To optimise the reaction condition, we carried out trial reactions with 5-bromothiophene-2-carboxaldehyde (1, 1mmol), ethyl acetoacetate (2c, 1mmol), and urea (3a, 1mmol) using CAN as a catalyst in different reaction conditions (Table 1).
In optimisation of reaction, our first target is to carry out the reaction at ambient temperature, but with this reaction we got lower yields at ambient temperature (Entry 2 and 3, Table 1). So, we carried out the reactions at 60°C with different amounts of catalyst at different reaction times, in which we got the best result with 20 mol % of CAN at 70 minutes (Entry 6, Table 1). The reaction was also optimised with different solvents, but we got the sticky product on work up except DMF, which is tedious to handle, while we got the crude product in solvent-free condition.
After these experiments, we further go with the solvent-free reaction. The targeted compounds 4(a-j) were synthesized from 5-bromothiophene-2-carboxaldehyde (1, 1mmol), ketoester (2a-2e, 1mmol), and urea/thiourea (3a-3b, 1mmol) using CAN (20 mol %) as catalyst in solvent-free condition at 60°C with average reaction time of 60–90 minutes (Table 2).
We successfully carried out the solvent-free synthesis of compounds 4(a-j) using CAN as a catalyst within 60–90 minutes of heating at 60°C. Structures of the synthesised compound were confirmed by spectral analysis, for which spectral data are given in supplementary material.
In 1H-NMR spectra, signals at δ 0.8–1.5 ppm confirm the presence of methyl group at C-1, whereas, for methyl, ethyl, iso-butyl, tert-butyl of ester give signals in a range of δ 1.5–3.0 ppm. A signal that appears as a singlet at a range of δ 5.0–6.0 ppm confirms the presence of proton at γ-position. For aromatic protons, we observe signals in the range of δ 6.8–7.6 ppm. For 2 –NH groups in some of the compounds, we observe singlet for both after an aromatic region in between δ 8.0-9.5 ppm and in some cases, we got singlet for 1 –NH around δ 6.0 ppm and for another around δ 8.5 ppm.
In 13C-APT spectra, signals in a range of δ 16–18 ppm confirm the presence of a methyl group, whereas signal for other aliphatic carbons of the ester group appears in the range of δ 30–55 ppm. For the quaternary carbon of the ring, we observe signals in a range of δ 100–110 ppm and signals in a range of δ 160–170 ppm that confirms the presence of the carbonyl group. Single-crystal XRD analysis of 4c also confirmed its structure.
2.2. Molecular structure of 4c
2.2.1. Description of crystal structure
The single-crystal structural data indicate that 4c was crystallised in P1 space group. The molecule of 4c is not symmetrical (Fig. 1a). The asymmetric unit revealed two molecules of 4c, and one of them contains a distorted thiophene ring. Pyrimidinone ring in 4c is observed in half chair configuration. Triclinic unit cell of crystal with cell dimensions a = 7.3244(3) Å, b = 13.5742(6) Å, c = 14.8486(7) Å, α = 94.044(2)°, β = 103.959(2)°, γ = 99.511(2)° show in Fig. 1b. In the crystal lattice, molecules of 4c have connected via strong N-H ····O = C hydrogen bonding interactions in a zigzag fashion and overall, a layered structure is formed (Fig. 1b). Each carbonyl oxygen able to interact with two neighbour atom’s hydrogens simultaneously with H ····O ····H bond angle 116.78° and 118.51°. Thus, each molecule interacts with two neighbour molecules by four hydrogen-bonding interactions having bond lengths 2.070 Å, 2.153 Å, 2.158 Å and 2.159 Å. XRD data were deposited online to Cambridge Crystallographic Data Centre (CCDC). CCDC deposition number 1970503 contains the Supporting Information crystallographic data for this paper.
2.2.2. Hirshfeld surfaces analysis
Hirshfeld surfaces for 4c were calculated as per established procedures. 27 These calculation help to understand effect of weak intermolecular interactions into the molecular packing. In Fig. 1c Hirshfeld surfaces mapped over dnorm in the − 0.5530 to + 1.3583 arbitrary unit range. Broad and bright-red spots on pyrimidone ring surface and near hydrogen atom of amino groups and oxygen atom of carbonyl group respectively recognise donor and acceptor of potential N-H...O hydrogen bond. Whereas the presence of diminutive and faint-red spots on the surface characterises weak intermolecular interactions in 4c. On thiophene ring surface, short interatomic Br···S/S···Br contacts in crystal packing of 4c are viewed as the faint-red spots. Diminutive-red spots are also observed which indicated short interatomic H···H contacts.
The two-dimensional fingerprint plot for 4c and fingerprint plots delineated into H··· H, O··· H/H··· O, C··· H/H··· C, Br··· H/H··· Br, S··· H/H··· S, N··· H/H··· N and Br··· S/S··· Br contacts are illustrated in Fig. 2(a-h) respectively. The H... H contacts show as a symmetrically dispersed point that covers a wide area of the plot and occupies a significant portion of the Hirshfeld area (37.5 percent ) The contribution of O...H/H...O, which corresponds to the NH...O interactions, is shown by a pair of sharp dots typical of hydrogen bonds. Here, the proportions of O ... H and H ... O interactions are remarkably not identical (O ... H (8.2%) and H ... O (7.3%)). Among these three contacts, only O-H interactions, with a total de + di smaller than the sum of the Van der Waals radii of participating atoms (H: 1.09 A, O: 1.52 A), are considered close together. The remaining contacts, like N...O/O...N, O...O, C...O/O...C, and N...H/H...N, barely contribute 6.1 % to the HS. These interactions fall under the category of far contacts in which summation di + de is higher than the sum of the van der Waals radii of the atoms, together with the C...H/H...C and H...H and contacts.
2.3. Biological evaluation
2.3.1. Antibacterial assay
The antibacterial activity of compounds 4(a-j) was performed on gram-positive and gram-negative bacteria by broth dilution method. The screening results were summarised in Table 3. The MIC values of compounds 4(a-j) are between 50–500 µg/mL against tested microorganisms. In the case of gram-negative bacteria, 4h shows good antibacterial activity against E.coli than the standard drug ampicillin, while 4b show good antibacterial activity against P.aeruginosa than standard drug ampicillin. In the case of gram-positive bacteria, 4a, 4b, 4d, 4g and 4i show good antibacterial activity against S.aureus than standard drug ampicillin, while 4a show good antibacterial activity against S.pyogenus. Overall, 4a, 4b and 4h exhibited maximal antibacterial activity.
2.3.2. Antifungal assay
Fungicidal activities of 4(a-j) were evaluated against three fungi C.albicans, A.niger, and A.clavatus and the minimum inhibitory concentrations were derived. The screening results were summarised in Table 4. Tabulated data show that compounds 4f, 4g, 4h and 4i are more effective on C.albicans than the standard drug griseofulvin. Entire antifungal data indicate that dihydropyrimidinthione 4(f-j) are more potent than dihydropyrimidinones 4(a-e).
2.4. ADMET prediction
ADMET properties of the compound are important for its drug-like profile. It might be important for novel drug discovery.28 Physicochemical properties of the compounds correlate to their drug-likeness via various rules like Lipinski’s, Ghose’s, Veber’s Egan’s and Muegee’s rule. Physicochemical properties must stay within limits defined in each rule. We evaluate our synthesised compounds for their ADMET properties with the help of the online web server SwissADME. (http://www.swissadme.ch) Calculated physicochemical properties of 4(a-j) are summarised in Table 5. The value of physicochemical properties remains in the limits defined for Lipinski’s, Ghose’s, Veber’s, Egan’s, and Muegee’s rule. Thus, all 5-bromothiophene based DHPMs incorporate all rule of drug-likeness, so they have good drug-like potential. Bioavailability radar of the compounds were derived based on six physicochemical properties namely lipophilicity, size, polarity, solubility, flexibility and saturation. The bioavailability radar showed that all 4(a-j) molecules exhibited drug-like radar plots (Bioavailability radar graph of 4(a-j) were included in supporting information file).
To predict the gastrointestinal absorption and blood-brain barrier permeability of the compounds, BOILED-Egg delineation was used. BOILED-Egg delineation of all the synthesised compounds is illustrated in Fig. 3. The white, elliptical region of the egg depicts a high probability of gastrointestinal absorption, while the yellow (Yolk) region of the egg depicts blood-brain permeation of molecule.29 All 5-bromothiophene based DHPMs show high gastrointestinal absorbance, and they have no blood-brain permeability. Red dots for all the 4(a-j) denoted that they are not P-gp substrate.