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Research Article
Synthesis and in vitro evaluation of new oxadiazole thioethers as antibacterials
expand article infoAli H. Abbas‡
‡ University of Tikrit, Tikrit, Iraq

Corresponding author: Ali H. Abbas ( alih.phchm@tu.edu.iq )

Academic editor: Emilio Mateev
© 2024 Ali H. Abbas.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Abbas AH (2024) Synthesis and in vitro evaluation of new oxadiazole thioethers as antibacterials. Pharmacia 71: 1-11. https://doi.org/10.3897/pharmacia.71.e139122
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Abstract

A study was conducted to synthesize a new set of compounds named comp.4–7 using the 1,3,4 tautomer of oxadiazole as the centroid unit. These compounds were subjected to various characterization processes, including thin-layer chromatography, infrared spectroscopy, and 1HNMR spectroscopy. The study was based on previous research that established several compounds’ diverse range of biological activities, such as hydrazide Schiff’s bases (hydrazones), oxadiazoles, thiophenes, and isoxazoles. These compounds had been found to possess properties against bacteria, fungi, TB, viruses, cancer cells, and inflammatory responses, as well as analgesic properties. The results of the docking study were conducted in MOE software, targeting the largest binding site of E. coli gyrase B (PDB: 6YD9) as identified by SITE FINDER, suggesting that these compounds had great potential to be effective antibacterial agents. To evaluate the synthesized compounds antibacterial activities, the well diffusion method was used, and the findings revealed that the synthesized compounds exhibit slight to moderate activities against E. coli, S. aureus, and K. pneumoniae.

Keywords

oxadiazoles, Schiff’s base, thiophenes, isoxazoles, antibacterial

Introduction

Heterocyclic compounds play a vital role in pharmaceutical and material sciences, and oxadiazole is one of the most widely used compounds due to its diverse properties. Among the structural isomers of oxadiazole, 1,3,4-oxadiazole is of particular interest in medicinal chemistry as a promising pharmacophore for developing new drugs with a wide range of activities (Balaji et al. 2015; Al-Mulla 2017; Kim et al. 2023).

Isoxazole is another five-membered heterocycle having two heteroatoms, which are oxygen and nitrogen, at the adjacent positions. Isoxazole compounds possess many biological activities that are explained by a wide spectrum of protein targets that isoxazole compounds are possible to interact with, such as anticancer, antibacterial, antifungal, antiviral, and anti-inflammatory (Zhu et al. 2018).

Thiophenes and their derivatives are an important class of heterocyclic compounds that possess a wide spectrum of biological properties, such as antibacterial and antifungal, anti-inflammatory, antioxidant, and antitumor (Shah and Verma 2018; Metwally et al. 2023).

In medicinal chemistry, new compounds with improved biological activity can be created by hybridization, which involves combining two or more distinct molecules. Hydrazones [Hydrazide Schiff’s base derivatives] can be considered scaffolds because they possess great potential for various pharmaceutical applications because of their high reactivity and excellent affinity toward numerous biological targets, so they are an attractive option for developing new drugs. A reactive (-CO-NH-N=CH-) group, commonly referred to as an azomethine group, is the unique structure included in these compounds. Because of their unique structure and favorable pharmacological properties, hydrazones have been extensively researched in medicinal chemistry, and a wide range of biological activities, including antibacterial, antifungal, antiviral, and anticancer properties, have been associated with them. In searching for a promising strategy for developing new drugs with enhanced pharmacological properties, hydrazide Schiff’s base derivatives represent attractive ones (Gilani et al. 2011; Babu et al. 2014; Sulaiman and Sarsam 2020). The current research utilizes molecular docking to investigate the interaction of novel compounds with E. coli DNA gyrase (PDB: 6YD9), a critical target for antibacterial therapy. The high-resolution crystal structure (1.60 Å) of chain, containing a co-crystallized ligand (ON2), was prepared by removing water molecules, delineating the binding site, and optimizing hydrogen geometry. Computational methods, including energy minimizing using AMBER10 force field and docking within MOE2022, ensured robust modeling. In silico physicochemical analyses, such as clogP (all < 5) and TPSA, aligned with Lipinski’s rule of five, underscoring the drug-like potential of the synthesized compounds. ADMET profiling via SwissADME and ADMETlab 3.0 further identified candidates for favorable pharmacokinetic and toxicity profiles, aiding in prioritization for further drug development (Lipinski et al. 2001; Trott and Olson 2010; Daina et al. 2017). The targeted compounds are shown in Fig. 1.

Figure 1. 

Structures of synthesized targeted compounds.

Materials and methods

The purity of the synthesized compounds was checked by thin-layer chromatography (TLC), which was conducted using pre-coated aluminum sheets. To facilitate visualization, the aluminum sheets were exposed to a UV light adjusted to 254 nm wavelength. Based on their distinct polarity and ability to separate and distinguish the synthesized compounds, two solvent systems (eluents) named E1 and E2, which were composed of toluene:ethylacetate:ethanol (3:2:1) and ethylacetate:methanol:ammonia (5:3.5:1.5) as parts, respectively, were utilized during the synthesis process. Furthermore, all the synthesized derivatives were characterized through spectroscopic analysis (IR and 1HNMR). (Silverstein et al. 2005a, 2005b; Pavia et al. (2015a, 2015b, 2015c). The infrared spectra were recorded using the Shimadzu Specac GS 10800-R IRAffnity-1 Spectrometer (Shimadzu, Japan) at the University of Baghdad, College of Pharmacy. The measurement unit (ύ, cm-1) and 1HNMR spectra were obtained on a Bruker and Varian model ultrashield (400 and 500 MHz) spectrophotometer with tetramethylsilane (TMS) as an internal standard, DMSO-d6 used as solvent for samples, chemical shift values expressed as (δ=ppm) and coupling constant in (j = Hz). 1HNMR was run at Tehran-University.

Chemical synthesis

The following sections involved the details of the synthesis from starting material to final products:

Synthesis of the first intermediate; comp. 1

A precise amount of vanillic acid weighing (7.0 g, 42 mmoles) was mixed with methanol, and the resulting solution was cooled to 0 °C. Concentrated H2SO4 (5 mL) was then slowly added drop by drop to the solution, which was stirred at room temperature [before being refluxed for 7 hrs] for 48 hours. TLC results indicate the formation of a product. A precipitate formed with time when the solution was transferred into a crushed ice contained in a suitable beaker, and after the compete precipitation, NaHCO3 (10%) was added wisely until pH was slightly alkaline to get rid of any excess acid and to neutralize the H2SO4. The product was collected by filtration and dried. The desired product was obtained as a yield of 7.0 g through this process (Abbas et al. 2021).

Comp. 1: whitish-brown powder, yield 91%, M.P: 60–62 °C.

ATR-FTIR spectrum in cm-1: (1686) C=O stretching vibration, (1276) C-(C=O)-O stretching vibration of aromatic ester.

1HNMR (500 MHz, DMSO-d6) in ppm.: 9.99(1H, br s, Ar-OH), 7.46–7.42(2H, m, aromatic protons at positions 2 and 6), 6.88–6.84(1H, d, aromatic proton at position 5), 3.80(3H, s, COOCH3), and 3.83(3H, s, OCH3).

Synthesis of the second intermediate; comp. 2

Comp.1 was dissolved in hot absolute ethanol (99.9%) using 5 mL. The amount of Comp.1 (27 mmoles), which is equivalent to (5.0 g). Then, 80% hydrazine hydrate (270 mmoles, 13.5 g) was added to the solution gradually. The reaction was monitored by TLC to track the progress of the reaction, and the results of TLC indicate that 4 hrs as reflux time was required. The reaction system was left to cool to r.t with overnight stirring and cooling, and a white precipitate formed as a solid mass, which was washed with cold ethanol, filtered out, and dried. The product yield was found to be 3.5 g after completion of the drying process (Yaseen et al. 2022).

Comp. 2: white powder, yield 70%, M.P: 208–210 °C.

ATR-FTIR spectrum in cm-1: (3310) phenolic OH stretching vibration overlapped with NH2 asymmetric stretching vibration, (3256) NH amide stretching vibration, (3210) NH2 symmetric stretching vibration, (1628) C=O stretching vibration of amide, (1600) NH bending vibration, and (1585) NH bending vibration of amide.

1HNMR (400MHz, DMSO-d6) in ppm: 9.52(2H, s, CONH and Ar-OH), 7.4–7.29(2H, m, aromatic protons at positions 2 and 6), 6.84–6.76(1H, d, aromatic proton at position 5), 4.38(2H, s, NH-NH2), and 3.78(3H, s, OCH3).

Synthesis of the third intermediate; comp. 3

A compound mixture was prepared by suspending comp.2 (6.86 mmoles, 1.25 g) in 30 mL of 50% ethanol. CS2 (0.0103 mmoles, 0.785 g) was then added to the mixture and stirred for a few minutes. Next, KOH (10.3 mmoles, 0.7 g) was introduced, and the whole mixture was refluxed for 12 hours. The progress of the reaction was monitored by TLC, and the evolution of H2S was noted for better observation. Upon completion of the refluxing process, conc. HCl was added dropwise to a beaker containing the reaction solution and 30 mL of crashed ice. Precipitate began to be formed and increased until the pH of the mixture became 2–3 [no further precipitate was formed]. The precipitate was then filtered, dried, and purified using the base to dissolve the product and then acidification to reform the pure product, which was 0.9 g (Karabanovich et al. 2016).

Comp. 3: faint yellow powder, yield 59%, M.P: 186–189 °C.

ATR-FTIR spectrum in cm-1: (3452) phenolic OH stretching vibration, (3155) NH (br stretching), 2670(w) SH stretching vibration.

1 HNMR (400 MHz, DMSO-d6) in ppm.: 14.58(1H, s, -SH), 10.04(1H, s, Ar-OH), 7.37–7.3(2H, m, aromatic protons at positions 2 and 6), 6.94–6.92(1H, d, aromatic proton at position 5), and 3.84(3H, s, OCH3).

Synthesis of the first final product; comp.4

A chemical compound known as comp.3, weighing (2.23 mmoles, 0.5 g) was dissolved completely in 5 mL of absolute ethanol. To the solution, triethylamine (0.00223 mmoles or 0.22564 g) was added gradually, and after a few minutes of gentle and constant stirring, [4-(chloromethyl) benzaldehyde (0.00223 mmoles or 0.345 g)] was added to the mixture. The solution was heated gently to a temperature of about 50 °C, which resulted in the formation of a precipitate. The precipitate was then filtered, dried, and finally crystallized from a mixture of boiled absolute ethanol and 2-methoxy ethanol (Hassan et al. 2023). This process led to the formation of a pure final product, which weighed 0.5 g.

Comp. 4: white crystals, yield 65.5%, M.P: 167–169 °C.

ATR-FTIR spectrum in cm-1: (3417–2830) broad phenolic OH stretching vibration, (2735) CH stretching vibration of aldehyde, and (1697) C=O stretching vibration of aldehyde carbonyl.

1 HNMR (400MHz, DMSO-d6) in ppm: 9.98(1H, s, Ar-OH), 9.97(1H, s, COH), 7.9–7.88(2H, d, aromatic protons at positions 10 and 12), 7.71–7.69(2H, d, aromatic protons at positions 9 and 13), 7.41–7.38(2H, m, aromatic protons at positions 2 and 6), 6.95–6.93(1H, d, aromatic proton at position 5), 4.65(2H, s, -S-CH2), and 3.85(3H, s, OCH3).

Synthesis of the second final product; comp.5

Comp.4 (0.3 mmole, 0.1 g) was suspended in 5 mL of absolute ethanol. Three drops of glacial acetic acid were added to the suspension with constant stirring for 15 minutes. Then, 4-hydroxybenzohydrazide (0.3 mmole, 0.044 g) was added to the mixture, and the reaction mixture was refluxed for 30 minutes. During this process, the suspension became a clear solution. The reaction mixture was then allowed to stir gently overnight. The formed precipitate was filtered and dried. The excess solvent was evaporated, and the product was crystallized from hot absolute ethanol. The final yield of pure product was 0.09 g (Han et al. 2018).

Comp. 5: white powder, yield 65%, M.P: 230–232 °C.

ATR-FTIR spectrum in cm-1: (3418) stretching vibration of two phenolic OH, (3244) NH amide stretching vibration, (1647) C=O stretching vibration of amide carbonyl, and (1608) C=N stretching vibration of imine.

1 HNMR (400MHz, DMSO-d6) in ppm: 11.64(1H, s, CONH), 10.12(1H, s, Ar-OH`), 9.96(1H, s, Ar-OH), 8.41(1H, s, -N=CH-), [7.81–7.79, 7.7–7.68, 7.56–7.54] (6H, d, aromatic protons at positions 9, 10, 12, 13, 17, and 21), 7.43–7.39(2H, m, aromatic protons at positions 2, and 6), 6.96–6.94(1H, d, aromatic proton at position 5), 6.87–6.85(2H, d, aromatic protons at positions 18, and 20), 4.6(2H, s, -SCH2-), and 3.86(3H, s, OCH3).

Synthesis of the third final product; comp.6

Comp.3, which had a weight of (0.67 mmole, 0.15 g), was dissolved in 3 mL of absolute ethanol. After that, (0.67 mmole, 0.0677 g) of triethylamine was added to the mixture and stirred for 10–15 minutes. Subsequently, (0.67 mmole, 0.1118 g) of 2-chloro-5-(chloromethyl)thiophene was added, and the reaction mixture was refluxed for 2 hours. Once the refluxing was complete, D.W. was added until a precipitate appeared, and the mixture was then filtered, dried, and subjected to crystallization using a two-solvent system of hot absolute ethanol and hot D.W (1:1) (Hassan et al. 2023).

Comp. 6: white crystals, yield 48%, M.P: 139–141 °C.

ATR-FTIR spectrum in cm-1: (2978 and 2893) asymmetric and symmetric stretching vibration of CH2, (1447) bending vibration of CH2.

1HNMR(400MHz, DMSO-d6) in ppm: 9.96(1H, s, Ar-OH), 7.44–7.42(2H, m, aromatic protons at positions 2 and 6), 7.01–6.93(3H, m, protons of thiophene ring and aromatic protons at positions 5, 9, and 10), 4.75 (2H, s, -SCH2-), 3.86(3H, s, OCH3).

Synthesis of the fourth final product; comp. 7

Comp. 7 was prepared by the same procedure that was followed in the preparation of comp. 6, except crystallization was from hot absolute ethanol only (Hassan et al. 2023).

Comp. 7: white crystals, yield 47%, M.P: 116–118 °C.

ATR-FTIR spectrum in cm-1: (2982 and 2835) asymmetric and symmetric stretching vibration of CH2, (1632) stretching vibration of (–O-C=N-), (1466) asymmetric bending vibration of CH3 and scissoring bending vibration of CH2, (1369) symmetrical bending vibration of CH3 groups.

1HNMR (400MHz, DMSO-d6) signals in ppm: 9.96 (1H, s, Ar-OH), 7.43–7.4 (2H, m, aromatic protons at positions 2 and 6), 6.97–6.93 (1H, d, aromatic proton at position 5), 4.39 (2H, s, -SCH2-), 3.85 (3H, s, OCH3), 2.35 (3H, s, methyl protons at position near to O), 2.24 (3H, s, methyl protons at position near to N).

Molecular induced fit (flexible) docking study

Molecular docking investigations were conducted on the E. coli DNA-binding protein 6YD9 (DNA Gyrase), leveraging its high-resolution (1.60 Å) crystal structure derived from X-ray crystallography. The protein is composed of a single chain (chain A) harboring a co-crystal ligand (ON2) binding site. Docking was executed on chain A following preparatory measures encompassing water removal, binding site delineation, and hydrogen addition. The AMBER10 force field was employed for energy minimization purposes. The MOE 2022 software facilitated molecular docking, with the SMILE representations of the investigated compounds generated via ChemBioDraw Ultra 13.0. These were subsequently transformed into 3D configurations within MOE 2022, followed by protonation and energy minimization utilizing the AMBER 10 force field with a 0.1 Å RMSD. Validation of the docking procedure involved re-docking the co-crystallized ligand (NO2). An RMSD value of 1.18 Å, computed using Discovery Studio Visualizer and VMD, substantiated the precision of the MOE program for docking the novel ligands (Prieto-Martinez et al. 2019; Hamdoon and Hadi 2024).

Antibacterial assay

To examine inhibition bacterial growth related to the synthesized compounds, diffusion assays were performed. In which McFarland turbidity of 0.5, having a concentration of around 1.5×108 colony-forming units per milliliter, was the standard to compare with the prepared bacterial suspension. The inoculated mixture was applied to the surface Mueller-Hinton agar plates. After inoculation, a current of sterile air under a hood was applied to remove any excess liquid. To assess the efficacy of the synthesized compounds in combating bacterial growth, in each agar plate of the examined bacteria, four wells were created. Then, 80 μl of each concentration of the compounds, at 1000 μg/mL, were poured into these wells. These plates were placed in an incubator set at 37 °C for 24 hours. Following the incubation period, the diameter of the inhibition zone formed around each well was measured to determine the potency of the targeted compounds (Bauer et al. 1966).

Results and discussion

Chemistry

A successful multi-step reaction process was executed, which involved the synthesis of several new compounds, as shown in Fig. 2. The process involved various chemical changes, starting with esterification of a carboxylic acid with an alcohol in the presence of an acid catalyst (Smith 2017). This produced the initial compound, Comp. 1, which was analyzed using various techniques. The FTIR spectrum of Comp. 1 showed a significant carbonyl group of aromatic ester at 1686 cm-1, while the 1HNMR analysis confirmed the presence of COOCH3 at 3.8 ppm.

Figure 2. 

Scheme showing the stepwise synthesis of targeted compounds.

Next, Comp. 1 was refluxed in absolute ethanol with hydrazine hydrate 80% to produce Comp. 2 (Sabzi and Al-Mudhafar 2023). The FTIR spectrum of Comp.2 was characterized by doublet bands (asymmetric and symmetric) for the primary amine of hydrazide at 3310 cm-1 and 3210 cm-1, respectively, and 3256 cm-1 NH amide stretching. Additionally, the 1628 cm-1 C=O stretching of amide and 1600 cm-1 of NH2 bending were observed. The presence of CONH at 9.53 ppm and 2H as a singlet for NH2 at 4.38 ppm were confirmed by 1HNMR analysis.

Furthermore, Comp. 3 was obtained by refluxing the ethanolic suspension of Comp. 2 with CS2 in the presence of KOH (Saoud 2017). The FTIR spectrum of Comp.3 was characterized by the phenolic OH stretching vibration at 3452 cm-1, the NH stretching vibration at 3155 cm-1, weak SH stretching at 2670 cm-1, and the absence of the amide band at 1628 cm-1. The 1HNMR spectrum showed the appearance of the SH proton at 14.58 ppm as a singlet and the absence of all protons related to hydrazide.

Comp. 4, Comp. 6, and Comp. 7 were obtained through a reaction between Comp. 3 as nucleophilic species and 4-(chloromethyl) benzaldehyde (Comp. 4), 2-chloro-5-(chloromethyl)thiophene (Comp. 6), or 4-(chloromethyl)-3,5-dimethyl isoxazole (Comp. 7) as electrophiles in the presence of a base catalyst and absolute ethanol as reaction solvent (Karty 2018). These new compounds were carefully characterized, using various analytical techniques to confirm their structures and properties. FTIR is characterized by 2735 cm-1 stretching of C-H aldehyde and 1697 cm-1 C=O stretching of aldehyde carbonyl. Comp.6 showed asymmetric and symmetric CH2 stretching at 2978 cm-1 and 2893 cm-1, and CH2 bending at 1447 cm-1. Comp. 7, in addition to (–O-C=N-) stretching vibration at 1632 cm-1, also showed asymmetrical stretching vibration of CH of –CH3 groups at 2982 cm-1, symmetric stretching vibration of CH3 at 2835 cm-1, and 1466 cm-1 asymmetric bending vibration of CH3 groups.

1 HNMR is characterized by the presence of a new proton at 9.97 ppm of COH as a singlet, four aromatic protons from 7.9–7.69 ppm related to the benzene ring of 4-(chloromethyl) benzaldehyde, and the absence of a SH proton at 14.58 ppm and instead the appearance of new two protons as a singlet at 4.65 ppm for comp. 4, 4.75 ppm for comp. 6, and 4.35 ppm for comp. 7, which related to –SCH2. The appearance of new protons in the aromatic region due to the thiophene ring in comp.6, and finally the appearance of six protons at their expected sites due to two methyl groups of 3,5-dimethylisoxazole in comp. 7.

Lastly, Comp. 5 is a Schiff base product of hydrazone type obtained by reacting aldehydes with primary amines in mildly acidic conditions (Klein 2021). FTIR was characterized by the absence of aldehyde CH stretching vibration at 2735 and aldehyde carbonyl at 1697 cm-1, which was replaced by imine stretching at 1608 cm-1, and the presence of amide carbonyl at 1647 cm-1. 1HNMR revealed the presence of new protons at 11.64 ppm as singlet, which was related to CONH; at 10.12 ppm due to OH` of 4-hydroxybenzohydrazidel; at 8.41 ppm as singlet, which was related to N=CH; and four aromatic protons at 7.81–7.79 ppm and at 6.87–6.85 ppm. This multi-step reaction process has resulted in the successful synthesis of the new compounds.

Molecular docking analysis

Molecular docking simulations were conducted in MOE software, targeting the largest binding site of E. coli gyrase B (PDB: 6YD9) as identified by SITE FINDER. An induced-fit docking protocol, incorporating ligand and protein flexibility, was employed. Each molecule was allowed a maximum of five interactions with the protein (Figs 3–6). The optimal docking pose for each molecule, along with its docking score and binding site information, was documented (Table 1). This data was utilized to predict the preferred binding mode and affinity. The predicted affinity for the evaluated substances with 6YD9 was considered representative of the binding free energy (∆G) (Al-Shuaeeb et al. 2024). The results of (∆G) indicate that all the synthesized compounds (4–7) show good affinity for binding to the target site in comparison with cocrystal ligand (ON2). The value of RMSD for all synthesized compounds less than 2 Å indicates that the docking pose closely matches the reference structure, suggesting good predictive accuracy.

Figure 3. 

Ligand (comp. 4) interactions.

Figure 4. 

Ligand (comp. 5) interactions.

Figure 5. 

Ligand (comp. 6) interactions.

Figure 6. 

Ligand (comp. 7) interactions.

Table 1.
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Scores for docking of tested compounds against the target site of co-crystallized ligand are represented in ∆G values measured in kcal/mol.

Ligand RMSD value Docking score (Kcal/mol)
Cocrystal (ON2) 1.18 -6.28
Comp. 4 1.68 -7.26
Comp. 5 2.01 -8.06
Comp. 6 1.58 -7.43
Comp. 7 1.75 -7.95

Antibacterial evaluation

There are different levels of activity that can be measured using a unit called ZI. When there is no activity, ZI is equal to zero. When activity is present, ZI can range from 5 to 10 mm for slightly active, 10 to 15 mm for moderately active, and more than 15 mm for highly active (Sahib and Mohammed 2020; Ali and Farhan 2023). In the study, several chemical compounds (comp. 4–7) were specifically targeted and evaluated for their antibacterial properties using the well diffusion technique. The antibacterial activities of these compounds were compared with two standard antibacterial agents, amoxicillin and nitrofurantoin, using both gram-positive and gram-negative bacteria. In addition, a control group was established using the solvent DMSO.

At a concentration of 1000 μg/mL, four of the compounds (comp. 4, 5, 6, and 7) showed excellent antibacterial activity against E. coli, which was comparable to that of amoxicillin. Another compound (comp. 5) demonstrated slightly better antibacterial activity than amoxicillin when tested against S. aureus, but its activity was lower than that of cefixime at a concentration of 1000 μg/mL.

Furthermore, comp. 6 showed similar activity to amoxicillin when tested against S. aureus, and it exhibited comparable activity to both amoxicillin and cefixime when tested against K. pneumoniae. Interestingly, comp. 5 demonstrated the best activity among all derivatives tested against S. aureus, while showing the least activity against E. coli. This can be attributed to the compound’s hydrophobicity, as more hydrophobic compounds tend to be more effective against gram-positive bacteria (Beale and Block 2011).

It is worth noting that none of the compounds synthesized in the study showed any significant activity against S. pyogenes, B. subtilis or P. aeruginosa (Table 2).

Table 2.
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The findings of the synthesized compounds’ antibacterial activities.

Comp. name Conc. μg/mL Gram (+)ve Gram (-)ve
S. pyogenes S. aureus B. subtilis P. aeruginosa E. coli K. pneumoniae
Zone of inhibition (mm)
Comp. 4 103 - 8 - - 11 -
Comp. 5 103 - 14 - - 10 -
Comp. 6 103 - 13 - - 12 11
Comp. 7 103 - 6 - - 11 -
Amoxicillin 103 5 13 40 28 11 11.5
Cefixime 103 6 16 20 6 22 13
Nitrofurantoin 103 9.5 21 31 17 16 20
DMSO Solvent and control - - - - - -

Physicochemical properties

Understanding the physicochemical characteristics of drugs is crucial to making them work better. One important factor is the partition coefficient (logP), which can be computed in silico (clogP). It gives an idea about how drugs move around inside the human body. Interestingly, all the synthesized compounds under consideration have a clogP value less than 5, which goes in accordance with a common rule called the Lipinski rule of five. Another important thing to consider is the total polar surface area (TPSA). This gives information about the surface area taken up by parts of the drug that are attracted to water. Drugs with lower TPSA values are usually better because they can pass through cell membranes more easily. So, by carefully studying these factors, it is possible to improve how well drugs work and help patients get better results from their treatments (Table 3).

Table 3.
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The properties related to physical and chemical characteristics of the compounds that were synthesized.

Comp. ClogP Ali class n. H-bond acceptors n. H-bond donors n. rotatable bonds TPSA / °A
Comp. 4 2.92 Moderately soluble 6 1 6 110.75
Comp. 5 3.50 Poorly soluble 9 3 9 155.37
Comp. 6 3.82 Poorly soluble 5 1 5 121.92
Comp. 7 2.76 Moderately soluble 7 1 5 119.71

In silico ADMET and toxicity properties

A rigorous in silico investigation of the ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiles of the newly synthesized compounds was conducted employing the SwissADME cheminformatics software and ADMETlab 3.0 web server. This comprehensive analysis facilitated the identification of promising drug candidates exhibiting favorable safety profiles and the exclusion of compounds demonstrating undesirable ADMET characteristics from further progression into subsequent drug development stages. A detailed tabulation of the predicted ADMET properties for the target compounds is presented in Tables 4, 5. The scores in the table reflect the probability of toxicity of each compound (Fu et al. 2024).

Table 4.
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Analysis of ADMET properties has been predicted for the mentioned compounds.

Comp. CYP2C9 CYP2D6 CYP3A4 BBB GI absorption P-gp substrate
S I S I S I
Comp. 4 P Yes No No No Yes No High No
Comp. 5 No Yes No No P Yes No Low No
Comp. 6 P Yes P No P Yes No High No
Comp. 7 No Yes No No P Yes No High Yes

S = substrate, I = inhibitor, P = probable.
Table 5.
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Predicted analysis of toxicity properties of the mentioned compounds.

Comp. Hepatotoxicity* Nephrotoxicity* Ototoxicity* Genotoxicity* Neurotoxicity* Hematotoxicity*
Comp. 4 0.646 0.271 0.292 0.819 0.34 0.126
Comp. 5 0.693 0.321 0.329 0.999 0.35 0.045
Comp. 6 0.735 0.542 0.435 0.979 0.133 0.144
Comp. 7 0.896 0.602 0.814 0.999 0.124 0.383

* Score 0 means non-toxic, while score 1 means toxic compound at targeted organ; scores between 0 and 1 indicate the compound is probably toxic.

Conclusion

Through a conventional synthesis method, a set of new oxadiazole-thioether derivatives was successfully developed and characterized by thin-layer chromatography, infrared spectroscopy, and 1HNMR spectroscopy. The docking studies were conducted in MOE software, targeting the largest binding site of E. coli gyrase B (PDB: 6YD9). In an effort to evaluate their potential as antibacterial agents, these derivatives were tested and found to exhibit activity against E. coli, K. pneumoniae, and S. aureus. Notably, Comp. 6 was found to have a particularly broad spectrum of activity. Future studies could focus on advanced modeling, SAR analysis, and testing against resistant strains to enhance potency and clinical potential. Investigating combination therapies and mechanisms of action may also address antimicrobial resistance. Comp. 6, with its broad spectrum activity, shows promise as a lead for next-generation antibacterial agents.

Additional information

Conflict of interest

The author has declared that no competing interests exist.

Ethical statements

The author declared that no clinical trials were used in the present study.

The author declared that no experiments on humans or human tissues were performed for the present study.

The author declared that no informed consent was obtained from the humans, donors or donors’ representatives participating in the study.

The author declared that no experiments on animals were performed for the present study.

The author declared that no commercially available immortalised human and animal cell lines were used in the present study.

Funding

No funding was reported.

Author contributions

The author solely contributed to this work.

Author ORCIDs

Ali H. Abbas https://orcid.org/0000-0002-2387-809X

Data availability

All of the data that support the findings of this study are available in the main text or Supplementary Information.

References

  • Abbas AH, Razzak Mahmood AA, Tahtamouni LH, Al-Mazaydeh ZA, Rammaha MS, Alsoubani F, Al-bayati RI (2021) A novel derivative of picolinic acid induces endoplasmic reticulum stress-mediated apoptosis in human non-small cell lung cancer cells: synthesis, docking study, and anticancer activity. Pharmacia 68(3): 679–692. https://doi.org/10.3897/pharmacia.68.e70654
  • Ali AA, Farhan MS (2023) Synthesis, characterization and preliminary anti-microbial evaluation of new ketorolac hydrazone derivatives. History of Medicine 9(2): 46–50.
  • Al-Mulla A (2017) A review: biological importance of heterocyclic compounds. Der Pharma Chemica 9(13): 141–172.
  • Al-Shuaeeb RAA, Abbas AH, Tawfeeq MF, Abood SJ (2024) Exploring natural medicinal plants for novel Bcl-2 inhibitors: In silico drug design and computational interaction mechanism for anti-cancer activity. Tikrit Journal of Pharmaceutical Sciences 18(1): 1–11. https://doi.org/10.25130/tjphs.2024.18.1.1.1.11
  • Babu RR, Naresh K, Ravi A, Reddy BM, Babu VH (2014) Synthesis of novel isoniazid incorporated styryl quinazolinones as anti-tubercular agents against INH sensitive and MDR M. tuberculosis strains. Medicinal Chemistry Research 23(10): 4414–4419. https://doi.org/10.1007/s00044-014-1020-2
  • Balaji K, Bhatt PR, Mallika D, Jha AN (2015) Design, synthesis and antimicrobial evaluation of some Mannich base derivative of 2 (2-substituted)-5-amino-thiadiazoles. International Journal of Pharmacy and Pharmaceutical Sciences 7: 145–149.
  • Bauer AW, Kirby WMM, Sherris JC, Truck M (1966) Antibiotic susceptibility testing by standardized single disk method. American Journal of Clinical Pathology 45(4): 493–496. https://doi.org/10.1093/ajcp/45.4_ts.493
  • Beale JM, Block JH (2011) Chapter 8, Antibacterial Antibiotics. In: Wilson and Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry (12th ed.). Philadelphia: Lippincott Williams & Wilkins, a Wolters Kluwer business, 258–329.
  • Daina A, Michielin O, Zoete V (2017) SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness, and medicinal chemistry friendliness of small molecules. Scientific Reports 7(1): 42717. https://doi.org/10.1038/srep42717
  • Fu L, Shi S, Yi J, Wang N, He Y, Wu Z, Cao D (2024) ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support. Nucleic Acids Research 52(W1): W422–W431. https://doi.org/10.1093/nar/gkae236
  • Gilani SJ, Khan SA, Alam O, Siddiqui NA (2011) Synthesis and in vitro antimicrobial evaluation of condensed heterocyclic 6-substituted 1, 2, 4-triazolo-[3, 4-b]-1, 3, 4-thiadiazole and 1, 3, 4-oxadiazole derivatives of isoniazid. Acta Poloniae Pharmaceutica 68(2): 205–211. https://doi.org/10.1002/chin.201103156
  • Han MI, Bekci H, Cumaoğlu A, Küçükgüzel ŞG (2018) Synthesis and characterization of 1, 2, 4-triazole containing hydrazide-hydrazones derived from (S)-Naproxen as anticancer agents. Marmara Pharmaceutical Journal 22: 559–569. https://doi.org/10.12991/jrp.2018.98
  • Hassan OM, Mahmood AA, Tahtamouni L (2023) Synthesis and docking studies of new 5-bromoindole-2-carboxylic acid oxadiazole derivatives as EGFR inhibitors. Tikrit Journal of Pharmaceutical Sciences 17(1): 58–77. https://doi.org/10.25130/tjphs.2023.17.1.6.58.77
  • Karabanovich G, Zemanová J, Smutný T, Székely R, Šarkan M, Centárová I, Vocat A, Pávková I, Čonka P, Němeček J, Stolaříková J, Vejsová M, Vávrová K, Klimešová V, Hrabálek A, Pávek P, Cole ST, Mikušová K, Roh J (2016) Development of 3,5-Dinitrobenzylsulfanyl-1,3,4-oxadiazoles and thiadiazoles as selective antitubercular agents active against replicating and nonreplicating Mycobacterium tuberculosis. Journal of Medicinal Chemistry 59(6): 2362–2380. https://doi.org/10.1021/acs.jmedchem.5b00608
  • Karty MJ (2018) Chapter 9, Nucleophilic Substitution and Elimination Reactions. In: Organic Chemistry Principles and Mechanisms (2nd ed.). New York-London: W. W. Norton & Company, Inc., 1, 442–502.
  • Kim H, Gu L, Yeo H, Choi U, Lee CR, Yu H, Koo S (2023) Rapid assembly of pyrrole-ligated 1, 3, 4-oxadiazoles and excellent antibacterial activity of iodophenol substituents. Molecules 28(8): 3638. https://doi.org/10.3390/molecules28083638
  • Klein D (2021) Organic Chemistry (4th ed.). Hoboken: John Wiley and Sons, Inc. Chapter 19, Aldehydes and Ketones, 884–837.
  • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews 46(1–3): 3–26. https://doi.org/10.1016/S0169-409X(00)00129-0
  • Metwally HM, Khalaf NA, Abdel-Latif E, Ismail MA (2023) Synthesis, DFT investigations, antioxidant, antibacterial activity and SAR-study of novel thiophene-2-carboxamide derivatives. BMC Chemistry 17(1): 1–21. https://doi.org/10.1186/s13065-023-00917-2
  • Pavia DL, Lampman GM, Kriz GS, Vyvyan JR (2015a) Chapter 2, Infrared Spectroscopy. In: Introduction to spectroscopy (5th ed.). United States: Cengage Learning, 14–106.
  • Pavia DL, Lampman GM, Kriz GS, Vyvyan JR (2015b) Chapter 5, Nuclear magnetic resonance spectroscopy Part One: Basic Concepts. In: Introduction to spectroscopy (5th ed.). United States: Cengage Learning, 215–289.
  • Pavia DL, Lampman GM, Kriz GS, Vyvyan JR (2015c) Chapter 5, Nuclear magnetic resonance spectroscopy Part Three: Spin–Spin Coupling. In: Introduction to spectroscopy (5th ed.). United States: Cengage Learning, 349–456.
  • Sabzi NA, Al-Mudhafar MM (2023) Synthesis, characterization, and antimicrobial evaluation of new Schiff bases derived from vanillic acid conjugated to heterocyclic 4H-1, 2, 4-triazole-3-thiol. Pharmacia 70(3): 657–663. https://doi.org/10.3897/pharmacia.70.e104579
  • Sahib HA, Mohammed MH (2020) Synthesis and preliminary biological activity evaluation of new N-substituted phthalimide derivatives. Iraqi Journal of Pharmaceutical Sciences 29(1): 247–252. https://doi.org/10.31351/vol29iss1pp247-252
  • Saoud SA (2017) Synthesis of some heterocyclic compounds at position six of 2-methyl phenol and evaluation of their antioxidant properties besides to antibacterial activities for some of them. University of Baghdad, College of Education for Pure Science/Ibn-AL-Haitham, Chemistry Department.
  • Silverstein RM, Webster FX, Kiemle DJ (2005a) Chapter 2, Infrared Spectrometry. In: Spectrometric identification of organic compounds (7th ed.). Hoboken: John Wiley & Sons, Inc., 72–126.
  • Silverstein RM, Webster FX, Kiemle DJ (2005b) Chapter 3, Proton NMR spectrometry. In: Spectrometric identification of organic compounds (7th ed.). Hoboken: John Wiley & Sons, Inc., 127–203.
  • Smith GJ (2017) Chapter 22, Carboxylic Acids and Their Derivatives—Nucleophilic Acyl Substitution. In: Organic Chemistry (5th ed.). New York: McGraw-Hill Education, 868–923.
  • Sulaiman AT, Sarsam SW (2020) Synthesis, characterization and antibacterial activity evaluation of new indole-based derivatives. Iraqi Journal of Pharmaceutical Sciences 29(1): 207–215. https://doi.org/10.31351/vol29iss1pp207-2015
  • Trott O, Olson AJ (2010) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry 31(2): 455–461. https://doi.org/10.1002/jcc.21334
  • Yaseen Y, Kubba A, Shihab W, Tahtamouni L (2022) Synthesis, docking study, and structure-activity relationship of novel niflumic acid derivatives acting as anticancer agents by inhibiting VEGFR or EGFR tyrosine kinase activities. Pharmacia 69(3): 595–614. https://doi.org/10.3897/pharmacia.69.e86504

Supplementary materials

Supplementary material 1 

ATR-FTIR

Ali H. Abbas

Data type: pdf

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
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Supplementary material 2 

1HNMR

Ali H. Abbas

Data type: pdf

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (500.82 kb)
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