Open access peer-reviewed chapter

Synthesis, Characterization and Antimicrobial Properties of Novel Benzimidazole Amide Derivatives Bearing Thiophene Moiety

Written By

Vinayak Adimule, Pravin Kendrekar and Sheetal Batakurki

Submitted: 10 September 2021 Reviewed: 12 April 2022 Published: 30 May 2022

DOI: 10.5772/intechopen.104908

From the Edited Volume

Benzimidazole

Edited by Pravin Kendrekar and Vinayak Adimule

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Abstract

In the present investigation, novel amide derivatives of benzimidazole (4a-f) with different thiophene acids (a-f) coupled in the presence of 1-[Bis (dimethylamino) methylene]-1H-1, 2, 3-triazolo [4, 5-b] pyridinium 3-oxide hexafluorophosphate (HATU) reagent at room temperature and as-synthesized derivatives were characterized by (1H-NMR and 13C-NMR) proton and carbon magnetic resonance, and high-performance liquid chromatography (HPLC) analytical techniques. The amide derivatives were tested for in vitro antimicrobial and antifungal activity and ciprofloxacin was used as standard. The antifungal activity was tested with Carbendazim and Fenbendazole cell lines using clotrimazole standard drug. The results indicated the potential activity toward S. bacillus with compounds having IC 50 of 4 (a), 4 (b), 4 (d) and 4 (e) against antimicrobial strains with IC50 of 51.8 μm, 57.4 μm, 54.5 μm and 56.5 μm respectively. However, compounds 4 (a), 4 (c) and 4 (d) showed greater inhibitions against Carbendazim fungal cell line with IC50 of 22.9, 26.8 and 28.8 μm. On the other hand IC50 values of the Fenbendazole for compounds 4 (a), 4(c) and 4 (d) were found to be 12.7, 10.2 and 12.7 μm, respectively. The thiophene-substituted benzimidazole amide derivatives are the potential candidate drug for antibacterial and antifungal activity.

Keywords

  • thiophene
  • antibacterial
  • antifungal
  • benzimidazole
  • amides
  • HATU

1. Introduction

In the present investigation, organic and medicinal chemistry involves the nitrogen containing heterocycles especially Benzimidazole derivatives [1, 2]. Benzimidazole has become nature and synthetic active structural part in the biological characteristics such as antibacterial [3], anticancer [4], antiviral [5], antifungal [6] and antioxidant [7] etc. It is widely accepted that the amidino moieties at the benzimidazole substituents terminal would generate numerous pathophysiological and biochemical processes in the human body. Additional biological activity can be found with the benzimidazole substituents carrying amide moiety and tetracyclic derivatives interaction with DNA is large enough to encounter the selectivity towards the drug molecules. Benzimidazole is indispensable nucleus for the discovery of the new biologically important molecules. Literature reports suggest that benzimidazole has potential interest in antimicrobial [8, 9] and anticancer agents [10, 11]. New class of oxadiazole and thiadiazoles containing thiophene and phenyl substituents reported for enhanced anticancer activity [12, 13, 14, 15]. Benzimidazole nucleus structurally analogues to purine and its derivatives and exhibit the synthesis of nucleic acids. Several DNA molecules will be cleaved upon interaction with the benzimidazole moiety and inhibit the growth of the microbial strains [16, 17, 18]. The development of new antimicrobial agents remains on priority [19]. Furthermore, Bisbezimidazole derivatives found to be biologically active towards antibacterial [20], antimicrobial [21] and anticancer [22] activities. On the other hand, benzylvanilline benzimidazole [23] derivatives were found to cleave DNA and potent towards leukemic cell lines. Distance between the benzimidazole molecule and ester containing phenyl group is very important factor for the antifungal activity. Extending the spacer between the benzimidazole and ester or amide substituents become important factor for the increased antifungal activity. Antitumor activity depends on the distance between the benzimidazole and spacer link of the ester or amide molecules. Thiophene and their derivatives which are sulfur compounds widely studied for their antifungal activity [24, 25, 26, 27, 28]. Some of the thiophene containing derivatives such as thicyofen, ethaboxam, silthiopham and penthiopyrad were widely used in agriculture as antifungal compounds [29, 30]. Recently certain amide, thiazole, 1, 3, 4-oxadiazoles has been designed, synthesized and studied for their enhanced anticancer properties [31, 32, 33, 34, 35, 36]. Incorporation of the thiophene moiety would enhance the antifungal activity of the benzimdiazole derivatives.

Based on the above literature evidences, Author envisaged by constructing the novel benzimidazole containing thiophene derivative could increase the antimicrobial and antifungal activity of the synthesized compounds. All the synthesized derivatives were characterized by 1H-NMR, 13C-NMR, LCMS spectroscopic studies and tested against microbial and fungal cell lines. The results indicated potential activity towards S. bacillus tested compound with IC 50 of 4 (a), 4 (b), 4 (d) and 4 (e) derivatives against antimicrobial strains with IC50 of 51.8 μm, 57.4 μm, 54.5 μm and 56.5 μm respectively. However, compounds 4 (a), 4 (c) and 4 (d) showed greater inhibitions against Carbendazim fungal cell line with IC50 of 22.9 μm 26.8 μm and 28.8 μm respectively. On the other hand IC50 values of the Fenbendazole for compounds 4 (a), 4(c) and 4 (d) was found to be 12.7 μm, 10.2 μm and 12.7 μm respectively.

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2. Materials and methods

All the chemicals, reagents and solvents are procured from Sigma-Aldrich, S-d fine chemicals Ltd., Spectrochem Ltd. and used without any further purification. Intermediate chemicals purchased directly (99.8% purity, thiophene-2-carboxylic acid, Sigma Aldrich India (a)), (98% purity, (thiophen-3-yl) acetic acid Sigma Aldrich India (b)), (99.1% purity, 3,6-dichloro-1-benzothiophene-2-carboxylic acid, Matrix Scientific, India (c)), (99.2% purity, 5-(4-fluorophenyl)thiophene-2-carboxylic acid.

Sigma Aldrich, India (d)), (98% purity, 4-bromo-5-chlorothiophene-2-carboxylic acid, Chem Src, China (e)), (99.2% purity, 3-chloro-1-benzothiophene-2-carboxylic acid, Sigma-Aldrich India (f)) and used without any further purifications. 1H-NMR, 13C-NMR spectral analysis was carried out using 300 MHz-1.2 GHz consisting of cryostat with excellent thermal efficiency, available with high performance vibration isolator make from Bruker Ascend series. LCMS (liquid crystal mass spectrometry) Triple quadrapole series of GCMS-TQ8050 NX fitted with high efficient trace level detection. In order to prepare the culture medium, the synthesized compounds were dissolved in DMSO and diluted with culture broth solution to 1 mg/mL. Serial dilutions were made to reach up to the 10 mL of the final concentration. About 100 μL of the each of the solution were distributed to 96 well plates and the sterility control and growth control solutions were placed into it. About 5 μL of the test and the growth solutions were inoculated into the well plates. All the experiments were carried out in triplicate. Bacterial growth was detected former by optical density (ELISA reader, CLX800 Biotech Instruments) and after by addition of 20 μL of an INT alcoholic solution (0.5 mg/mL). 7 mm filter paper discs (Whatman, no. 3) were impregnated with 10 mL of each of the different dilutions [37, 38]. The discs were allowed to remain at RT until complete diluent evaporation and kept under refrigeration until ready to be used. Discs loaded with synthesized derivatives which were placed onto the surface of the agar. Commercial chloramphenicol discs and paper discs impregnated with 20 mL of diluents used to dilute concentration of the synthesized products were used as control.

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3. Experimental

3.1 Synthesis of 1H-benzimidazole-2-carboxylic acid

In a 100 mL round bottom flask fitted with a reflux condenser, 2-methyl-1H-benzimidazole (5.69 g, 1.1 mole), KMnO4 (4 mole), K2CO3 (3 mole) were dissolved in 100 mL of absolute ethanol and 20 mL of water under stirring. The contents of the reaction mixture heated to 90 C for 5 h. The progress of the reaction was monitored by TLC (thin-layer chromatography) (ethyl acetate: hexane: 40:60). After completion of the reaction, contents of the RB flask cooled to room temperature (RT), filtered over celite bed, filtrate was concentrated to half of its initial volume, acidified with concentrated HCl to PH ∼ 2. Off white colored solid separated out was filtered, washed with cold water and dried. Yield: 5.2 g. The solid was taken to next step without any purification [39, 40].

3.2 Synthesis of 1-(1H-benzimidazol-2-yl) methanamine

In a 100 mL RB flask fitted with an inert nitrogen atmosphere, 1H-benzimidazole-2-carboxylic acid (5.2 g) dissolved in dry THF solvent and LiAlH4 (1 mole) were added under stirring at RT. Progress of the reaction was monitored by TLC, after completion of the reaction. LiAlH4 was quenched in carbonate solution. The reaction mixture was concentrated to remove the organic solvent and filtered. The product was extracted in ethyl acetate (100 mL × 3 times), washed with Na2CO3 (25 mL × 2 times), brine (25 mL × 2 times) and dried over Na2SO4. Solid that are separated out was filtered in 10 mL of n-hexane solvent and obtained as 1-(1H-benzimidazol-2-yl) methanamine (Figure 1). Yield: 3.87 g.

Figure 1.

Synthetic pathway of Benzimidazole intermediates.

3.3 General procedure for the synthesis of benzimidazole amide derivatives

In a 100 mL RB flask fitted with a condenser, 1-(1H-benzimidazol-2-yl) methanamine (1mole) added with different thiophene substituted acids (a-f), Dichloromethane (DCC) (10 mL), HATU (0.25mole), Triethyl amine (TEA) (1.5mole) and stirred at RT for 24 h, after completion of the reaction (monitored by TLC), solvent and other volatile reagents are evaporated, solid obtained was mixed with 60–120 silica gel and purified by column-chromatography (ethyl acetate: hexane: 30:70), Solids obtained after the solvent evaporation was used for the antimicrobial property studies [41].

3.4 Characterization of the synthesized compounds (Benzimidazole 2, 3 and 4a-4f)

1H-NMR Spectrum of the compounds 2, 3, 4a to 4 f.

1H-NMR, 13C-NMR and LCMS analysis of the synthesized compounds.

Compound 2.

Yellow solid; m.p-157.8°C; Yield = 97.8%; LCMS-98.1%; 1H-NMR: δ1H NMR: δ 7.04 (1H, ddd, J = 7.7, 6.9, 1.3 Hz), 7.23 (1H, ddd, J = 8.2, 6.9, 1.7 Hz), 7.77 (1H, ddd, J = 8.2, 1.3, 0.5 Hz), 7.90 (1H, ddd, J = 7.7, 1.7, 0.5 Hz). 13C-NMR: δ13C NMR: δ 114.3 (1C, s), 118.4 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 137.9 (1C, s), 138.4 (1C, s), 150.9 (1C, s), 156.7 (1C, s) (Figure 2) (Figures 36).

Figure 2.

Synthesis of amide derivatives of Benzimidazoles.

Figure 3.

1H-NMR of the spectrum of 2 and 3.

Figure 4.

1H-NMR of the spectrum 4a and 4b.

Figure 5.

1H-NMR of the compounds 4c and 4d.

Figure 6.

1H-NMR Spectrum of the compounds 4e and 4 f.

Compound 3.

Pale yellow solid; m.p-159.2°C; Yield = 98.8%; LCMS-98.7%;1H-NMR: δ 1H NMR: δ 4.32 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.19 (1H, ddd, J = 8.1, 7.6, 1.4 Hz), 7.59–7.75 (2H, 7.65 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz). 13C-NMR: δ13C NMR: δ 49.1 (1C, s), 114.3 (1C, s), 118.4 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 137.9 (1C, s), 138.4 (1C, s), 150.9 (1C, s).

Compound 4a.

Pale yellow solid; m.p-163.4°C; Yield = 97.8%; LCMS- 98.1%;1H NMR: δ 4.93 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.12–7.27 (2H, 7.19 (ddd, J = 8.1, 7.6, 1.4 Hz), 7.21 (dd, J = 7.2, 5.0 Hz)), 7.60–7.83 (4H, 7.66 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz), 7.76 (dd, J = 5.0, 1.2 Hz), 7.76 (dd, J = 7.2, 1.2 Hz). 13C-NMR: δ13C NMR: δ 44.7 (1C, s), 114.3 (1C, s), 118.4 (1C, s), 127.5 (1C, s), 127.8 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 131.0 (1C, s), 137.9 (1C, s), 138.4 (1C, s), 139.9 (1C, s), 150.9 (1C, s), 160.1 (1C, s).

Compound 4b.

Off white colored solid; m.p-171.8°C; Yield = 97.8%; LCMS- 98.3%; 1H NMR: δ 3.88 (2H, s), 4.99 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.10–7.26 (2H, 7.16 (dd, J = 7.5, 5.0 Hz), 7.19 (ddd, J = 8.1, 7.6, 1.4 Hz), 7.31–7.45 (2H, 7.37 (dd, J = 5.0, 1.3 Hz), 7.39 (dd, J = 7.5, 1.3 Hz), 7.59–7.76 (2H, 7.66 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz). 13C-NMR: δ13C NMR: δ 29.2 (1C, s), 44.7 (1C, s), 114.3 (1C, s), 118.4 (1C, s), 126.6 (1C, s), 127.5 (1C, s), 127.8 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 137.9 (1C, s), 138.1 (1C, s), 138.4 (1C, s), 150.9 (1C, s), 172.7 (1C, s).

Compound 4c.

Pale Yellow Solid; m.p−174.5°C; Yield = 99.4%; LCMS- 97.8%; 1H NMR: δ 4.90 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.19 (1H, ddd, J = 8.1, 7.6, 1.4 Hz), 7.42 (1H, dd, J = 8.6, 1.9 Hz), 7.60–7.76 (2H, 7.66 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz), 7.94–8.07 (2H, 8.00 (dd, J = 1.9, 0.5 Hz), 8.01 (dd, J = 8.6, 0.5 Hz)). 13C-NMR: δ13C NMR: δ 44.7 (1C, s), 114.3 (1C, s), 118.4–118.5 (2C, 118.4 (s), 118.5 (s)), 127.0 (1C, s), 127.8 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 128.7 (1C, s), 130.3 (1C, s), 132.6 (1C, s), 136.6 (1C, s), 137.9 (1C, s), 138.4 (1C, s), 139.3 (1C, s), 150.9 (1C, s), 160.1 (1C, s).

Compound 4d.

Yellow solid; m.p-157.8°C; Yield = 97.8%; LCMS- 96.8%; 1H NMR: δ 4.92 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.12–7.32 (3H, 7.19 (ddd, J = 8.1, 7.6, 1.4 Hz), 7.25 (ddd, J = 8.9, 1.4, 0.5 Hz)), 7.40 (1H, d, J = 8.7 Hz), 7.60–7.82 (5H, 7.66 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.66 (d, J = 8.7 Hz), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz), 7.76 (ddd, J = 8.9, 1.5, 0.5 Hz). 13C-NMR: δ13C NMR: δ 44.7 (1C, s), 114.3 (1C, s), 115.4 (2C, s), 118.4 (1C, s), 124.0 (1C, s), 127.8 (2C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s)), 129.6 (1C, s), 134.3 (1C, s), 137.8–138.0 (2C, 137.8 (s), 137.9 (s), 138.4 (1C, s), 150.9 (1C, s), 151.1 (1C, s), 160.1 (1C, s), 162.5 (1C, s).

Compound 4e.

Pale Yellow Solid; m.p-179.2°C; Yield = 95.1%; LCMS- 98.2%; 1H NMR: δ 4.92 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.19 (1H, ddd, J = 8.1, 7.6, 1.4 Hz), 7.60–7.76 (3H, 7.66 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.65 (s), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz). 13C-NMR: δ13C NMR: δ 44.7 (1C, s), 110.5 (1C, s), 114.3 (1C, s), 118.4 (1C, s), 123.0 (1C, s), 128.0 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 134.4 (1C, s), 137.9 (1C, s), 138.4 (1C, s), 150.9 (1C, s), 160.1 (1C, s).

Compound 4f.

White colored solid; m.p-178.5°C; Yield = 94.3%; LCMS- 99.2%; 1H NMR: δ 4.91 (2H, s), 6.94 (1H, ddd, J = 7.7, 7.6, 1.2 Hz), 7.19 (1H, ddd, J = 8.1, 7.6, 1.4 Hz), 7.40–7.59 (2H, 7.47 (ddd, J = 8.0, 7.8, 1.4 Hz), 7.52 (ddd, J = 8.5, 7.8, 1.6 Hz), 7.60–7.80 (3H, 7.66 (ddd, J = 8.1, 1.2, 0.5 Hz), 7.69 (ddd, J = 7.7, 1.4, 0.5 Hz), 7.74 (ddd, J = 8.0, 1.6, 0.5 Hz)), 8.47 (1H, ddd, J = 8.5, 1.4, 0.5 Hz). 13C-NMR: δ13C NMR: δ 44.7 (1C, s), 114.3 (1C, s), 118.4–118.5 (2C, 118.4 (s), 118.5 (s), 122.5 (1C, s), 123.3 (1C, s), 128.1–128.3 (2C, 128.2 (s), 128.2 (s), 128.3–128.6 (2C, 128.4 (s), 128.5 (s), 132.6 (1C, s), 136.1 (1C, s), 136.6 (1C, s), 137.9 (1C, s), 138.4 (1C, s), 150.9 (1C, s), 160.1 (1C, s).

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4. Results and discussion

4.1 Antimicrobial activity of the synthesized derivatives

Antibacterial and antifungal activities of the synthesized compounds were tested by Agar well diffusion method. One mL of the fresh bacterial or fungi was placed in the sterile petri dish. Cooled Muller Hi was placed over it and upon solidification. 5 μL of the compounds dissolved in DMSO solvent was added to respective wells. The concentration has been fixed as per the previous reported literature [42, 43]. The Agar well plates were incubated for 30 minutes and subsequently kept at 35°C for 24 h. Antimicrobial activity was detected by measuring the zone of inhibition (including the wells diameter) appeared after the incubation period. DMSO at a concentration of 10% was employed as a negative control. All tested samples and their antimicrobial activity were expressed in terms of minimum inhibitory concentration (MIC values) (Tables 13). Different concentrations of the test solution are prepared and zone of inhibition and MIC values compared with the standards used for the evaluation [44]. The MIC was considered as the lowest concentration which inhibited the growth of the respective microorganisms. All assays were performed in triplicate. DMSO was served as a control for all the synthesized samples. Tables 1 and 2 depicts the minimum inhibitory concentration of the antibacterial and antifungal activity (Table 3) of the synthesized derivatives. The results indicated potential activity towards S. bacillus tested compound with IC50 of 4 (a), 4 (b), 4 (d) and 4 (e) derivatives against antimicrobial strains with IC50 of 51.8 μm, 57.4 μm, 54.5 μm and 56.5 μm respectively. However, compounds 4 (a), 4 (c) and 4 (d) showed greater inhibitions against Carbendazim fungal cell line with IC50 of 22.9 μm 26.8 μm and 28.8 μm respectively. The compounds 4 (a), 4(c) and 4 (d) tested for anti micro (IC50) of the Fenbendazole for compounds were found to be 12.7 μm, 10.2 μm and 12.7 μm respectively [45].

CompoundsE. coliS-BacillusStaphylococcus ASalmonella Typhi
Zone of InhibitionIC50Zone of InhibitionIC50Zone of InhibitionIC50Zone of InhibitionIC50
(mm)(μm)(mm)(μm)(mm)(μm)(mm)(μm)
11.212.9 ± 0.123.214.8 ± 0.144.118.9 ± 0.137.126.9 ± 0.10
21.715.4 ± 0.183.418.9 ± 0.154.825.7 ± 0.118.722.7± 0.10
32.822.1 ± 0.173.825.7 ± 0.122.722.8 ± 0.029.124.8 ± 0.11
4a13.929.9 ± 0.1212.851.8 ± 0.192.221.8 ± 0.256.923.7 ± 0.12
4b12.428.7 ± 0.1210.857.4 ± 0.187.629.6 ± 0.218.119.7 ± 0.22
4c2.814.7± 0.153.415.9± 0.114.726.9± 0.225.429.6 ± 0.24
4d9.830.2 ± 0.1418.954.5 ± 0.138.816.9 ± 0.197.524.7 ± 0.21
4e7.129.1 ± 0.1622.856.5 ± 0.186.615.4 ± 0.187.222.7 ± 0.27
4f6.814.7 ± 0.184.115.9 ± 0.226.918.7 ± 0.155.526.8 ± 0.26
Ciprofloxacin18.948.7 ± 0.0117.651.8 ± 0.0114.942.6 ± 0.0116.843.3± 0.02

Table 1.

Antimicrobial activity data of the synthesized compounds against E. Coli and S. Bacillus.

*Potent Antimicrobial Compounds.


CompoundsCarbendazimFenbendazole
Zone of Inhibition (mm)IC50 (μm)Zone of Inhibition (mm)IC50 (μm)
16.111.8 ± 0.112.28.9 ± 0.13
29.816.1 ± 0.112.44.7 ± 0.15
32.210.4 ± 0.101.818.1 ± 0.14
4a7.822.9 ± 0.251.912.7 ± 0.18
4b2.314.4 ± 0.231.813.7± 0.19
4c12.226.8 ± 0.282.210.2 ± 0.29
4d10.228.8 ± 0.342.712.7 ± 0.22
4e2.412.5 ± 0.282.713.8 ± 0.11
4f2.813.8 ± 0.145.511.8± 0.10
Clotrimazole12.222.8 ± 0.132.210.226.1 ± 0.13

Table 2.

Antimicrobial activities of the compounds against Staphylococcus A and Salmonella Typhi.

*Potent antimicrobial compounds.


CompoundsCarbendazim Fenbendazole% change in the activity
Zone of Inhibition (mm)IC50 (μm)Zone of Inhibition (mm)IC50 (μm)
2-methyl-1H-benzimidazole (1)6.111.8 ± 0.112.28.9 ± 0.132.2
1H-benzimidazole-2-carboxylic acid (2)9.816.1 ± 0.112.44.7 ± 0.153.6
1-(1H-benzimidazol-2-yl) methanamine (3)2.210.4 ± 0.101.818.1 ± 0.144.8
N-[(1H-benzimidazol-2-yl) methyl]thiophene-2-carboxamide (4a)7.822.9 ± 0.251.912.7 ± 0.18*12.4
N-[(1H-benzimidazol-2-yl) methyl]-2-(thiophen-2-yl) acetamide (4b)2.314.4 ± 0.231.813.7± 0.191.8
N-[(1H-benzimidazol-2-yl) methyl]-3, 6-dichloro-1-benzothiophene -2-carboxamide (4c)12.226.8 ± 0.282.210.2 ± 0.29*32.4
N-[(1H-benzimidazol-2-yl)methyl]-5-(4-fluorophenyl) thiophene-2-carboxamide (4d)10.228.8 ± 0.342.712.7 ± 0.22*24.7
N-[(1H-benzimidazol-2-yl) methyl]-4-bromo-5-chlorothiophene-2-carboxamide (4e)2.412.5 ± 0.282.713.8 ± 0.115.9
N-[(1H-benzimidazol-2-yl)methyl]-3-chloro-1-benzothiophene-2-carboxamide (4f)2.813.8 ± 0.145.511.8 ± 0.103.6
Clotrimazole12.222.8 ± 0.1310.226.1 ± 0.131.8

Table 3.

Antifungal activity data of the synthesized compounds.

Potent antifungal agent.


4.2 Structure activity relationships (SAR)

The SAR may be attributed from the presence of halo, phenyl and aliphatic linkage present in the benzimidazoles derivatives and deduced from the following points. The minimum inhibitory concentration of the Cl, Br substituted aliphatic amide linkage draw attention for the enhanced binding and increased solubility of the compounds with respect to the target sites. Compounds of benzimidazoles derivatives bearing most active one 4(a), 4 (c) and 4 (d) as a lead compound to develop novel antimicrobial agent [46]. The appreciable antimicrobial activity of the synthesized Benzimidazole derivatives compared to the standard drugs show that only minor structural changes needed for the derivatives to improve the binding of the molecules. The excellent antimicrobial activity of the synthesized Benzimidazole derivatives compared to the standard drug indicated a fact that for developing novel antimicrobial agent based on synthesized Benzimidazole derivatives. The above results also indicated a fact that different structural requirements are necessary for a compound to show different activities.

SAR study of synthesized compounds showed that the presence of electron-withdrawing moieties phenyl thiophene substituted with Cl, Br groups adjacent to the amide linkage in the benzimidazoles enhanced ant mycobacterial activity [47]. Further SAR of most of the derivatives indicated the attachment of thiophene-2-carboxamide moieties at amide position of the benzimidazoles increased antibacterial activity and the presence of 3, 6-dichloro-1-benzothiophene (compound 4c) at 2nd position of Benzimidazole carboximide also important for antimicrobial activities [48, 49]. The presence of electron withdrawing Cl and Br groups at 3rd and 4th position (compound 4f and 4e) required for antimicrobial activity. However substitution of 4-fluorophenyl) thiophene at 5th position of benzimidazoles carboxamide moiety increases the solubility of the compound (compound 4d) as well as the presence of phenyl ring increases the antibacterial properties (Figure 7).

Figure 7.

SAR of the novel derivatives of benzimidazoles containing thiophene moiety.

Further, (thiophen-2-yl) acetamide and thiophene-2-carboxamide (compound 4a and 4b) attached to the benzimidazoles moiety at 2nd position of the ring system results in basicity of the –NH2 (amine) linker and thus increases the Clog P values where, C is the concentration of the compounds and P is permeability. On the other hand compound 4c contains 3, 6-dichloro-1-benzothiophene-2-carboxamide group attached at 2nd position of the benzimidazoles moiety responsible for moderate antibacterial and antiviral activities. If the 3, 6 dichloro groups present in the opposite direction of the ring system results in enhanced bioavailability of the benzimidazoles derivatives.

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5. Conclusion

In the present research, novel series of thiophene amide derivatives containing benzimidazole moiety has been synthesized by the reaction with HATU at room temperature. All the synthesized derivatives are characterized by 1H-NMR, 13C-NMR and LCMS spectroscopic studies. Synthesized compounds are purified by column-chromatography, and tested for antimicrobial strains (antibacterial and antifungal). The cell lines used was E. coli, S. bacillus, Staphylococcus Aures and Salmonella Typhi and ciprofloxacin used as standard. The results indicated potential activity towards S. bacillus tested compound with IC50 of 4 (a), 4 (b), 4 (d) and 4 (e) derivatives against antimicrobial strains with IC50 of 51.8 μm, 57.4 μm, 54.5 μm and 56.5 μm respectively. However, compounds 4 (a), 4 (c) and 4 (d) showed greater inhibitions against Carbendazim fungal cell line with IC50 of 22.9 μm 26.8 μm and 28.8 μm respectively. Compared with the activity (IC50) of the Fenbendazole for compounds 4 (a), 4(c) and 4 (d) was found to be 12.7 μm, 10.2 μm and 12.7 μm respectively. The newly synthesized derivatives find its potential application in antibacterial and antifungal cells and replacing the existing drug in the market.

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Acknowledgments

All the authors are thankful to corresponding author Dr. Pravin Kendrekar, School of Natural Sciences, University of central Lancashire, Preston PR12HE, United Kingdom for carrying out antibacterial and antifungal activity of the synthesized compounds and M. S. Ramaiah University of Applied Science, Karnataka, Bangalore for synthesis of the thiophene substituted benzimidazole derivatives.

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Conflict of interest

All the authors declare that they do not have any conflict of interest.

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Data availability

All the obtained data has been incorporated in the main manuscript and more data can be obtained from the corresponding author on request.

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Written By

Vinayak Adimule, Pravin Kendrekar and Sheetal Batakurki

Submitted: 10 September 2021 Reviewed: 12 April 2022 Published: 30 May 2022