4.62

In this rapid mouse model, the compounds were administered via oral gavage for nine consecutive days at 300 mg/kg. Four compounds gave a significant reduction of the bacterial load in the lungs (Table 5) and in spleen (results not shown) (P > 0.05). The bacterial numbers in the lung were reduced between 0.5 and 1.04 Log₁₀ CFU (up to 90% killing of the bacterial load). The control drug isoniazid (INH) at 25 mg/kg reduced the bacterial load in this experiment with 4.62 Log₁₀CFU in the lungs.

Discussion

In this study we detail the synthesis and evaluation of an advanced series of nitrofuranyl amides. The compounds were produced in good yields and the synthesis offered no barrier to scale-up synthesis for larger quantities required for in vivo testing. The compounds were tested for MIC activity against M. tuberculosis and clear structure-activity relationships were observed for this series. The substituted benzyl series had much greater antituberculosis activity than the substituted phenyl series. In both the phenyl and the benzyl amides, para-substitution with the cyclic secondary amine produced better antituberculosis activity. Compounds from the benzyl series are extremely potent and are the most active compounds developed in this class to date. Among them, 4c with benzyl-piperazine at para-position is the most active compound with an MIC value of 0.0125 μg/mL against M. tuberculosis H₃₇Rv. The addition of a fluorine to the meta position of the benzyl ring of 4c produced 5a which also had excellent activity (0.025 μg/mL)

The in vivo testing shed new light on the relative bioavailability of compounds in this series. It was noted that while some compounds in this series were well absorbed, the compounds appear to be rapidly eliminated with short half lives, as was seen for the compound with best in vitro activity 4c (T_1/2 1.1hrs). 4c contains both an amide and benzyl piperazine bonds, both likely candidates for rapid metabolism. It is our current hypothesis that rapid degradation is limiting the in vivo efficacy. Current studies are ongoing to understand the metabolism and distribution of this series and to design a new generation of compounds with a longer serum half life to retain potent antituberculosis activity.

Experimental

All the anhydrous solvents and starting materials were purchased from Aldrich Chemical Company (Wilwaukee, WI). All reagent grade solvents used for chromatography were purchased from Fisher Scientific (Suwanee, GA) and Flash column chromatography silica cartridges were obtained from Biotage Inc. (Lake Forest, VA). The reactions were monitored by thin layer chromatography (TLC) on pre-coated Merck 60 F₂₅₄ silica gel plates and visualized using UV light (254 nm). A Biotage FLASH 25+ column chromatography system was used to purify mixtures. All ¹H and ¹³C NMR spectra were recorded on a Bruker ARX-300 (300 and 75 MHz for ¹H and ¹³C NMR, repectively) or Varian INOVA-500 (500 and 125 MHz for ¹H and ¹³C NMR, respectively) spectrometers. Chemical shifts (δ) are reported in ppm relative to the residual solvent peak or internal standard (tetramethylsilane), and coupling constants (J) are reported in hertz (Hz). Mass spectra were recorded on a Bruker Esquire LCMS using ESI. Purity of the final products was confirmed before testing by analytical HPLC using an Alltech platinum C-18 reverse phase column (4.5×150mm) and an H₂O (0.1% TFA) to acetonitrile 0–100% linear gradient at a flow rate of 1.0 mL min⁻¹ and UV detection at 254nm.

General Procedure I: for preparation of 12a–j and 14a–h: Secondary amine (2 eq) was added to a mixture of substituted fluoro benzene (1 eq.) and K₂CO₃ (1.5 eq.) in dimethyl sulfoxide (7 mL/g). The reaction mixture was stirred at 90° C and followed by TLC. After completion of the reaction, the mixture was diluted with ethyl acetate (60 mL/g), and washed with water (2 × 50 mL/g), followed by brine (50 mL/g). The ethyl acetate fraction was dried over Na₂SO₄ and concentrated. The crude products were purified by flash column chromatography to afford pure products.

1-Benzyl-4-(4-nitro-phenyl)-piperazine (12c)

1-Benzyl piperazine (1.04 mL, 6.02 mmol) was added to a mixture of 4-fluoro nitro benzene 6 (425 mg, 3.01 mmol) and K₂CO₃ (623 mg, 4.52 mmol) in dimethyl sulfoxide (3 mL) and the reaction continued as described in general procedure I to afford 805 mg of amine 12c in 90% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.59 (4Hs, t, J = 4.88 Hz), 3.42 (4Hs, t, J = 5.12 Hz), 3.57 (2Hs, s), 6.81 (2Hs, d, J = 7.32 Hz), 7.29 (1H, sextet, J = 1.22 Hz), 7.34 (4Hs, d, J = 7.39 Hz), 8.12 (2Hs, d, J = 7.32 Hz); ESI-MS: 298.2 (M+1).

4-Benzyl-1-(4-nitro-phenyl)-piperidine (12d)

4-Benzyl piperidine (1.06 mL, 6.02 mmol) was added to a mixture of 4-fluoro nitro benzene 6 (425 mg, 3.01 mmol) and K₂CO₃ (623 mg, 4.52 mmol) in dimethyl sulfoxide (3 mL) and the reaction continued as described in general procedure I to afford 847 mg of amine 12d in 95% yield. ¹H-NMR (500 MHz, CDCl₃): δ 1.33 (2Hs, dq, J = 3.9, 12.45 Hz), 1.74–1.88 (3Hs, m), 2.57 (2Hs, d, J = 6.83 Hz), 2.91 (2Hs, t, J = 15.13 Hz), 3.93 (2Hs, d, J = 13.18 Hz), 6.78 (2Hs, d, J = 9.52 Hz), 7.15 (2Hs, d, J = 7.08 Hz), 7.22 (1H, t, J = 7.32 Hz), 7.30 (2Hs, t, J = 7.56 Hz), 8.1 (2Hs, d, J = 9.52 Hz); ESI-MS: 319.1 (M+23).

4-(3-Nitro-phenyl)-morpholine (12f)

Morpholine (0.52 mL, 6.02 mmol) was added to a mixture of 3-fluoro nitro benzene 7 (425 mg, 3.01 mmol) and K₂CO₃ (623 mg, 4.52 mmol) in dimethyl sulfoxide (3 mL) and the reaction continued as described in general procedure I to afford 589 mg of amine 12f in 94% yield. ¹H-NMR (300 MHz, CDCl₃): δ 3.27 (4Hs, t, J = 4.83 Hz), 3.9 (4Hs, t, J = 4.95 Hz), 7.21 (1H, ddd, J = 1.03, 2.25, 9.06 Hz), 7.42 (1H, t, J = 8.19 Hz), 7.68–7.76 (2Hs, m); ESI-MS: 231.0 (M+23).

1-Methyl-4-(3-nitro-phenyl)-piperazine (12g)

1-Methyl piperazine (0.66 mL, 6.02 mmol) was added to a mixture of 3-fluoro nitro benzene 7 (425 mg, 3.01 mmol) and K₂CO₃ (623 mg, 4.52 mmol) in dimethyl sulfoxide (3 mL) and the reaction continued as described in general procedure I to afford 619 mg of amine 12g in 93% yield. ¹H-NMR (300 MHz, CDCl₃): δ 2.38 (3Hs, s), 2.6 (4Hs, t, J = 5.0 Hz), 3.32 (4Hs, t, J = 5.14 Hz), 7.2 (1H, dd, J = 2.16, 8.26 Hz), 7.39 (1H, t, J = 8.14 Hz), 7.67 (1H, dd, J = 1.43, 8.01 Hz); ESI-MS: 222.4 (M+1).

General Procedure II: for preparation of 13a–j, except 13c and 13h

The substituted nitro compound (1 eq. in a mixture of methanol-ethyl acetate, 1:2, 20 mL) was treated with 10% Pd-carbon (5% w/w). The reaction was subjected to hydrogenation under 50 Psi hydrogen gas pressure at room temperature and the reaction was monitored by TLC. After completion of the reaction, the mixture was filtered thorough a celite bed and concentrated in a vacuum to afford pure product in quantitative yields.

4-(4-Benzyl-piperidin-1-yl)-phenylamine (13d)

4-Benzyl-1-(4-nitro-phenyl)-piperidine 12d, (600 mg, 2.02 mmol) was treated with 10% Pd-carbon (5% w/w) under the conditions described in general procedure II to afford amine 13d in quantitative yield. ¹H-NMR (500 MHz, CD₃OD): δ 1.44 (2Hs, q, J = 9.27, 21.23 Hz), 1.6–1.7 (1H, m), 1.75 (1H, d, J = 12.2 Hz), 2.55 (2Hs, t, J = 11.47 Hz), 2.6 (2Hs, d, J = 7.08 Hz), 3.39 (2Hs, d, J = 11.23 Hz), 6.71 (2Hs, d, J = 7.81 Hz), 6.87 (2Hs, d, J = 8.05 Hz), 7.16–7.21 (3Hs, m), 7.28 (2Hs, t, J = 7.07 Hz); ESI-MS: 267.1 (M+1).

3-Morpholin-4-yl-phenylamine (13f)

4-(3-Nitro-phenyl)-morpholine 12f, (600 mg, 2.88 mmol) was treated with 10% Pd-carbon (5% w/w) under the conditions described in general procedure II to afford amine 13f in quantitative yield. ¹H-NMR (300 MHz, CDCl₃): δ 3.145 (4Hs, t, J = 4.79 Hz), 3.86 (4Hs, t, J = 4.89 Hz), 6.24–6.29 (2Hs, m), 6.37 (1H, ddd, J = 0.73, 2.21, 8.20 Hz), 7.08 (1H, t, J = 8.28); ESI-MS: 201.3 (M+23).

3-(4-Methyl-piperazin-1-yl)-phenylamine (13g)

1-Methyl-4-(3-nitro-phenyl)-piperazine 12g, (600 mg, 2.71 mmol) was treated with 10% Pd-carbon (5% w/w) under the conditions described in general procedure II to afford amine 13g in quantitative yield. ¹H-NMR (300 MHz, CDCl₃): δ 2.36 (3Hs, s), 2.57 (4Hs, t, J = 4.94 Hz), 3.2 (4Hs, t, J = 5.11 Hz), 3.59–3.67 (2Hs, bs), 6.22 (1H, dd, J = 2.07, 8.41 Hz), 6.28 (1H, t, J = 2.21 Hz), 6.39 (1H, dd, J = 1.89, 7.82 Hz), 7.06 (1H, t, J = 8.02 Hz); ESI-MS: 192.1 (M+1).

General Procedure III: For preparation of 13c and 13h

SnCl₂.H₂O (1.125 g/mmol) was added to a solution of the substituted nitro benzene in ethyl acetate (10 mL/mmol). The solution was refluxed for 2 hours. The cooled solution was diluted with water and the pH was adjusted to 8 by addition of a saturated NaHCO₃ solution. The aqueous phase was extracted with EtOAc (3 × 75 mL) and the combined organic extracts were thoroughly washed with brine and dried over Na₂SO₄. The products obtained after the removal of the solvent were used without further purification.

4-(4-Benzyl-piperazin-1-yl)-phenylamine (13c)

1-Benzyl-4-(4-nitro-phenyl)-piperazine 12c (750 mg, 2.52 mmol) was treated with SnCl₂.H₂O (14.4 g, 63.9 mmol) under the conditions described in general procedure III to afford 552 mg of amine 13c in 82% yield. ¹H-NMR (300 MHz, CDCl₃): δ 2.6–2.8 (4Hs, bs), 3.11 (4Hs, t, J = 4.38 Hz), 3.64 (2Hs, s), 6.66 (2Hs, d, J = 8.76 Hz), 6.82 (2Hs, d, J = 8.76 Hz), 7.25–7.45 (5Hs, m); ESI-MS: 268.2 (M+1).

General Proceure IV: For preparation of 2 and 3a–j

5-Nitro-furan-2-carbonyl chloride (438 mg, 2.5 mmol) in CH₂Cl₂ (10 mL) was added to a mixture of amine (2.0 mmol) in Et₃N (1.04 mL, 7.5 mmol). The mixture was stirred for 12 hrs at room temperature and was followed by TLC. After completion of reaction, 100 mL of ethyl acetate was added to the reaction mixture, and it was sequentially washed with saturated aq. NaHCO₃ (2 × 50 mL), water (2 × 50 mL) and brine (2 × 50 mL). The organic phase was dried over Na₂SO₄, filtered, concentrated and purified by flash column chromatography to provide the corresponding pure amides.

5-Nitro-furan-2-carboxylic acid [4-(4-benzyl-piperazin-1-yl)-phenyl]-amide (3c)

5-Nitro-furan-2-carbonyl chloride (438 mg, 2.5 mmol) in CH₂Cl₂ (10 mL) was added to amine 13c (534 mg, 2.0 mmol) in Et₃N (1.04 mL, 7.5 mmol) and the reaction continued as described in general procedure IV to afford 755 mg of amide 3c in 93% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.66–2.76 (4Hs, bs), 3.26–3.33 (4Hs, bs), 3.64–3.7 (2Hs, bs), 7.99 (2Hs, d, J = 9.03 Hz), 7.32–7.37 (2Hs, m), 7.38–7.46 (4Hs, m), 7.47 (1H, d, J = 3.90), 7.61 (2Hs, d, J = 9.03 Hz), 8.14 (1H, bs); ¹³C-NMR (300 MHz, CDCl₃-DMSO-D₆, 5:1): 48.13, 51.98, 61.85, 111.94, 114.87, 114.91, 121.36, 126.12, 127.29, 128.12, 128.67, 137.17, 147.65, 148.11, 150.69, 153.39; ESI-MS: 407.5 (M+1). Anal. (C₂₂H₂₂N₄O₄) C, H, N.

5-Nitro-furan-2-carboxylic acid [4-(4-benzyl-piperidin-1-yl)-phenyl]-amide (3d)

5-Nitro-furan-2-carbonyl chloride (438 mg, 2.5 mmol) in CH₂Cl₂ (10 mL) was added to a mixture of amine 13d (532 mg, 2.0 mmol) in Et₃N (1.04 mL, 7.5 mmol) and the reaction continued as described in general procedure IV to afford 728 mg of amide 3d in 90% yield. ¹H-NMR (500 MHz, CDCl₃): δ 1.50–1.65 (3Hs, m), 1.65–1.85 (2Hs, m), 2.6–2.8 (4Hs, m), 3.68 (2Hs, d, J = 10.98 Hz), 6.9–7.02 (2Hs, bs), 7.2–7.3 (3Hs, m), 7.3–7.39 (2Hs, m), 7.41 (1H, d, J = 3.66), 7.47 (1H, t, J = 2.1, 3.6), 7.515–7.65 (2Hs, bs), 8.12–8.22 (1H, bs); ¹³C-NMR 300 MHz, (CDCl₃): 31.37, 37.26, 42.58, 49.36, 112.13, 115.74, 116.16, 121.15, 125.38, 127.34, 127.70, 128.59, 139.84, 147.74, 149.11, 153.06; ESI-MS: 406.4 (M+1); Anal. (C₂₃H₂₃N₃O₄) C, H, N.

5-Nitro-furan-2-carboxylic acid (3-morpholin-4-yl-phenyl)-amide (3f)

5-Nitro-furan-2-carbonyl chloride (438 mg, 2.5 mmol) in CH₂Cl₂ (10 mL) was added to a mixture of amine 13f (356 mg, 2.0 mmol) in Et₃N (1.04 mL, 7.5 mmol) and the reaction continued as described in general procedure IV to afford 494 mg of amide 3f in 78% yield. ¹H-NMR (500 MHz, CDCl₃): δ 3.23 (4Hs, t, J = 4.63 Hz), 3.89 (4Hs, t, J = 4.88 Hz), 6.77 (1H, dd, J = 2.19, 8.3 Hz), 7.1 (1H, dd, J = 1.46, 7.81 Hz), 7.30 (1H, t, J = 8.05 Hz), 7.38 (1H, d, J = 3.66 Hz), 7.46–7.5 (2Hs, m), 8.20 (1H, bs); ¹³C-NMR (300 MHz, CDCl₃): 51.75, 69.37, 110.78, 114.99, 115.26, 115.31, 119.17, 132.16, 140.47, 150.80, 154.44, 157.39; ESI-MS: 318.3 (M+1); Anal. (C₁₅H₁₅N₃O₅) C, H, N.

5-Nitro-furan-2-carboxylic acid [3-(4-methyl-piperazin-1-yl)-phenyl]-amide (3g)

5-Nitro-furan-2-carbonyl chloride (438 mg, 2.5 mmol) in CH₂Cl₂ (10 mL) was added to a mixture of amine 13g (382 mg, 2.0 mmol) in Et₃N (1.04 mL, 7.5 mmol) and the reaction continued as described in general procedure IV to afford 593 mg of amide 3g in 90% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.38 (3Hs, s), 2.60 (4Hs, t, J = 4.64 Hz), 3.28 (4Hs, t, J = 4.51 Hz), 6.8 (1H, d, J = 8.3 Hz), 7.08 (1H, d, J = 8.05 Hz), 7.25–7.32 (2Hs, m), 7.37–7.45 (2Hs, m), 7.48 (1H, dd, J = 1.22, 3.66 Hz), 8.17 (1H, bs); ¹³C-NMR (300 MHz, CD₃OD): 44.16, 47.92, 53.98, 107.99, 111.48, 111.70, 112.26, 115.49, 128.50, 137.57, 147.55, 151.16, 154.73; ESI-MS: 331.3 (M+1). Anal. (C₁₆H₁₈N₄O₄) C, H, N.

4-(4-Methyl-piperazin-1-yl)-benzonitrile (14b)

1-Methyl piperazine (1.36 mL, 12.38 mmol) was added to a mixture of 4-fluoro-benzonitrile 8 (1.0 g, 8.25 mmol) and K₂CO₃ (2.27 mg, 16.51 mmol) in dimethyl sulfoxide (7 mL) and the reaction continued as described in general procedure I to afford amine 1.54 g of 14b in 93% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.36 (3Hs, s), 2.55 (4Hs, t, J = 4.88 Hz), 3.35 (4Hs, t, J = 4.88 Hz), 6.87 (2Hs, d, J = 8.78 Hz), 7.49 (2Hs, d, J = 8.78 Hz); ESI-MS: 202.1 (M+1).

3-(4-Benzyl-piperidin-1-yl)-benzonitrile (14g)

1-Methyl piperazine (2.17 mL, 12.38 mmol) was added to a mixture of 3-fluoro-benzonitrile 9 (1.0 g, 8.25 mmol) and K₂CO₃ (2.27 mg, 16.51 mmol) in dimethyl sulfoxide (7 mL) and the reaction continued as described in general procedure I to afford amine 2.05 g of 14g in 90% yield. ¹H-NMR (500 MHz, CDCl₃): δ 1.43 (2Hs, dq, J = 3.9, 12.45 Hz), 1.73–1.86 (3Hs, m), 2.65 (2Hs, d, J = 6.83 Hz), 2.88 (2Hs, dt, J = 2.68, 12.45 Hz), 3.73 (2Hs, d, J = 12.45 Hz), 7.1 (1H, td, J = 0.97, 7.56 Hz), 7.14–7.17 (2Hs, m), 7.22 (2Hs, d, J = 6.83 Hz), 7.27 (1H, t, J = 7.32 Hz), 7.34–7.38 (3Hs, m); ESI-MS: 299.5 (M+23).

4-Thiomorpholin-4-yl-benzonitrile (14h)

Thio morpholine (2.35 mL, 24.79 mmol) was added to a mixture of 4-fluoro-benzonitrile 8 (2.0 g, 16.52 mmol) and K₂CO₃ (4.56 mg, 33.05 mmol) in dimethyl sulfoxide (10 mL) and the reaction continued as described in general procedure I to afford amine 2.93 g of 14h in 87% yield. ¹H-NMR (300 MHz, CDCl₃): δ 2.71 (4Hs, t, J = 5.07 Hz), 3.78 (4Hs, t, J = 5.11 Hz), 6.82 (2Hs, d, J = 9.0 Hz), 7.51 (2Hs, d, J = 9.05 Hz); ESI-MS: 227.4 (M+23).

General Procedure V: Preparation of (4a–l) and (5a–e)

(a) 65% Red-Al in toluene was added drop wise to a mixture of nitrile in THF (5 mL) at 0° C while stirring under argon atmosphere. After, the reaction was stirred for 3 hrs at room temperature; it was quenched by adding 5 mL water, drop wise, at 0° C. The reaction mixture was then filtered through a celite bed, washed with THF, and the combined fractions were concentrated under vacuum. The resulting crude mixture was used in further reactions without further purification and characterization. (b) 5-Nitro-furan-2-carbonyl chloride was added to the crude amine in THF and Et₃N. The mixture was stirred for 12 hrs at room temperature and was followed by TLC After completion of reaction, 100 mL of ethyl acetate was added to the reaction mixture, and it was sequentially washed with saturated aq. NaHCO₃ (2 × 50 mL), water (2 × 50 mL) and brine (2 × 50 mL). The organic phase was dried over Na₂SO₄, filtered, concentrated and purified by flash column chromatography to provide the corresponding pure amides.

5-Nitro-furan-2-carboxylic acid 4-(4-methyl-piperazin-1-yl)-benzylamide (4b)

65% Red-Al in toluene (5.79 mL, 18.6 mmol) was reacted with nitrile 14b (1.25 g, 6.21 mmol) as described in general procedure V(a) to yield a crude amine mixture. 5-Nitro-furan-2-carbonyl chloride (1.63 mg, 9.29 mmol) was added to the crude amine in THF (10 mL) and Et₃N (2.58 mL, 18.58 mmol). The reaction was then carried out as described in general procedure V(b) to afford 1.49 g of amide 4b in 70% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.41 (3Hs, s), 2.63 (4Hs, t, J = 4.88 Hz), 3.27 (4Hs, t, J = 4.88 Hz), 4.6 (2Hs, d, J = 5.61 Hz), 6.78–6.83 (1H, bs), 6.97 (2Hs, d, J = 8.78 Hz), 7.31 (2Hs, d, J = 8.78 Hz), 7.33 (1H, d, J = 3.90 Hz), 7.41 (1H, d, J = 3.90 Hz); ¹³C-NMR (300 MHz, CDCl₃): 41.71, 44.02, 48.06, 53.94, 111.31, 114.88, 115.52, 127.89, 128.91, 147.54, 149.95, 156.61; ESI-MS: 345.3 (M+1); Anal. (C₁₇H₂₀N₄O₄) C, H, N.

5-Nitro-furan-2-carboxylic acid 3-(4-benzyl-piperidin-1-yl)-benzylamide (4g)

65% Red-Al in toluene (3.81 mL, 12.28 mmol) was reacted with nitrile 14g (1.13 g, 4.09 mmol) as described in general procedure V(a) to yield a crude amine mixture. 5-Nitro-furan-2-carbonyl chloride (1.06 g, 6.1 mmol) was added to the crude amine in THF (10 mL) and Et₃N (1.7 mL, 12.28 mmol), and the reaction was carried out as described in general procedure V(b) to afford 1.42 g of amide 4g in 83% yield. ¹H-NMR (500 MHz, CDCl₃): δ 1.44 (2Hs, dq, J = 3.66, 11.71, 23.92 Hz), 1.68–1.77 (1H, m), 1.78 (2Hs, d, J = 13.18 Hz), 2.62 (2Hs, d, J = 2.83 Hz), 2.7 (2Hs, dt, J = 2.19, 12.20 Hz), 3.72 (2Hs, d, J = 12.45 Hz), 4.61 (2Hs, d, J = 5.61 Hz), 6.81–6.88 (2Hs, m), 6.9–6.94 (2Hs, m), 7.21 (2Hs, d, J = 7.07 Hz), 7.22–7.36 (5Hs, m), 7.40 (1H, d, J = 3.66 Hz); ¹³C-NMR (300 MHz, CDCl₃): 31.41, 37.30, 42.57, 43.54, 49.17, 111.84, 115.27, 115.48, 118.09, 125.28, 127.70, 128.59, 129.10, 137.20, 139.85, 147.52, 151.74, 155.52; ESI-MS: 420.4 (M+1); Anal. (C₂₄H₂₅N₃O₄) C, H, N.

5-Nitro-furan-2-carboxylic acid 4-thiomorpholin-4-yl-benzylamide (4h)

65% Red-Al in toluene (6.84 mL, 22.02 mmol) was reacted with nitrile 14h (1.5 g, 7.32 mmol) as described in general procedure V(a) to yield a crude amine mixture. 5-Nitro-furan-2-carbonyl chloride (1.92 mg, 11.02 mmol) was added to the crude amine in THF (10 mL) and Et₃N (3.0 mL, 21.92 mmol), and reaction was carried out as described in general procedure V(b) to afford 1.96 g of amide 4h in 79% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.75–2.82 (4Hs, m), 3.61–3.64 (4Hs, m), 4.6 (2Hs, d, J = 5.85 Hz), 6.8–6.85 (1H, bs), 6.93 (2Hs, d, J = 8.78 Hz), 7.31 (2Hs, d, J = 8.78 Hz), 7.33 (1H, d, J = 3.66 Hz), 7.41 (1H, d, J = 3.66 Hz); ¹³C-NMR (300 MHz, CDCl₃): 26.04, 42.6, 51.37, 111.86, 115.42, 116.55, 127.26, 128.82, 147.57, 150.33, 155.48; ESI-MS: 346.0 (M+1).

4-(4-Cyclopropylmethyl-piperazin-1-yl)-benzonitrile (16)

Bromomethyl-cyclopropane (0.64 mL, 6.63 mmol) was added drop wise to a mixture of 4-piperazin-1-yl-benzonitrile (1 g, 4.42 mmol) and K₂CO₃ (915 mg, 6.63 mmol) in dry N,N-dimethylformamide (5 mL), under argon atmosphere at 0° C. The reaction mixture was stirred at room temperature for 12 h, diluted with water (50 mL) and extracted with ethyl acetate (3 × 40 mL). The combined organic fractions were washed with saturated brine (50 mL) and dried over Na₂SO₄ followed by solvent evaporation under vacuum which gave the crude product. The crude product was subsequently purified by column chromatography (4:1 petroleum ether: ethyl acetate) to afford 991 mg of product 16 (93% yield). ¹H-NMR (500 MHz, CDCl₃): δ0.01 (2Hs, q, J = 4.63 Hz), 0.43 (2Hs, q, J = 5.85 Hz), 0.73 (1H, m), 2.19 (2Hs, d, J = 6.59 Hz), 2.54 (4Hs, t, J = 5.51 Hz), 3.23 (4Hs, t, J = 5.12 Hz), 6.74 (2Hs, d, J = 9.03 Hz), 7.37 (2Hs, d, J = 9.03 Hz), 7.89 (1H, bs); ESI-MS: 242.5 (M+1).

5-Nitro-furan-2-carboxylic acid 4-(4-cyclopropylmethyl-piperazin-1-yl)-benzylamide (4k)

65% Red-Al in toluene (3.09 mL, 9.9 mmol) was reacted with nitrile 16 (800 mg, 3.3 mmol) as described in general procedure V(a) to yield a crude amine mixture. 5-Nitro-furan-2-carbonyl chloride (873 mg, 4.9 mmol) was added to the crude amine and Et₃N (1.3 mL, 9.9 mmol) in CH₂Cl₂ (10 mL), and the reaction was carried out as described in general procedure V(b) to afford mg of amide 4k in 82% yield. ¹H-NMR (500 MHz, CDCl₃): δ0.0 – 0.04 (2Hs, m), 0.38 – 0.45 (2Hs, m), 0.74 – 0.82 (1H, m), 2.19 (2Hs, d, J = 6.34 Hz), 2.56 (4Hs, t, J = 5.12 Hz), 3.07 (1H, t, J = 5.12 Hz), 3.11 (3Hs, t, J = 5.12 Hz), 4.42 (2Hs, d, J = 5.85 Hz), 6.62 – 6.68 (1H, bs), 6.8 (2Hs, d, J = 8.54 Hz), 7.12 (2Hs, d, J = 8.54 Hz), 7.13 (1H, d, J = 3.66 Hz), 7.23 (1H, d, J = 3.66 Hz); ¹³C-NMR (300 MHz, CDCl₃): 2.94, 4.42, 41.63, 46.0, 50.83, 60.72, 111.35, 114.89, 116.05, 128.05, 130.25, 147.49, 148.56, 156.68; ESI-MS: 385.6 (M+1).

5-Nitro-furan-2-carboxylic acid 4-(1-oxo-1λ⁴-thiomorpholin-4-yl)-benzylamide (4i) and 5-Nitrofuran-2-carboxylic acid 4-(1,1-dioxo-1 λ⁶-thiomorpholin-4-yl)-benzylamide (4j)

A mixture of compound 4k (1 g, 2.87 mmol) and NaHCO₃ (1.2 g, 14.39 mmol) in CH₂Cl₂ (10 mL) at 0° C was treated with m-chloroperbenzoicacid (1.29 g, 5.75 mmol) and stirred at room temperature for 30 min. The reaction mixture was quenched with 10% aqueous NH₄OH solution (10 mL) and diluted with CH₂Cl₂ (30 mL). The organic layer was washed with 10% aqueous NH₄OH solution (30 mL), water (30 mL), brine (30 mL), and dried over Na₂SO₄. The organic solution was concentrated in a vacuum followed by flash column purification with petroleum ether and ethyl acetate in 5:1 ratio, which afforded 261 mg of 4i and 173 mg of 4j in 25% and 15% yields respectively. 4i: ¹H-NMR (500 MHz, CDCl₃): δ 2.87 – 2.99 (4Hs, m), 3.63 (2Hs, td, J = 3.66, 14.89 Hz), 4.04 (2Hs, dt, J = 2.68, 13.82 Hz), 4.6 (2Hs, d, J = 5.85 Hz), 6.98 (3Hs, d, J = 8.54 Hz), 7.32 – 7.36 (3Hs, m), 7.41 (2Hs, d, J = 3.66 Hz); ¹³C-NMR (300 MHz, CDCl₃): 40.31, 42.49, 43.92, 111.89, 115.49, 116.09, 128.1, 129.04, 147.56, 148.48, 155.53; ESI-MS: 386.1 (M+23); 4j: ¹H-NMR (300 MHz, CDCl₃): δ3.12 (4Hs, t, J = 5.43 Hz), 3.88 (4Hs, t, J = 5.28 Hz), ), 4.57 (2Hs, d, J = 5.9 Hz), 6.81 – 6.90 (1H, bs), 6.92 (2Hs, d, J = 8.71 Hz), 7.27 – 7.36 (3Hs, m), 7.38 (2Hs, d, J = 3.79 Hz); ¹³C-NMR (300 MHz, CDCl₃): 42.41, 47.08, 49.98, 111.86, 115.56, 116.04, 128.71, 129.25, 146.89, 147.41, 155.52; ESI-MS: 402.2 (M+1).

5-Nitro-furan-2-carboxylic acid 4-hydroxymethyl-benzylamide (18)

Acid chloride 11 in CH₂Cl₂ (10 mL) was added to (4-aminomethyl-phenyl)-methanol 17 (200 mg, 1.45 mmol) in Et₃N (205 μL). The reaction mixture was stirred for 14 hrs at room temperature. After completion of the reaction, 100 mL of ethyl acetate was added and washed sequentially with 10% aqueous NaHCO₃ (2 × 50 mL), water (2 × 50 mL) and brine (2 × 50 mL). The organic phase was dried over Na₂SO₄, filtered and concentrated followed by flash column purification to yield 260 mg (65%) of compound 18; TLC: R_f 0.5 (ethyl acetate); ¹HNMR (500 MHz, CDCl₃): δ 4.6 (2H, d, J = 5.85 Hz), 4.68 (2H, s), 7.15–7.25 (1H, bs), 7.27–7.29 (1H, m), 7.3–7.36 (4H, m), 7.37 (1H, d, J = 2.68 Hz); ESI-MS, m/z: 275 (M−1).

5-Nitro-furan-2-carboxylic acid 4-[(4-methyl-piperazin-1-ylimino)-methyl]-benzylamide (4l)

Pyridine (175 μL) was added to alcohol 18 (120 mg, 0.434 mmol) in CH₂Cl₂ (10 mL) followed by Dess-Martin periodinane reagent (184 mg, 0.434 mmol). The resulting reaction mixture was stirred at room temperature for two hours and was quenched with aqueous NaHCO₃. The reaction mixture was extracted with CH₂Cl₂, dried over Na₂SO₄, and concentrated under vacuum to give 80 mg of the corresponding aldehyde (5-nitro-furan-2-carboxylic acid 4-formyl-benzylamide). 4-Methyl-piperazin-1-ylamine (36 μL, 0.291 mmol) was added to the crude aldehyde (80 mg, 0.291 mmol) in 10 mL ethanol. The reaction mixture was refluxed for an hour, then stirred at room temperature for 14 hrs. The reaction mixture was concentrated in vacuum, column purified and recrystallized to yield 80 mg (74%) of compound 4l; TLC: R_f 0.4 (9:1 chloroform: methanol); ¹HNMR (500 MHz, CDCl₃): δ 2.38 (3H, s), 2.58–2.72 (4H, bs), 3.32–3.19 (4H, bs), 4.64 (2H, d. J = 5.85 Hz), 6.82–6.88 (1H, bs), 7.31 (1H, d, J = 3.66 Hz), 7.34 (2H, d, J = 8.3 Hz), 7.38 (1H, d, J = 3.66 Hz), 7.54 (1H, s), 7.61 (2H, d, J = 8.05 Hz); ¹³CNMR (300 MHz, CDCl₃): 42.84, 45.39, 50.39, 53.92, 111.82, 115.65, 125.98, 127.66, 134.31, 135.65, 136.11, 147.4, 155.59; ESI-MS, m/z: 372.1 (M+1).

General procedure VI: For preparation of 19a–e

Secondary amine (1 eq.) was added to a mixture of 3,4-difluoro-benzonitrile (1 eq.) and K₂CO₃ (1.5 eq.) in dimethyl sulfoxide (7 mL/g). The reaction mixture was stirred at 90° C and followed by TLC. After completion of the reaction, the mixture was diluted with ethyl acetate (60 mL/g), and washed with water (2 × 50 mL/g), followed by brine (50 mL/g). The ethyl acetate fraction was dried over Na₂SO₄ and concentrated. The crude products were purified by flash column chromatography to afford pure products.

4-(4-Benzyl-piperazin-1-yl)-3-fluoro-benzonitrile (19a)

1-Benzyl piperazine (1.25 mL, 7.19 mmol) was added to a mixture of 3,4-difluoro-benzonitrile 10 (1.0 g, 7.19 mmol) and K₂CO₃ (1.48 g, 10.78 mmol) in dimethyl sulfoxide (7 mL) and the reaction continued as described in general procedure VI to afford amine 1.86 g of 19a in 88% yield. ¹H-NMR (300 MHz, CDCl₃): δ 2.64 (4Hs, t, J = 4.84 Hz), 3.25 (4Hs, t, J = 4.8 Hz), 3.59 (2Hs, s), 6.92 (1H, t, J = 8.54 Hz), 7.25–7.42 (7Hs, m); ESI-MS: 296.4 (M+1).

3-Fluoro-4-thiomorpholin-4-yl-benzonitrile(19c)

Thiomarpholine (0.68 mL, 7.19 mmol) was added to a mixture of 3,4-difluoro-benzonitrile 10 (1.0 g, 7.19 mmol) and K₂CO₃ (1.48 g, 10.78 mmol) in dimethyl sulfoxide (7 mL) and the reaction continued as described in general procedure VI to afford amine 1.2 g of 19c in 81% yield. ¹H-NMR (300 MHz, CDCl₃): δ2.8 (4Hs, t, J = 5.06 Hz), 3.5 (4Hs, t, J = 5.12 Hz), 6.94 (1H, t, J = 8.51 Hz), 7.28 (1H, dd, J = 1.92, 12.35 Hz), 7.37 (1H, ddd, J = 0.86, 1.86, 8.38 Hz); ESI-MS: 245.5 (M+23).

5-Nitro-furan-2-carboxylic acid 4-(4-benzyl-piperazin-1-yl)-3-fluoro-benzylamide (5a)

65% Red-Al in toluene (3.15 mL, 10.15 mmol) was reacted with nitrile 19a (1 g, 3.38 mmol) as described in general procedure V(a). 5-Nitro-furan-2-carbonyl chloride (1.12 g, 6.75 mmol) was added to the crude amine and Et₃N (1.4 mL, 10.15 mmol) in THF (10 mL), and the reaction was carried out as described in general procedure V(b) to afford 1.21 g of amide 5a in 82% yield. ¹H-NMR (500 MHz, CDCl₃): δ2.74 – 2.82 (4Hs, m), 3.09 – 3.18 (4Hs, m), 3.62 (2Hs, s), 4.59 (2Hs, d, J = 5.85 Hz), 6.85 – 6.9 (1H, bs), 6.96 (1H, t, J = 8.3 Hz), 7.08 (2H, dt, J = 1.95, 12.93 Hz), 7.3 – 7.42 (7Hs, m); ¹³C-NMR (300 MHz, CDCl₃): 42.22, (49.91, 49.95), 52.54, 62.53, 111.83, 115.23, (115.51, 115.62), (118.56, 118.61), (123.5, 123.54), 126.6, 127.72, 128.69, (130.53, 130.62), 137.41, 147.34, 153.4, 155.55, 156.68; ESI-MS: 437.1 (M−1).

5-Nitro-furan-2-carboxylic acid 3-fluoro-4-thiomorpholin-4-yl-benzylamide (5c)

65% Red-Al in toluene (4.14 mL, 13.49 mmol) was reacted with nitrile 19c (1 g, 4.49 mmol) as described in general procedure V(a) to yield a crude amine mixture. 5-Nitro-furan-2-carbonyl chloride (1.5 g, 8.99 mmol) was added to the crude amine and Et₃N (1.8 mL, 13.49 mmol) in THF (10 mL), and the reaction was carried out as described in general procedure V(b) to afford 1.3 g of amide 5c in 79% yield. ¹H-NMR (500 MHz, CDCl₃): δ 2.82 – 2.88 (4Hs, m), 3.32 – 3.4 (4Hs, m), 4.6 (2Hs, d, J = 5.85 Hz), 6.86 – 6.91 (1H, bs), 6.98 (1H, t, J = 8.3 Hz), 7.09 (2H, dt, J = 1.95, 12.93 Hz), 7.34 (1H, d, J = 3.9 Hz), 7.41 (1H, d, J = 3.9 Hz); ¹³C-NMR (300 MHz, CDCl₃): 27.41, (42.18, 42.19), (52.63, 52.67), 111.85, 115.32, (115.60, 115.65), 118.39, (119.71, 119.75), (123.49, 123.54), (131.26, 131.35), (140.12, 140.23), 147.3, 153.55, 155.59, 156.83; ESI-MS: 363.9 (M−1); Anal. Calcd. for C₁₆H₁₆FN₃O₄S: C, 52.59, H, 4.41; N, 11.50. Found: C, 51.90; H, 4.38; N, 11.08.

MIC determinations against M. tuberculosis H37Ra and H37Rv

MIC values of the nitrofuranyl amides against M. tuberculosis H37Rv were determined by the micro broth dilution method according to NCCLS guidelines. A broth culture of M. tuberculosis was grown in Middlebrook 7H9 medium with 10% ADC supplement to an OD₆₀₀ of 0.4 – 0.6. The culture was diluted with 7H9 medium to an OD₆₀₀ of 0.01 and 100 μL of these cells were then added to a microtiter plate containing serial dilutions of the nitrofuranyl amides for a final volume of 200 μL. The plates were incubated at 37° C for 8 days. The MIC₉₀ was determined by visual inspection for wells with greater than 90% inhibition of growth.

Maximum Tolerated Dose Assay (MTD)

Three healthy mice were given one single dose of the compound by oral gavage and were observed at regular times for any adverse effects. Three different concentrations were tested, generally at 100, 300 and 500 mg/kg. The latter dose was about twice to five times the dose used for efficacy testing of the compound in mice. After 7 days of observation the mice are sacrificed and the organs are studied by gross necropsy.

Determination of the in vivo biological activity and basic bioavailability after oral administration

8–10 Week old female C57BL/6 mice were dosed (at a dose lower than the maximum tolerated dose of the compound used, generally 300 mg/kg), via oral gavage. At 20 min., 2 hr, 4 hr and 8 hr after dosing, 3 mice were bled from the tail vein. Blood samples were collected aseptically, stored on ice, and centrifuged to collect serum. The drug concentration in the collected serum samples was determined by a microdilution MIC method using M. tuberculosis H37Rv. Serum samples were prepared as two-fold dilutions using serum from naïve mice as diluent (ranging from 10% to 0.312% from collected mouse serum samples). The serum dilutions were subsequently added in 10 μL to the 96-well assay plate, starting with a maximum of 10% serum collected from drug treated mice in the top well. Standards of the tested compounds were tested on the same 96-well microtiter plate using 3-fold dilutions of the compound ranging from 30 μg/mL up to 0.51 ng/mL final concentrations, in presence and without 10% mouse serum. Compounds in standard lanes were diluted in 100% DMSO to avoid any solubility problems (2% final DMSO concentration). The M. tuberculosis H37Rv suspension was grown as a mid-Log culture and frozen in aliquots until further use. A frozen stock was added at 10⁴ CFU per well in a volume of 50 μL 7H9 medium to the 96-well plates (total volume per well is adjusted to 100 μL with 7H9 culture medium). The plates were incubated at 35 °C for 2 weeks. Optical density was measured after 3, 6, 9 and 12 days at 600 nm, and results were confirmed by visual inspection at 10 days. Inhibition of bacterial growth in the bioassay indicated sufficient high concentrations of bioactive product in the bloodstream. Wells were scored as positive (drug containing) wells when the OD₆₀₀ values were less than 50% of the OD₆₀₀ value of the untreated control wells. An estimation of serum drug levels (in μg per mL serum) was obtained by using the MIC data from the standard drug lanes.

GKO Mouse Model

Mice were infected via low dose aerosol with M. tuberculosis to reproducibly deliver approximately 50 bacilli in the lungs as described previously.¹⁹ Treatment is initiated 18 days post infection for 9 daily treatments for one single dose (at 300 mg/kg). Bacterial load is determined 27 days post infection in lungs and spleens of the mice by serial dilution of the tissue homogenates on nutrient Middlebrook 7H11 agar plates (GIBCO BRL, Gaithersburg, Md.). The plates were incubated at 37° C in ambient air for 4 weeks prior to the counting of viable M. tuberculosis colonies (CFU). The viable bacterial numbers were converted to logarithms, which were then evaluated by multiplecomparison analysis of variance by a one-way Dunnett test (SigmaStat software program). Differences were considered significant at the 95% level of confidence.