Synthesis and Quantitative Structure Activity Relationship (QSAR) of Arylidene

SUPPLEMENTARY MATERIAL

Synthesis and quantitative structure activity relationship (QSAR) of arylidene (benzimidazol-1-yl)acetohydrazones as potential antibacterial agents

Yeldez El-kilany • Nariman M. Nahas • Mariam A. Al-Ghamdi • Mohamed E. I. Badawy • El Sayed H. El Ashry

Yeldez El-kilany • Nariman M. Nahas • Mariam A. Al-Ghamdi

Chemistry Department, Faculty of Applied Science, Umm Al-Qura University, Mekkah, Kingdom of Saudi Arabia.

Mohamed E. I. Badawy*

Department of Pesticide Chemistry and Technology, Faculty of Agriculture, 21545-El-Shatby, Alexandria University, Alexandria, Egypt. E-mail: Tel.: 002039575269; Fax: 002035972780

El Sayed H. El Ashry

Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt.

Abstract Ethyl (benzimidazol-1-yl)acetate was subjected to hydrazinolysis with hydrazine hydrate to give (benzimidazol-1-yl)acetohydrazide. The latter was reacted with various aromatic aldehydes to give the respective arylidene (1H-benzimidazol-1-yl)acetohydrazones. Solutions of the prepared hydrazones were found to contain two geometric isomers. Similarly (2-methyl-benzimidazol-1-yl)acetohydrazide was reacted with various aldehydes to give the corresponding hydrazones. The antibacterial activity was evaluated in vitro by minimum inhibitory concentration (MIC) against Agrobacterium tumefaciens (A. tumefaciens), Erwinia carotovora (E. carotovora), Corynebacterium fascians (C. fascians) and Pseudomonas solanacearum (P. solanacearum). MIC result demonstrated that salicylaldehyde(1H-benzimidazol-1-yl)acetohydrazone (4) was the most active compound (MIC = 20, 35, 25 and 30 mg/L against A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively). Quantitative structure activity relationship (QSAR) investigation using Hansch analysis was applied to find out the correlation between antibacterial activity and physicochemical properties. Various physicochemical descriptors and experimentally determined MIC values for different microorganisms were used as independent and dependent variables, respectively. pMICs of the compounds exhibited good correlation (r = 0.983, 0.914, 0.960 and 0.958 for A. tumefaciens, C. fascians, E. carotovora and P. solanacearum, respectively) with the prediction made by the model. QSAR study revealed that the hydrophobic parameter (ClogP), the aqueous solubility (LogS), calculated molar refractivity (CMR), topological polar surface area (tPSA) and hydrogen bond acceptor (HA) were found to have overall significant correlation with antibacterial activity. The statistical results of training set, correlation coefficient (r and r2), the ratio between regression and residual variances (f, Fisher's statistic), the standard error of estimates (SE) and significant (s) gave reliability to the prediction of molecules with activity using QSAR models. However, QSAR equations derived for the MIC values against the tested bacteria showed negative contribution of molecular mass.

Keywords Hydrazones · Geometric isomers · Benzimidazole · Benzimidazolyl-acetohydrazones · Antibacterial activity · QSAR

Materials and methods

General procedure for the synthesis of arylidene (benzimidazol-1-yl)acetohydrazones

Ethyl(benzimidazol-1-yl)acetate

A stirred suspension of the benzimidazole (11.8 g, 0.1 mol) with ethylchloroacetate (14.7 g, 0.12 mol) and anhydrous potassium carbonate (13.8 g, 0.1 mol) in DMF (4.0 mL) and acetone (30 mL) was heated under reflux for 2 h. The reaction mixture was filtered and the solid was washed with acetone. The filtrate was concentrated under reduced pressure and the resulting syrup was washed with water (2.18 g, 97.14% yield). TLC: Rf = 0.63 (ethyl acetate/petroleum ether 1:1). The product was recrystallized from ethanol to give colorless needles; m.p. 169˚C (Habib and El-Hawash 1989). 1H-NMR (DMSO-d6): δ 1.17 (t, 3H, CH3), 4.14 (q, 2H, CH2), 5.24 (s, 2H, CH2), 7.21 (t, 1H, J6′,7′ = 6.85 Hz, J6′,5′ = 6.10 Hz, H-6'), 7.24 (t, 1H, J5',6' = 8.4 Hz, J5',4' = 6.1 Hz, H-5'), 7.53 (d, 1H, J7′,6′ = 6.85 Hz, H-7'), 7.68 (d, 1H, J4′,5′ = 6.1 Hz, H-4'), and 8.22 (s, 1H, H-2'). 13C-NMR (DMSO-d6): δ 14.5 (CH3), 45.9 (CH2), 61.8 (CH2), 111.0 (C-7'), 119.9 (C-4'), 122.3 (C-6'), 123.1 (C-5'), 134.8 (C-8'), 143.6 (C-9'), 145.2 (C-2'), and 168.9 (C=O). Anal. Calc. for C11H12N2O2 (204.21): C, 64.69%, H, 5.92%, and N, 13.72%. Found: C, 65.02%, H, 6.10%, and N, 14.00 %.

(Benzimidazol-1-yl)acetohydrazide (1)

A solution of the ethyl (benzimidazol-1-yl)acetate (2.04 g, 0.01 mol) in ethanol (20 mL) was treated with hydrazine hydrate (1.9 mL). The reaction mixture was heated under reflux for 3 h then concentrated and allowed to cool to give the product (1.8 g, 94.73% yield). TLC: Rf = 0.46 (ethyl acetate/petroleum ether 1:1). The product was recrystallized from ethanol to give colorless needles; m.p. 152 ˚C. IR (KBr): ν 3309 cm-1 (NH) and 1662 cm-1 (NCO). Anal. Calc. for C9H10N4O (190.20): C, 56.83%, H, 5.30%, and N, 29.46%. Found: C, 56.79%, H, 5.59%, and N, 29.36%.

2-(2-Methyl-benzimidazol-1-yl)acetohydrazide (2)

A solution of the ethyl 2-(2-methyl-benzimidazol-1-yl) acetate (2.18 g, 0.01 mol) in ethanol (20 mL) was treated with hydrazine hydrate (1.9 mL). The reaction mixtures was heated under reflux for 3 h then concentrated and allowed to cool to give the product (2.18 g, 89.97% yield). TLC: Rf = 0.37 (ethyl acetate/petroleum ether 1:1). The product was crystallized from ethanol to give white needles (Shetgiri and Kokitkar 2001), m.p. 245 ˚C. IR (KBr): ν 3305 cm-1 (NH) and 1660 cm-1 (NCO). 1H-NMR (DMSO-d6 + D2O): δ 2.46 (s, 3H, CH3), 4.76 (s, 2H, CH2), 7.10 (dt, 1H, J6',5' = 5.35Hz, J6',7′ = 1.55Hz, H-6'), 7.13 (2dt, 1H, J5',4’ = 1.55Hz, J5',6′ = 5.35 Hz, H-5'), 7.35 (dd, 1H, J7',6' = 7.70 Hz, H-7'), 7.48 (dd, 1H, J4',5' = 6.9 Hz, J4',6' = 1.5 Hz, H-4'), Signals appeared before addition of D2O: 4.31 (bs, 2H, NH2), and 9.50 (s, 1H, NH). 13C-NMR (DMSO-d6): δ 14.0 (CH3), 45.0 (CH2), 110.1 (C-7'), 118.7 (C-4'), 121.8 (C-6'), 122.0 (C-5'), 136.1 (C-8'), 142.7 (C-9'), 153.1 (C-2'), 166.6 (C=O). Anal. Calc. for C10H12N4O (204.23): C, 58.81%, H, 5.92%, and N, 27.43%. Found: C, 58.74%, H, 6.05%, and N, 27.07%.

Benzaldehyde (1H-benzimidazol-1-yl) acetohydrazone (3)

A solution of the (1H-benzo[d]imidazol-1-yl)acetohydrazide (1.9 g, 0.01 mol) in ethanol (60 mL), benzaldehyde (1.06 g, 0.01 mol) and glacial acetic acid (1 drop) was added. The reaction mixture was boiled under reflux for 6 h. The mixture was concentrated, then cooled to give a solid product (1.81 g, 65.10% yield). TLC: Rf = 0.39 (ethyl acetate/petroleum ether 1:1). The product was crystallized from ethanol to give white needles, m.p. 202-204 ˚C. 1H-NMR (DMSO-d6): δ 5.07 and 5.54 (2s, 2H, (1.0 : 4.0), CH2 minor and major), 7.20 (m, 2H, H-5′, 6′), 7.43 (m, 2H, H-3,5), 7.50 (d, 1H, H-7′), 7.63 (d, 1H, H-4′), 7.67 (m, 1H, H-4), 7.75 (m, 2H, H-2,6), 8.05 (s, 1H, H-2′), 8.20 and 8.21 (2s, 1H, (1.0 : 4.0), HC=N minor and major ) and 11.80 (s, 1H, NH). 13C-NMR: δ 40.3 and 40.35 (CH2), 111.0 and 111.2 (C-7′), 119.8, 121.7, 122.6 and 122.9, 127.6, 127.7, 129.3, 129.5, 130.5, 130.8, 134.5 and 135.3 (12Ar-C), 143.7 (C-2′), 144.5 and 144.7 (HC=N); 169.1 (C=O). Anal. Calc. for C16H14N4O (278.31): C, 69.05%, H, 5.07%, and N, 20.13%. Found: C, 68.78%, H, 5.10%, and N,19.87%.

Salicylaldehyde(1H-benzimidazol-1-yl)acetohydrazone(4)

Crystaline solid (2.00 g, 68.80% yield) with m.p. 214-216 ˚C. TLC: Rf = 0.72 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6) δ: 5.09 and 5.52 (2s, 2H (1.0 : 2.0), CH2 minor and major), 6.95 (m, 2H, H-3,5), 7.19 (m, 2H, H-5′,6′), 7.38 (t, 1H, H-4), 7.51 (m, 2H, H-7′), 7.67 (d, 1H, H-6), 7.79 (q, 1H, H-4′), 8.19 (s, 1H, H-2′), 8.34 and 8.45 (2s, 1H (1.0 : 2.0), HC=N minor and major), 10.88 (s, 1H, OH) and 12.07 (s, 1H, NH). 13C-NMR: δ 40.17 (CH2), 111.0 and 111.2 (C-7′), 116.9, 117.3, 119.9, 121.7, 122.8, 122.9, 129.6, 133.9, 134.9 and 142.0 (11Ar-C), 143.7 (C-2′), 147.9 and 148.1 (HC=N), 157.8 (C-1) and 168.7 (C=O). Anal. Calc. for C16H14N4O2 (294.31): C, 65.30%, H, 4.79% and N, 19.04%. Found: C,65.27%, H, 4.72%, and N, 18.82%.

4-Hydroxybenzaldehyde(1H-benzimidazol-1-yl)acetohydrazone (5)

Crystaline solid (1.96 g, 66.67% yield) with m.p. 189-191 ˚C. TLC: Rf = 0.69 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 5.05 and 5.51 (2s, 2H (1.0 : 3.0), CH2 minor and major), 6.83 (s, 1H, H-3), 6.86 (s, 1H, H-5), 7.22 (m, 2H, H-5′,6′), 7.51 (m, 1H, H-7′), 7.59 and 7.61 (s, 2H, H-2,6), 7.66 (m, 1H, H-4′), 7.97 (s, 1H, H-2′), 8.15 and 8.22 (2s, 1H (1.0 : 3.0), HC=N minor and major), 9.94 (s, 1H, OH), 11.55 and 11.68 (2s, 1H, NH). 13C-NMR: δ 45.42 (CH2), 110.38 and 110.63 (C-7′), 115.64 and 115.73 (C-3,5), 119.25 and 119.42 (C-4′), 122.29 and 122.47 (C-5′,6′), 124.94 and 125.01 (C-1), 128.81 and 129.03 (C-2,6), 134.77 (C-8′), 143.18 and 143.21 (C-2′), 144.43 (C-9′), 145.03 and 145.21 (HC=N), 162.96 (C-4), 168.04 and 168.14 (C=O). Anal. Calc. for C16H14N4O2 (294.31): C, 65.30%, H, 4.79%, and N, 19.04%. Found: C, 65.40%, H, 4.70%, and N, 18.80%.

Anisaldehyde(1H-benzimidazol-1-yl)acetohydrazone (6)

Crystaline solid (1.79 g, 58.11% yield) with m.p. 197-199 ˚C. TLC: Rf = 0.70 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 3.75 and 3.77 (2s, 3H, OCH3), 5.06 and 5.52 (2s, 2H (1.0 : 3.0), CH2 minor and major), 6.98 (m, 2H, H-3,5), 7.18 (m, 2H, H-5′,6′), 7.50 (m, 1H, H-7′), 7.64 (m, 1H, H-4′), 7.69 (d, 2H, H-2,6), 8.00 (s, 1H, H-2′), 8.19 and 8.22 (t, 1H (1.0 : 3.0), HC=N, minor and major), and 11.68 (s, 1H, NH).13C-NMR: δ 40.01 and 45.94 (CH2), 55.7 (CH3), 111.1 and 111.4 (C-7′), 114.6, 115.2, 119.9, 121.9, 122.6, 127.1, 129.1, 129.2, and 134.9 (10Ar-C), 143.7 (C-2′), 144.5 (C-9′), 145.6 and 145.8 (HC=N), 163.6 (C-4), and 168.8 (C=O). Anal. Calc. for C17H16N4O2 (308.33): C, 66.22%, H, 5.23%, and N, 18.17%. Found: C, 65.94%, H, 5.43% and N, 17.97%.

Benzaldehyde(2-methyl-1H-benzimidazol-1-yl)acetohydrazone (7)

Crystaline solid (1.96 g, 67.12% yield) with m.p. 230-232 ˚C. TLC: Rf = 0.62 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 2.53 (s, 3H, CH3), 5.03 and 5.46 (2s, 2H (3.0 : 1.0), CH2 minor and major), 7.15 (m, 2H, H-5′,6′), 7.43 (m, 3H, H-3,4,5), 7.58 (m, 1H, H-7′), 7.49 (d, 1H, H-4′), 7.57 (t, 2H, H-2,6), 8.09 and 8.25 (2s, 1H (3.0 : 1.0), HC=N minor and major), and 11.91 (s, 1H, NH). 13C-NMR: δ 13.9 (CH3), 40.15 and 40.31 (CH2), 110.2 and 110.3 (C-7′), 118.8, 121.8, 122.3, 127.6, 127.7, 129.0, 129.3, 130.6, 134.5, 136.6, and 142.9 (12Ar-C), 144.8 and 145.0 (HC=N), 148.5 (C-2′), and 168.9 (C=O). Anal. Calc. for C17H16N4O (292.33): C, 69.85%, H, 5.52% and N, 19.17%. Found: C, 69.48%, H, 5.15%, and N, 19.57%.

Salicylaldehyde(2-methyl-1H-benzimidazol-1-yl)acetohydrazone (8)

Crystaline solid (2.15 g, 69.80% yield) with m.p. 294-296 ˚C. TLC: Rf = 0.72 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 3.32 (s, 3H, CH3), 5.02 and 5.45 (2s, 2H, (1.0 : 2.0 ), CH2 minor and major), 6.90 (m, 2H, H-3,5), 7.16 (m, 2H, H-5′,6′), 7.26 (m, 1H, H-4), 7.44 (d, 1H, H-7′), 7.52 (m, 1H, H-6), 7.82 (dd, 1H, H-4′), 8.38 and 8.49 (2s, 1H, (1.0 : 2.0), HC=N minor and major), 10.01 (s, 1H, OH), 10.90 (s, 1H, NH) and 11.70 (s, 1H, NH). 13C-NMR: δ 13.31 and 13.38 (CH3), 39.48 (CH2), 109.45 and 109.60 (C-7′), 117.93 (C-3), 118.51 (C-1), 119.24 and 119.29 (C-4′), 121.24 and 121.25 (C-5), 126.34 (C-5′,6′), 128.82 (C-6), 131.24 (C-4), 135.87 (C-8′), 142.12 and 142.14 (C-9′), 147.41 (HC=N), 152.66 (C-2′), 157.12 (C-2), and 167.89 (C=O). Anal. Calc. for C17H16N4O2 (308.33): C, 66.22%, H, 5.23%, and N, 18.17%. Found: C, 65.57%, H, 4.92%, and N, 18.32%.

4-Hydroxybenzaldehyde(2-methyl-1H-benzimidazol-1-yl) acetohydrazone (9)

Crystaline solid (2.11 g, 68.50% yield) with m.p. 285-287 ˚C. TLC: Rf = 0.45 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 3.33 (s, 3H, CH3), 4.97 and 5.42 (2s, 2H, (1.0 : 3.0), CH2 minor and major), 6.83 and 6.85 (s, 2H, H-3,5), 7.14 (m, 2H, H-5′,6′), 7.43 (m, 1H, H-7′), 7.52 (m, 2H, H-2,6), 7.60 (s, 1H, H-4′), 7.62 (s, 1H, H-2′), 7.97 and 8.15 (2s, 2H (1.0 : 3.0), HC=N minor and major), 9.93 (s, 1H, OH), 11.57 and 11.67 (s, 1H, 2NH). 13C-NMR: δ 13.32 and 13.39 (CH3), 39.76 (CH2), 109.42 and 109.56 (C-7′), 115.52 (C-3,5), 117.93 and 118.06 (C-4′), 120.97, 121.18, 121.26 and 121.40 (C-5′,6′), 124.76 and 124.85 (C-1), 128.71 and 128.85 (C-2,6), 135.56 and 135.86 (C-8′), 142.10 and 142.14 (C-9′), 144.42 (HC=N), 152.49 and 152.64 (C-2′), 159.25 and 159.43 (C-4), 167.70 and 167.81 (C=O). Anal. Calc. for C17H16N4O2 (308.33): C, 66.22%, H, 5.23%, and N, 18.17%. Found: C, 65.95%, H, 5.52%, and N, 17.88%.

Furfural(1H-benzimidazol-1-yl)acetohydrazone(10)

Crystaline solid (1.74 g, 64.92% yield) with m.p. 204-206 ˚C. TLC: Rf = 0.18 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 5.06 and 5.45 (2s, 2H (1.0 : 3.0), CH2 minor and major), 6.61 (d, 1H, H-4), 6.93 (d, 1H, H-3), 7.18 (m, 2H, H-5′,6′), 7.49 (d, 2H, H-7′), 7.64 (d, 1H, H-4′), 7.83 (s, 1H, H-5), 8.12 (s, 1H, H-2′), 7.94 and 8.20 (2s, 1H ( 1.0 : 3.0) HC=N minor and major), and 11.85 (s, 1H, NH). 13C-NMR: δ 40.01 and 40.17 (CH2), 111.0 and 111.2 (C-7′), 112.1, 119.8, 121.7, 122.8, 122.9, 134.9 (7Ar-C), 137.7 and 138.0 (HC=N), 143.7 (C-2′), 145.5 (C-9′), 145.8 (C-3), 149.5 (C-1), and 168.8 (C=O). Anal. Calc. for C14H12N4O2 (268.27): C, 62.68%, H, 4.51%, and N, 20.88%. Found: C,62.70%, H, 4.56%, and N, 20.82%.

Furfural (2-methyl-1H-benzimidazol-1-yl)acetohydrazone (11)

Crystaline solid (1.64 g, 58.15% yield) with m.p. 222-22 ˚C. TLC: Rf = 0.54 (ethyl acetate/petroleum ether 1:1). 1H-NMR (DMSO-d6): δ 2.43 and 2.47 (2s, 3H, CH3), 4.97 and 5.34 (2s, 2H (3.0 : 1.0), CH2 minor and major), 6.61 (d, 1H, H-4), 6.92 (q, 1H, H-3), 7.10 (m, 2H, H-5′,6′), 7.40 (m, 1H, H-7′), 7.49 (m, 1H, H-4′), 7.80 (s, 1H, H-5), 7.94 and 8.12 (2s, 1H (3.0 : 1.0), HC=N), 11.73 and 11.84 (s, 1H, NH). 13C-NMR: δ 13.88 and 13.99 (CH3), 39.9 and 40.16 (CH2), 110.20 and 110.33 (C-7′), 112.7 and 112.8 (C-4), 118.5 and 118.7 (C-5), 118.8 (C-4′), 121.8 (C-5′), 122.1 (C-6′), 134.9 and 135.1 (C-8′), 137.9 and 138.1 (HC=N), 142.8 (C-9′), 145.7 and 145.8 (C-3), 149.5 and 149.6 (C-1), 153.1 and 153.3 (C-2ꞌ), and 169.6 (C=O). Anal. Calc. for C15H14N4O2 (282.29): C, 63.82%, H, 5.00%, and N, 19.85%. Found: C, 63.70%, H, 4.66%, and N, 20.22%.

References

Habib NS and El-Hawash SA (1989) Il Farmaco, Ed. Sci 44:1225-1232

Shetgiri NP and Kokitkar SV (2001) Synthesis and biological activity of new benzimidazoles. Ind J Chem 40B:163-166

Table S1. Development of QSAR Equation 1

Constant
(Intercept) / Coefficienta / r / f / SE / s
MW / ClogP / LogS / CMR / tPSA / HA
0.772 / 0.010 / 0.737 / 10.732 / 0.388 / 0.010
2.475 / 0.001 / 0.335 / 0.760 / 5.457 / 0.396 / 0.032
2.226 / 0.004 / 0.306 / -0.164 / 0.763 / 3.242 / 0.421 / 0.091
4.414 / 0.039 / 0.927 / 0.459 / -1.883 / 0.861 / 4.294 / 0.358 / 0.056
1.359 / -0.024 / 0.737 / 1.891 / -0.413 / 0.062 / 0.887 / 3.701 / 0.355 / 0.089
-9.339 / -0.526 / 0.441 / 0.932 / 14.421 / 0.017 / 6.557 / 0.983 / 18.934 / 0.150 / 0.007

a Dependant variable is a pMIC; ClogP: Calculated hydrophobic parameter (logarithm of partition coefficient); LogS: The aqueous solubility of a compound; CMR: Calculated molar refractivity; NVE: Number of valence electrons; tPSA: Topological Polar Surface Area; HD: Hydrogen bond donors. HA: H bond acceptors.