Home Design, synthesis, biological evaluation, and bio-computational modeling of imidazo, thieno, pyrimidopyrimidine, pyrimidodiazepene, and motifs as antimicrobial agents
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Design, synthesis, biological evaluation, and bio-computational modeling of imidazo, thieno, pyrimidopyrimidine, pyrimidodiazepene, and motifs as antimicrobial agents

  • Maged F. El-Ahwany , Mohamed G. Assy , Mohamed H. Sherif , Mohamed R. Soliman , Abderrahim Titi , Rachid Touzani , Marwa S. El-Gendey , Wesam S. Shehab EMAIL logo and Magda H. Abdellattif EMAIL logo
Published/Copyright: August 31, 2023
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Heterocyclic Communications
From the journal Heterocyclic Communications Volume 29 Issue 1

Abstract

In the drug chemistry industry, synthesizing a talented exclusive series of aza-polyheterocyclic compounds was crucial. Aminopyrimidine nucleus reacted with two equivalents of benzaldehyde in the presence of KOH as a starting material to bring about imidazopyrimidine derivative, which experienced intermolecular cyclization using carbon disulfide, Br2/AcOH, and/or HNO2 to produce thiazole, thieno, and/or nitro pyrimidine derivative, respectively. Accordingly, the nucleus of Aminopyrimidine was prepared and used to develop the novel polyheterocyclic systems acylated with two moles of succinic anhydride to furnish the imidazolopyrimidine derivative. Benzylidene ethyl cyanoacetate and aminopyrimidine undergo (3 + 4) intermolecular cycloaddition 1,3 H shift followed by hydrolysis and after CO2 evolution provided diazepine derivative. The diazepine derivative was attained due to the cyclo-condensation of the starting material and acetylacetone. Moreover, the structure of the novel synthesized compound series was exploited and verified via spectroscopic approaches. The synthesized series were tested for antimicrobial activity against gram-positive and gram-negative bacterial strains and antifungal activity. The thienopyrimidine derivatives and diazepine exhibited unusual antimicrobial activity. Furthermore, the molecular docking studies confirmed the biological studies with Molecular Operating Environment and petro orisis molinspiration studies, which proved the activity of compounds 4, 5, 7, 10, 13, and 16.

Keywords: imidazopyrimidine; thienopyrimidine; pyrimidopyrimidine; pyrimidodiazepene; molecular docking; POM studies

1 Introduction

Drug innovation is the most crucial field in chemistry applications. Therefore, poly-functionalized heterocyclic rings have a great significance in medicinal chemistry and drug discovery. Modern synthetic chemistry’s challenge was designing highly efficient chemical reaction sequences, providing molecules containing maximum complexity and structural diversity with interesting bioactivities with the minimum number of synthetic steps. For instance, pyrimidine and condensed pyrimidine showed a broad range of biological activities, such as antiviral [1], antitumor [2], and antimicrobial agents [3]. Moreover, many pyrimidine derivatives were described to own potential central nervous system depressant properties [4] and, also, act as calcium channel blockers [5].

Moreover, pyrimidine-fused benzodiazepines had remarkable pharmacological properties, such as antihypoxic, antipyretic, and analgesic consequences [6,7]. Recently, our interests were in the progress of new heterocyclic frames with convenient biological activities [8,9,10,11]. As regard to earlier studies on the biological activities of pyrimidine and its fused derivatives [12,13,14,15,16,17], the functionalization of 2-amino-3-benzyl-6-(benzylthio) pyrimidine-4(3H)-one (1) as a synthetic key for polycyclic fused pyrimidine derivatives as antimicrobial agents will be pronounced. Molecular docking studies are essential in proving or predicting the biological activities obtained from experimental studies. Petro orisis molinspiration (POM) analyses reveal that the compounds are only slightly toxic and potentially exhibit antibacterial activity. Furthermore, most of the synthesized compounds’ drug scores were an essential parameter for the compound possessing the drug properties.

2 Results and discussion

2.1 Chemistry

As designated in the literature, 2-amino pyrimidine of type 1 was synthesized [7]. Condensation of benzaldehyde with compound 1 in the presence of KOH afforded imidazolopyrimidine 4 via the addition of dehydrogenation and enolization. Acid protons of 4 led to downfield signals at 11.38, 10.65, and 10.61 ppm (Scheme 1). [1,4]-cycloaddition of carbon disulfide and compound 4 resulted in thiazolocyclization forming 5 ( Scheme 1). The exchangeable downfield signals of SH and OH were located at 10.58 and 11.33 ppm, respectively. The IR of 5 contained OH, C═O, and C═N frequencies, while carbon signals for 5 led to sp2, sp3 carbon of C═O, and aliphatic carbon at 162.24 and 30.76 ppm.

Scheme 1 Synthetic routes for imidazo[1,2-a] pyrimidines.
Scheme 1

Synthetic routes for imidazo[1,2-a] pyrimidines.

Imidazolopyrimidine 4 experienced bromination trailed by intramolecular cycloalkylation, whereas on reacting with Br2/AcOH mixture, the thienopyrimidine 7 was attained (Scheme 1). Compound 7 led to NH signals recorded at 12.4 and 12.7. In addition, the OH, C═O, and C═N frequencies were perceived at 3,426, 1,706, and 1,607 cm−1.

Upon treatment of 4 with NaNO2/AcOH mixture, N-nitrosation and the intramolecular cyclodehydration generated thiophene ring which afforded 8. However, compound 8 displayed a deficiency of NH signal; the carbonyl group frequency was identified at 1,617 cm−1.

Succinic anhydride undergoes cyclo-condensation with compound 1 to furnish imidazolopyrimidine derivative 10. The OH broad signal was located at 11.99 ppm, while the OH and C═O frequencies were depicted at 3,377 and 1,612 cm−1, respectively (Scheme 2).

Scheme 2 The reaction of pyrimidine 1 with succinic anhydride.
Scheme 2

The reaction of pyrimidine 1 with succinic anhydride.

(4 + 3) Cycloaddition of compound 1 and benzylidene ethyl cyanoacetate led to aza-Michael through conjugate addition of benzylic anion to cyano function 1,3 H shift followed by hydrolysis and subsequent evolution of CO2 to furnish diazepine derivative 13, the NH protons were resonated at 8.05 and 10.41 ppm (Scheme 3).

Scheme 3 Synthetic routes for Pyrimido[1,2-a] [1,3] diazepines.
Scheme 3

Synthetic routes for Pyrimido[1,2-a] [1,3] diazepines.

β-Electrophilic acetylacetone experienced a cyclo-condensation reaction with compound 1 providing 15 that rearranged through 1,3 H shift to 16, the NH protons lead to exchangeable signals at 10.96 and 10.98 ppm. IR led to NH and C═O groups at 3,365 and 1,644 cm−1, while the C13 provided sp2 oxo and sp3 carbon (Scheme 3).

2.2 Biological studies

2.2.1 Antimicrobial assessment

The produced compounds from 4 to 16 were in vitro inspected against 4 microbial strains (S. aureus, E. coli, A. flavus, and C. Albicans) using the disc diffusion method. Results for each tested compound were noted as the average diameter of inhibition zones (IZs) of bacterial or fungal growth around the discs in mm, as presented in Table 1.

Table 1

Diameter of inhibition zone (mm) for the newly synthesized compounds as antibacterial and antifungal activity

Compound no. Inhibition zone diameter (mm/mg sample)
Gram (+) bacteria Gram (−) bacteria Fungi
S. aureus E. coli A. flavus C. Albicans
4 12 10 15 14
5 12 11 16 20
7 29 27 12 22
10 14 13 12 14
13 11 11 11 12
16 28 28 10 20
Ampicillin 25 21 — —
Amphotericin B — — 17 21

It was noticed that compounds 7 and 16 showed high antibacterial activity against S. aureus and E. coli. Other compounds displayed moderate activity against S. aureus and E. coli. In the meantime, compounds 4 and 5 exhibited the uppermost antifungal activity against A. flavus, and compounds 5, 7, and 16 showed high activity against C. Albicans (Figure 1).

Figure 1 The Inhibition % of the tested compounds as anti-fungal and anti bacterial.
Figure 1

The Inhibition % of the tested compounds as anti-fungal and anti bacterial.

2.2.2 Molecular modeling

Molecular modeling studies were performed using the Molecular Operating Environment (MOE, 2019) software on an Intel Core i5 processor 2.6 GHz, 8 GB memory with Windows 10, and a 64-bit operating system. First, energy minimizations were executed with an RMSD gradient of 0.05 kcal/mol and an MMFF94X force field, utilizing the MOE. Additionally, the partial charges were automatically calculated [18,19,20,21,22,23]. Next the target enzymes were prepared for docking by removing the ligand from the enzyme’s active site. Then, the structure was completed by adding the hydrogen atoms, considering their standard geometry, and detecting the enzyme’s active site through the MOE Alpha Site Finder.

Molecular docking was performed using the investigated protein 6YH4, found in Escherichia coli BL21(DE3), classified as lyase, and isolated with crystal structure of chimeric carbonic anhydrase XII with 2,3,5,6-tetrafluoro-4-(propylthio)benzenesulfonamide.

Docking scores with synthesized compounds 4, 5, 7, 10, 13, and 16 were −7.6148, −7.2549, −6.4948, −6.8758, −6.9387, and −6.0642, respectively. This means that they have higher activity toward lyase protein, although compounds 5, 4, and 13 have higher activity than the others. Compounds 13 and 16 showed intellectual activity as they are new seven-membered ring compounds, as shown in Table 2.

Table 2

Docking score and energy of the compounds and 6YH4 protein

Compound no. S RMSD-refine E_conf E_place E_score1 E_refine E_score2
4 −7.6148 2.3225 2.0997 −48.0119 −9.5520 −44.4244 −7.6148
5 −7.2549 1.9522 2.1454 −81.7684 −9.1137 −37.4933 −7.2549
7 −6.4948 2.5389 0.5566 −20.4384 −9.2915 −32.2745 −6.4948
10 −6.8758 1.6265 39.9518 −71.7156 −12.9965 −42.8328 −6.8758
13 −6.9387 0.8172 −124.7472 −86.2801 −9.9730 −37.8826 −6.9387
16 −6.0642 0.8788 −84.2089 −61.0727 −9.9091 −2.4426 −6.0642

Most newly synthesized compounds were connected to protein from the same side of protein–ligand interaction, indicating their efficiency [24,25] (Figures 2 and 3).

Figure 2 2D interactions between 6YH4 and docked pyrimidine series.
Figure 2

2D interactions between 6YH4 and docked pyrimidine series.

Figure 3 3D interactions between 6YH4 and docked pyrimidine series.
Figure 3

3D interactions between 6YH4 and docked pyrimidine series.

2.2.3 POM analyses

The POM theory is considered one of the best and most reliable bioinformatics platforms to predict crucial and precise bioinformatics properties, especially in designing and synthesizing novel and small compounds as bioactive agents. In addition, it can improve the significant parameters to solve or reduce many obstacles. The most important properties were calculated, like lipophilicity (clogP ≤ 5), the polar surface area (TPSA ≤ 140), bioactivity scores, and toxicity risks [26,27,28,29,30]. Furthermore, the type, size, and the number of pharmacophore sites were identified based on the atomic charge as tabulated in Tables 3–6 and Figure 4.

Table 3

Interaction table between the compounds and 6YH4: LYASE

Compound Ligand Receptor Interaction Distance E (kcal/mol)
4 O⋯19⋯N THR (A) 199 H-acceptor 2.80 −3.9
ZN⋯301⋯NE2 HIS (A) 94 Metal 1.97 −6.6
ZN⋯301⋯NE2 HIS(A) 96 Metal 2.02 −4.7
ZN⋯301⋯ND1 HIS (A) 119 Metal 2.04 −4.7
ZN⋯301⋯NE2 HIS(A) 94 Ionic 1.97 −16.8
ring⋯5-ring HIS(A) 96 pi–pi 1.93 −0.0
ring⋯5-ring HIS(A) 96 pi–pi 3.41 −0.6
6-ring⋯5-ring HIS (A) 96 pi–pi 3.56 −0.0
6-ring⋯5-ring HIS (A) 119 pi–pi 1.89 −0.0
5 ZN⋯301⋯NE2 HIS (A) 94 Metal 1.97 −6.6
ZN⋯301⋯NE2 HIS (A) 96 Metal 2.02 −4.7
ZN⋯301⋯ND1 HIS(A) 119 Metal 2.04 –4.7
ZN⋯301⋯NE2 HIS (A) 94 Ionic 1.97 −16.8
6-ring⋯CA LEU (A) 198 pi–H 4.43 −1.0
7 O⋯11⋯N HIS (A) 94 H-acceptor −0.8 −0.8
ZN⋯301⋯NE2 HIS (A) 94 Metal −6.6 −6.6
ZN⋯301⋯NE2 HIS (A) 96 Metal −4.7 −4.7
ZN⋯301⋯ND1 HIS (A) 119 Metal −4.7 −4.7
ZN⋯301⋯NE2 HIS (A) 94 Ionic 1.97 −16.8
6-ring⋯5-ring HIS (A) 94 pi–pi 1.13 −0.0
10 S⋯19⋯OE1 GLU (A) 106 H-donor 2.99 −5.4
ZN⋯301⋯NE2 HIS (A) 94 Metal 1.97 −6.6
ZN⋯301⋯NE2 HIS (A) 96 Metal 2.02 −4.7
ZN⋯301⋯ND1 HIS (A) 119 Metal 2.04 −4.7
ZN⋯301⋯NE2 HIS 94 (A) Ionic 1.97 −16.8
ring⋯5-ring HIS (A) 119 pi-pi 3.86 −0.0
ring⋯5-ring HIS(A) 119 pi–pi 1.61 −0.0
ring⋯6-ring TRP (A) 209 pi–pi 2.20 −0.0
6-ring⋯5-ring TRP (A) 209 pi–pi 3.74 −0.0
13 N⋯22⋯O THR 208 (A) H-donor 3.37 −0.7
ZN⋯301⋯NE2 HIS 94(A) Metal 1.97 −6.6
ZN⋯301⋯NE2 HIS 96(A) Metal 2.02 −4.7
ZN⋯301⋯ND1 HIS 119(A) Metal 2.04 −4.7
N⋯20⋯5-ring HIS 119 (A) H–pi 3.76 −1.7
ring⋯6-ring TRP 209 (A) pi–pi 2.75 −0.6
6-ring⋯5- ring TRP 209 pi–pi 3.82 0
16 O⋯13⋯CA PHE 95 (A) H-acceptor 3.09 −0.8
ZN⋯301⋯NE2 HIS 94 (A) Metal 1.97 −6.6
ZN⋯301⋯NE2 HIS 96 (A) Metal 2.02 −4.7
ZN⋯301⋯ND1 HIS 119 (A) Metal 2.04 −4.7
ZN⋯301⋯NE2 HIS 94 (A) Ionic 1.97 −16.8
7- ring⋯5-ring HIS 94 (A) pi–pi −3.72 −0.0
7-ring⋯5-ring HIS 119 (A) pi–pi 3.91 −0.0
Table 4

Physico-chemical properties and Bioactivity scores of compounds (4, 5, 6, 7, 10, 13, and 16)

Compound Calculation of molecular properties[1] Calculation of bioactivity scores[2]
TPSA NONH NR NV VOL GPCRL ICM KI NRL PI
4 70 2 7 5 410 −0.06 0.08 −0.21 −0.22 −0.04
5 59 1 5 5 476 −0.07 0.02 −0.31 −0.19 −0.05
7 50 1 4 4 433 −0.01 0.19 −0.57 −0.38 −0.00
10 93 2 5 7 393 −0.11 −0.15 −0.20 −0.25 −0.20
13 72 3 5 5 407 −0.32 −0.20 −0.42 −0.42 −0.20
16 50 4 4 4 351 −0.32 −0.25 −0.65 −0.20 −0.30

[1]TPSA: The polar surface area; NONH: number of OH–N or 0–NH interaction, NV: number of violation of five Lipinsky rules; VOL: volume. [2]GPCRL: GPCR ligand; ICM: ion channel modulator; KI: kinase inhibitor; NRL: nuclear receptor ligand; PI: protease inhibitor; EI: enzyme inhibitor.

Table 5

Estimation of toxicity hazards of prepared compounds by Osiris
Table 6

Atomic charge and their identified pharmacophore sites of the novel prepared compounds

Compound Atomic charge of O, N, and S heteroatoms Pharmacophore site
O1 O2 O1 H O2 H N1 N2 N3 N1 H S SH
4 −0.38 — 0.7 — −0.18 −0.08 — 0.2 −0.7 — (O1–O2H); (N1–N2); (N1–N3H); (N3H–S)
5 −0.35 — 0.12 — −0.17 −0.08 — — −0.15 0.06 (O1–O2H); (N1–N2); (N1–SH); (N3–S)
7 −0.38 — — — −0.18 −0.19 — 0.06 −0.12 — (N1–N2); (N1–N3H); (N3H–S)
10 −0.37 −0.3 0.24 0.06 0 −0.17 −0.29 — — — (O1–O2); (O2–O1H); (N1–N2); (N3–O2H)
13 — — — — −0.01 −0.18 −0.31 0.06 — — (N1–N2); (N1–N1H);
16 — — — — −0.09 −0.21 −0.19 0.06 −0.05 — (N1–N2); (N1–N3H); (N3H–S)
Figure 4 Calculated atomic charge of heteroatoms of pharmacophore sites.
Figure 4 Calculated atomic charge of heteroatoms of pharmacophore sites.
Figure 4

Calculated atomic charge of heteroatoms of pharmacophore sites.

The calculated data bio-screening demonstrated that all the tested compounds are not toxic and presented attractive drug scores. The tested compounds show more respect to Lipinski’s rule or five-rule exhibit 5, and 7 have clogp >5, which means they have a weak water solubility, but these compounds possess another feature that gives them a significant advantage chance to transit with the facility to the lipophilicity pocket. Therefore, they have the power to kill bacteria and viruses living in the hydrophobe zone. This fact is still vital even if the clogp not very high than five. In addition, the tested compounds have exceptional features: pharmacophore sites are broadly responsible for bioactivity; these pharmacophore sites are affected by numbers, sizes, and types. The experimental data have shown excellent agreement with this analysis. For example, The more antifungal pharmacophore sites, the more antifungal activity, and more antibacterial activity with more antibacterial pharmacophore sites. In addition, we have noted that most tested compounds will be good candidates as anticancer agents, especially compounds (13 and 16).

3 Experimental method

3.1 Chemistry

Chemicals were purchased from Sigma-Aldrich (Taufkirchen, Germany), while solvents were purchased from El-Nasr Pharmaceutical Chemicals Company (analytical reagent grade, Egypt). All chemicals were used as supplied without further purification. The melting points were measured by a Digital Electrothermal IA 9100 Series apparatus (Cole-Parmer, Beacon Road, Stone, Staffordshire, ST15 OSA, UK) and were uncorrected. C, H, and N analyses were carried out on a PerkinElmer CHN 2400. In addition, 1H and 13C NMR spectra were recorded on a Bruker 400 MHz NMR Spectrometer using tetramethylsilane as the internal standard, and chemical shifts were expressed in δ (ppm), and DMSO-d 6 was used as the solvent.

(7-(Benzylthio)-5-(methyl-l3-oxidanylidene)-2,3-diphenyl-1,5dihydroimidazo[1,2- a ] pyrimidin-6-yl) (phenyl)methanol (4)

0.01 mmol compound 1 was supplemented with absolute ethanol (30 mL) and benzaldehyde (0.01 mol) and then heated under reflux for 4 h. The achieved solid product was filtered off, dried, and recrystallized from ethanol, producing a yellow compound 4. Yield 85%, mp 290–292°C. IR spectrum, υ, cm−1 3,391, 3,179, 3,060 (OH, 2NH), 1,641 (C═N). 1H NMR spectrum, δ, ppm: 1H NMR δ 7.77–7.71 (m, 1H), 7.66–7.60 (m, 1H), 7.49–7.22 (m, 7H), 5.85 (dt, J = 4.7, 0.7 Hz, 0H), 4.59 (d, J = 4.7 Hz, 0H), 4.37 (d, J = 0.8 Hz, 1H). 13C NMR δ 159.19, 153.93, 144.95, 141.12, 139.85, 136.10, 135.26, 131.47, 129.39, 129.34, 129.12, 128.57, 128.42, 128.37, 127.62, 127.47, 126.88, 126.26, 121.53, 103.17, 71.37, 36.76. Found, %: C, 74.54; H, 4.89; N, 8.15; S, 6.22. C32H25N3O2S. (515.63). Calculated, %: C, 74.53; H, 4.88; N, 8.15.

6-(Hydroxy(phenyl)methyl)-9-mercapto-2,3,8-triphenyl-5 H -imidazo[1,2- a ] thiazolo[3,2- c ] pyrimidin-5-one (5)

Carbon disulfide (0.02 mol) was added to a solution of compound 4 in potassium hydroxide in absolute ethanol. The mixture was refluxed for 7 h, then poured into a water/ice mixture containing HCl. The solid was dried and recrystallized from DMF to yield 5 yellow crystals. Yield 85%, mp 320–321°C. IR spectrum, υ, cm−1: 3,381 (OH), 1,647 (C═O), 1,601(C═N). 1H NMR spectrum, δ, ppm: 5.54 (s, 1H, Hmethine), 8.05–7.13 (m, 20H, H-aryl), 10.58 (s, 1H, OH, D2O exchangeable), 11.33 (s, 1H, SH, D2O exchangeable). 13C NMR: 30.76, 33.67, 35.76, 124.4, 126.7, 127.2, 127.3, 128.2, 128.3, 128.4, 129.1, 129.2, 129.3, 134.3, 140.6, 142.6, 142.7, 142.8, 145.6, 146.1, 150.6, 155.5, 162.2. Found, %: C, 70.06; H, 4.10; N, 7.50; C33H23N3O2S2. (557.69). Calculated, %: C, 71.07; H, 4.16; N, 7.53.

2,3,6,7-Tetraphenylimidazo[1,2- a ] thieno[2,3- d ] pyrimidin-5(9 H )-one (7)

0.01 mol bromine in (5 mL) acetic acid was added dropwise to (0.01 mol) of compound 4 in 10 mL of acetic acid and stirred for 4 h. The solid product was formed, filtered off, dried, and recrystallized from acetic acid, thus forming yellow crystals of compound 7. Yield 85%, mp 240–241°C. IR spectrum, υ, cm−1 2,923 (NH), 1,706 (C═O), 1,607(C═N). 1H NMR spectrum, δ, 9.57 (s, 0H), 7.78–7.71 (m, 1H), 7.66–7.61 (m, 1H), 7.61–7.55 (m, 1H), 7.53–7.37 (m, 7H). 13C NMR (125 MHz, Chloroform-d) δ 163.96, 157.66, 150.43, 139.12, 137.78, 136.55, 135.21, 129.71, 129.63, 129.24, 129.16, 129.11, 129.09, 129.02, 128.97, 128.89, 128.80, 128.74, 127.97, 127.75, 127.01, 124.79, 124.47, 116.53. Found, %: C, 77.52; H, 4.25; N, 8.40 C32H21N3OS. (495.60). Calculated, %: C, 77.55; H, 4.27; N, 8.48.

1-Nitroso-2,3,6,7-tetraphenylimidazo[1,2- a ] thieno[2,3- d ] pyrimidin-5(1 H )-one (8)

0.01 mmol cold solution of pyrimidine 4 in acetic acid was added to a cold sodium nitrite solution (0.01 mol in 20 mL of water), the mixture was stirred for 2 h, the gained precipitate was filtered and recrystallized from dilute ethanol to give compound 8 as blue crystals. Yield 95%, mp 240−242°C. IR spectrum, υ, cm−1: 1,617 (C═O). 1H NMR spectrum, δ, ppm: 7.95–7.28 (m, 20H, H-aryl). Found, %: C, 73.20; H, 3.80; N, 10.69. C32H20N4O2S (524.60), Calculated, %: C, 73.27; H, 3.84; N, 10.68.

2-(Benzylthio)-9-hydroxy-3-(5-hydroxyfuran-2-yl)-6-phenyl-4H,6 H -pyrrolo[1′,2′:3,4] imidazo[1,2- a ]pyrimidin-4-one (10)

A solution of pyrimidine 1 (0.01 mol), succinic anhydride (0.02 mol) in DMF (20 mL), and three drops of TEA were refluxed for 10 h. The solution was poured into an ice/HCl mixture; the resulting precipitate was filtered, dried, and recrystallized from DMF to give compound 9. Yield 80%, mp 330–332°C. IR spectrum, υ, cm−1 3,377 (OH), 1,612 (C═O). 1 H NMR: 1H NMR δ 9.34 (s, 1H), 7.42–7.36 (m, 2H), 7.39–7.31 (m, 4H), 7.35–7.22 (m, 6H), 6.95 (d, J = 6.4 Hz, 1H), 6.55–6.47 (m, 2H), 6.43 (d, J = 0.8 Hz, 1H), 5.91 (d, J = 6.4 Hz, 1H), 4.50 (t, J = 0.8 Hz, 2H). 13C NMR δ 163.63, 160.05, 155.03, 154.07, 150.86, 143.93, 135.48, 133.89, 133.08, 129.37, 128.77, 128.57, 128.32, 127.63, 127.62, 114.04, 111.43, 103.71, 101.08, 97.58, 54.85, 35.86. Found, %: C, 66.50; H, 3.95; N, 8.93 C26H19N3O4S. (469.52). Calculated, %: C, 66.51; H, 4.08; N, 8.95.

7-Amino-2-(benzylthio)-6,9-diphenyl-9,10-dihydropyrimido[1,2- a ][1,3]diazepin-4(6 H )-one (13)

A mixture of 1 (0.01 mol) and benzylidene ethyl cyanoacetate (0.01 mol) in ethoxide (0.01 mmol) was heated under reflux for 12 h. The reaction mixture was cooled, poured into crushed ice, and neutralized by HCl. The separated product was filtered off, dried, and recrystallized from ethanol to give yellowish crystals of compound 12, yielding 90%, mp 300–301°C. IR spectrum, υ, cm−1: 3,425 (NH2), 2,923 (NH), 1,639 (C═O). 1 H NMR: 3.38 (d, 1H, enamenic proton), 3.39 (d, 1H, Hmethine proton), 5.54(s, 2H, SCH2), 7.89–8.07 (m, 15H, H-aryl), 8.05 (s, 2H, NH2, D2O exchangeable), 10.96 (s, 1H, NH, D2O exchangeable). C27H24N4OS: (452.58). Found, %: C, 71.60; H, 5.35; N, 12.38; Calculated, %: C, 71.66; H, 5.35; N, 12.38.

2-(Benzylthio)-7,9-dimethyl-6-phenylpyrimido[1,2- a ][1,3]diazepin-4(1 H )-one (16)

A mixture of compound 1 (0.01 mol) and acetylacetone (0.01 mol) in the presence of TEA (3 drops), was heated under reflux for 10 h. After cooling and pouring into the ice mixture, the solid product was filtered off, dried, and recrystallized from ethanol, and compound 15 as yellow crystals were obtained. Yield 90%, mp 310–311°C. IR spectrum, υ, cm−1: 3,294 (NH), 1,644 (C═O). 1 H NMR: δ 9.31 (s, 1H), 7.75–7.69 (m, 2H), 7.55–7.47 (m, 1H), 7.47–7.40 (m, 2H), 7.37–7.22 (m, 5H), 6.17 (hept, J = 1.2 Hz, 1H), 5.97 (s, 1H), 4.30 (t, J = 0.8 Hz, 2H), 2.28 (s, 2H), 2.12 (d, J = 1.0 Hz, 3H). 13 C NMR δ 159.62, 157.44, 151.91, 151.71, 148.01, 135.93, 134.00, 129.77, 129.36, 129.11, 128.97, 128.72, 128.57, 127.62, 115.89, 97.36, 36.30, 22.00, 19.04. Found, %: C, 71.20; H, 5.40; N, 10.80; C23H21N3OS. (387.50) Calculated, %: C, 71.29; H, 5.46; N, 10.84.

3.2 Biological activity

3.2.1 Antimicrobial activity

A modified Kirby-Bauer disc diffusion method [31] was used to expedient the tested samples’ antimicrobial activity. It was intended to use 100 µL of the test bacteria grown in 10 mL of fresh media until they reached a count of approximately 108 cells/mL for bacteria [32]. Therefore, 100 µL of bacterial suspension was spread onto agar plates corresponding to the conserved broth. Plates inoculated with the Gram (−) bacteria and Gram (+) bacteria were incubated at 35–37°C for 24–48 h, then the diameters of the inhibition zones were measured in millimeters [33]. Ampicillin (antibacterial agent) standard discs served as positive controls for antimicrobial activity, but filter discs were impregnated with 10 µL of solvent (distilled water, chloroform, DMSO) as a negative control.

The agar exploited was Mueller-Hinton agar which was rigorously tested for composition and pH. Moreover, the agar depth in the plate was a factor to be considered in the disc diffusion method. This method was well documented, and standard IZs have been determined for susceptible and resistant values. Blank paper disks (Schleicher & Schuell, Spain) of 8.0 mm diameter were impregnated with 10 µL of tested concentration of the stock solutions. When a filter paper disc impregnated with a tested chemical is placed on agar, a chemical will diffuse from the disc into the agar. This diffusion will place the chemical in the agar only around the disc. The solubility of the chemical and its molecular size will determine the size of the area of chemical infiltration around the disc. The area of no growth around the disc was recognized as a “Zone of inhibition” or” Clear zone.” The zone diameters were measured with slipping calipers of the National Committee for Clinical Laboratory Standards for disc diffusion.

3.2.2 Molecular docking study

The protein data bank obtained the crystal structures of the proteins identified for Escherichia coli (6YH4). Water molecules around the duplex were removed, and hydrogen atoms were added. The parameters and charges were allocated with the MMFF94x force field. After alpha-site spheres were generated using the site finder module of MOE, our compound was docked in the active site, utilizing the dock module of MOE. The dock scoring in MOE software was calculated by the London dG scoring function and was refined using two different methods. The planarity of the system was maintained, and the best poses were analyzed for the best score [30,31,32,33].

4 Conclusion

Synthesis and antimicrobial activities of some new imidazopyrimidine derivatives, aminopyrimidine, were prepared and used to obtain polycyclic heterocyclic systems. 2-(Benzylthio)-7,9-dimethyl-6-phenylpyrimido[1,2-a][1,3] diazepam-4(1H)-one preparation was a challenge, which directed high antibacterial activity against S. aureus, E. coli, and high action against C. Albicans. Finally, this study has indicated that the pyrimidine with polycyclic hetero systems was vital for antimicrobial activity. The molecular docking and POM studies explain that the antibacterial and anticancer pharmacophore sites are related to the functional groups, while the antifungal pharmacophore sites are related to the heteroatoms.

Acknowledgments

M.H.A author thanks Deanship of Scientific research Taif University for its support of this manuscript.

  1. Author contributions: Authors state no conflict of interest.

  2. Conflict of interest: All authors are equally shared work.

  3. Data availability statement: The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Received: 2022-08-03
Revised: 2022-10-26
Accepted: 2022-11-23
Published Online: 2023-08-31

© 2023 the author(s), published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/hc-2022-0156
Keywords for this article
imidazopyrimidine; thienopyrimidine; pyrimidopyrimidine; pyrimidodiazepene; molecular docking; POM studies
Creative Commons
BY 4.0

Articles in the same Issue

  1. Research Articles
  2. Synthesis, characterization, and antibacterial activity of a new poly azo compound containing N-arylsuccinimid and dibenzobarrelene moieties
  3. Design, synthesis, and antiviral activities evaluation of novel quinazoline derivatives containing sulfonamide moiety
  4. Design, synthesis, and anticancer activity of novel 4,6-dimorpholinyl-1,3,5-triazine compounds
  5. Design, synthesis, biological evaluation, and bio-computational modeling of imidazo, thieno, pyrimidopyrimidine, pyrimidodiazepene, and motifs as antimicrobial agents
  6. Synthesis of a novel phosphate-containing ligand rhodium catalyst and exploration of its optimal reaction conditions and mechanism for the polymerization of phenylacetylene
  7. Design, synthesis, and antiproliferative activity of novel 1,2,4-triazole-chalcone compounds
  8. Synthesis of metal–organic nanofiber/rGO nanocomposite as the sensing element for electrochemical determination of hypoxanthine
  9. Design and synthesis of various 1,3,4-oxadiazoles as AChE and LOX enzyme inhibitors
  10. Bis(2-cyanoacetohydrazide) as precursors for synthesis of novel azoles/azines and their biological evaluation
  11. Synthesis, characterization, and biological target prediction of novel 1,3-dithiolo[4,5-b]quinoxaline and thiazolo[4,5-b]quinoxaline derivatives
  12. Sustainable conversion of carbon dioxide into novel 5-aryldiazenyl-1,2,4-triazol-3-ones using Fe3O4@SP-vanillin-TGA nanocomposite
  13. Erratum
  14. Erratum to “Design, synthesis and study of antibacterial and antitubercular activity of quinoline hydrazone hybrids”
  15. SI: Undergraduate Research in the Synthesis of Biologically Active Small Molecules and Their Applications
  16. Preparation of novel acyl pyrazoles and triazoles by means of oxidative functionalization reactions
  17. Synthesis and conformational analysis of N-BOC-protected-3,5-bis(arylidene)-4-piperidone EF-24 analogs as anti-cancer agents
  18. SI: Development of Heterocycles for Biomedical and Bioanalytical Applications
  19. Influence of octreotide on apoptosis and metabolome expression in lipopolysaccharide-induced A549 cells
  20. Crude extract of J1 fermentation promotes apoptosis of cervical cancer cells
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