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Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds.

ABSTRACT: The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance.

SUBMITTER: Ramachandran V

PROVIDER: S-EPMC4733073 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds.

Ramachandran Vanitha V Arumugasamy Karthiga K Singh Sanjeev Kumar SK Edayadulla Naushad N Ramesh Penugonda P Kamaraj Sathish-Kumar SK

Journal of chemical biology 20150704 1

The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors ...[more]

PMID: 26855679

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Project description:The presence of alkaline phosphatases has been observed in several species and has been known to play a crucial role in various biological functions. Higher expressions of alkaline phosphatase have been found in several multifactorial disorders and cancer patients, which has led it to be an interesting target for drug discovery. A strong structural similarity exists between intestinal alkaline phosphatases (IAPs) and tissue-nonspecific alkaline phosphatases (TNAPs), which has led to the discovery of only a few selective inhibitors. Therefore, a series of 22 derivatives of 6-(chloromethyl)-4-(4-hydroxyphenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (1) and ethyl 6-(chloromethyl)-4-(2-hydroxyphenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (2) were synthesized to evaluate the anticancer potential of these compounds against breast cancer. The compounds were characterized through spectral and elemental analyses. The inhibitory effect of dihydropyrimidinone derivatives on alkaline phosphatases was evaluated using the calf alkaline phosphatase assay. The antioxidant activity of these compounds was performed to study the radical scavenging effect. In silico molecular docking and molecular dynamic simulations were performed to elucidate the binding mode of active compounds. Moreover, the two-dimensional qualitative-structure-activity relationship (2D-QSAR) was performed to study the structural requirements for enzyme inhibition. The calf alkaline phosphatase inhibitory assay revealed significant inhibition of the enzyme by compound 4d with IC50 1.27 μM at 0.1 mM concentration as compared to standard KH2PO4 having IC50 2.80 μM. The compounds 4f, 4e, and 4i also showed very good inhibition with IC50 values of 2.502, 2.943, and 2.132 μM, respectively, at the same concentration. The antioxidant assay revealed efficient radical scavenging activity of compounds 4f, 4e, and 4g at 100 μg/mL with IC50 values of 0.48, 0.61, and 0.75 μg/mL, respectively. The molecular docking and simulation studies revealed efficient binding of active compounds in the active binding site of the target enzyme. The final QSAR equation revealed good predictivity and statistical validation having R 2 = 0.958 and Q 2 = 0.903, respectively, for the generated model. The compound 4d showed the highest inhibitory activity with stable binding modes acting as a future lead for identifying alkaline phosphatase inhibitors. The molecular simulations suggested the stable binding of this compound, and the QSAR studies revealed the importance of autocorrelated descriptors in the inhibition of alkaline phosphatase. The investigated compounds may serve as potential pharmacophores for potent and selective alkaline phosphatase inhibitors. We intend to further investigate the biological activities of these compounds as alkaline phosphatase inhibitors.

Project description:Background: Toll-like receptor 4 (TLR4) initiates both innate and adaptive immune responses, which plays an important protective role in self-defense mechanisms. Excessive or inappropriate TLR4 activation causes the development of many autoimmune diseases. Dihydropyrimidinone derivatives are medicinally important molecules with diverse pharmacological activities, including anti-inflammatory activity. The present study focused on novel synthesized 3,4-dihydropyrimidinone derivatives and evaluated their inhibitory effects on TLR4. Methods: A series of 3,4-dihydropyrimidinone derivatives were recently synthesized and evaluated for their TLR4 inhibition activities and cytotoxic on HEK-BlueTM hTLR4 cells with the help of QUANTI-Blue assay and MTS assay. Selected compound 3 was analyzed for its molecular docking with TLR4 by using Autodock vina 1.1.2. Its effect on the TLR4 pathway related cytokines was also evaluated in THP-1 cells and human peripheral blood mononuclear cells by using real-time PCR, ELISA and western blot. Results: Five compounds were synthesized and characterized for effectiveness based on 3,4-dihydropyrimidinone. Compound 3 was found to be the potent hybrid among the synthesized compounds, with high TLR4 inhibition activities and low cytotoxic activities against HEK-BlueTM hTLR4 cells. Molecular docking analysis showed that two hydrogen bonds between compound 3 and residues Asp209(TLR4) and Asp99(MD-2) mainly contribute to the TLR4 inhibition. In addition, compound 3 suppressed LPS-induced of the mRNA expression of TLR4, IP-10, TNF-?, IL-6, IL-12A, and IL-12B, the protein expression of pIRF3 and pNF?B and the secretion of IP-10, TNF-? in THP-1 cell line. Compound 3 also inhibited LPS-induced expression of TNF-?, IL-6, and IL-1? but increased IP-10 at mRNA levels in human peripheral blood mononuclear cells. Conclusion: Our study reveals compound 3, a novel 3,4-dihydropyrimidinone derivative, is a potential TLR4 antagonist, which opens up new research avenues for the development of promising therapeutic agents for inflammatory and autoimmune diseases.

Dataset Information

Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds.

Publications

Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds.

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