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

Palladium-catalyzed/copper-mediated carbon-carbon cross-coupling reaction for synthesis of 6-unsubstituted 2-aryldihydropyrimidines

Dihydropyrimidines (DPs) show a wide range of biological activities for medicinal applications. Among the DP derivatives, 2-aryl-DPs have been reported to display remarkable pharmacological properties. In this work, we describe a method for the synthesis of hitherto unavailable 6-unsubstituted 2-aryl-DPs by Pd-catalyzed/Cu-mediated carbon–carbon cross-coupling reaction of 1-Boc 2-methylthio-DPs with organostannane reagents. The Boc group of the substrate significantly increases the substrate reactivity. Aryl tributylstannanes having various substituents such as MeO, Ph, CF₃, CO₂Me, and NO₂ groups smoothly afforded the corresponding products in high yields. Various heteroaryl tributylstannanes having 2-, or 3-thienyl, 2-, or 3-pyridinyl groups were also applicable to the reaction. Regarding the substituents at the 4-position, the reactions of DPs bearing various aryl and alkyl substituents proceeded smoothly to give the desired products. The Boc group of the products was removed under a standard acidic condition to produce N-unsubstituted DP as a mixture of the tautomers in quantitative yields. The synthetic procedure was also applied to 4,4,6-trisubstituted 2-methylthio-DP to give novel 2,4,4,5,6-pentasubstituted DP. Therefore, the Pd-catalyzed/Cu-mediated reaction should help expand the DP-based molecular diversity, which would impact biological and pharmacological studies.

This protocol enables the synthesis of 6-unsubstituted 2-aryldihydropyrimidines using various substituents at the 2- and 4-positions, which would impact dihydropyrimidine-based biological and pharmacological studies.

Synthesis of 3,4-Dihydropyrimidin(thio)one Containing Scaffold: Biginelli-like Reactions

The interest in 3,4-dihydropyrimidine-2(1H)-(thio)ones is increasing every day, mainly due to their paramount biological relevance. The Biginelli reaction is the classical approach to reaching these scaffolds, although the product diversity suffers from some limitations. In order to overcome these restrictions, two main approaches have been devised. The first one involves the modification of the conventional components of the Biginelli reaction and the second one refers to the postmodification of the Biginelli products. Both strategies have been extensively revised in this manuscript. Regarding the first one, initially, the modification of one of the components was covered. Although examples of modifications of the three of them were described, by far the modification of the keto ester counterpart was the most popular approach, and a wide variety of different enolizable carbonylic compounds were used; moreover, changes in two or the three components were also described, broadening the substitution of the final dihydropyrimidines. Together with these modifications, the use of Biginelli adducts as a starting point for further modification was also a very useful strategy to decorate the final heterocyclic structure.

Dihydropyrimidinones Against Multiresistant Bacteria

The increase in bacterial resistance to antimicrobials has led to high morbidity and mortality rates, posing a major public health problem, requiring the discovery of novel antimicrobial substances. The biological samples were identified as the Gram-negative bacilli Acinetobacter baumannii, Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, Morganella morgannii, Pseudomonas aeruginosa and Serratia marcescens and the Gram-positive cocci Enterococcus faecium, and Staphylococcus aureus, all of them resistant to at least three classes of antimicrobials. The antibacterial activity of the compounds was checked in vitro by determining the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) by the broth microdilution method and plating in brain heart infusion (BHI) agar, respectively. The chemical characterization of the compounds was performed by measuring the melting point and gas chromatography coupled with mass spectrometry (GC–MS) on a Shimadzu GC–MS-QP system 2010SE. Synthetic compounds showed antimicrobial activity against Gram-positive cocci at MIC concentrations 0.16–80 μg/ml and Gram-negative bacilli at MIC concentrations 23.2–80 μg/ml. Enterococcus faecium and S. aureus had the best MIC values. The results of the cytotoxicity test indicated that the synthetic compounds showed no significant difference in three concentrations tested (5, 20, and 80 μg/ml), allowing cell viability not different from that assigned to the control, without the tested compounds. In this context, the development of DHPM derivatives brings an alternative and perspective on effectiveness of drugs as potential future antimicrobial agents.

Synthesis, Molecular docking, and in silico ADME Studies of Dihydropyrimidine Derivatives using Tetrabutylphosphonium Methanesulphonate Ionic Liquid as a catalyst Under Solvent Free Conditions

This paper describes the synthesis and characterization of tetrabutylphosphonium methanesulphonate ionic liquid and its use for the first time as a catalyst in multicomponent reaction for one-pot synthesis of Dihydropyrimidine derivatives from various aromatic aldehydes, methyl or ethyl acetoacetate and urea or thio-urea under the solvent-free conditions at 120 oC. About twenty-one different dihydropyrimidine derivatives have been synthesized in excellent yields. The advantage of this method is a solvent-free condition, the requirement of a small amount of catalyst, shorter reaction time, easy workup procedure and non-involvement of any hazardous organic solvent and toxic catalyst. This catalyst was easily prepared and showed excellent level of reusability. Also the molecular docking study was performed to evaluate interactions between the active compounds with Leishmania Pteridine reductase 1(PTR1). Further the theoretical evaluation of ADME properties in silico was investigated for their oral bioavailability to predict the safer efficacy of the synthesized compounds.

Synthesis of 4,4-Disubstituted 3,4-Dihydropyrimidin-2(1H)-ones and -thiones, the Corresponding Products of Biginelli Reaction Using Ketone, and Their Antiproliferative Effect on HL-60 Cells

An efficient synthetic method for novel 4,4-disubstituted 3,4-dihydropyrimidin-2(1H)-ones 5 and -thiones 6 was developed. The cyclocondensation reaction of O-methylisourea hemisulfate salt 11 with 8 gives a tautomeric mixture of dihydropyrimidines 12 and 13 following acidic hydrolysis of the cyclized products to produce 5 in high yields. Thionation reaction of 5 at the 2-position smoothly proceeds to give 2-thioxo derivatives 6. These compounds 5 and 6, corresponding to the products of a Biginelli-type reaction using urea or thiourea, a ketone and a 1,3-dicarbonyl compound, have long been inaccessible and hitherto unavailable for medicinal chemistry. These methods are invaluable for the synthesis of 5 and 6, which have been inaccessible by conventional methods. Therefore, the synthetic methods established in this study will expand the molecular diversity of their related derivatives. These compounds were also assessed for their antiproliferative effect on a human promyelocytic leukemia cell line, HL-60. Treatment of 10 µM 6b and 6d showed high inhibitory activity similarly to 1 µM all-trans retinoic acid (ATRA), indicating that the 2-thioxo group and length of two alkyl substituents at the 4-position are strongly related to activity.

Biginelli Reaction Mediated Synthesis of Antimicrobial Pyrimidine Derivatives and Their Therapeutic Properties

Antimicrobial resistance was one of the top priorities for global public health before the start of the 2019 coronavirus pandemic (COVID-19). Moreover, in this changing medical landscape due to COVID-19, finding new organic structures with antimicrobial and antiviral properties is a priority in current research. The Biginelli synthesis that mediates the production of pyrimidine compounds has been intensively studied in recent decades, especially due to the therapeutic properties of the resulting compounds, such as calcium channel blockers, anticancer, antiviral, antimicrobial, anti-inflammatory or antioxidant compounds. In this review we aim to review the Biginelli syntheses reported recently in the literature that mediates the synthesis of antimicrobial compounds, the spectrum of their medicinal properties, and the structure-activity relationship in the studied compounds.

In-silico strategies for identification of potent inhibitor for MMP-1 to prevent metastasis of breast cancer

Matrix Metalloproteinase-1 (MMP-1) has been often upregulated in advanced breast cancers, known to participate in ECM degradation, migration, invasion, thus leading to metastasis. Due to these effects, the condition is often reported to inversely correlate with survival in advanced breast cancers. In the present study, in-silico method was adopted based on selective non zinc binding inhibitors of MMP-1. ADME properties were predicted for PASS filtered compounds and docking calculations were performed using Glide XP and IFD protocols of Schrodinger program. We identified six ligands as potent inhibitors and validated by observing structures and the interactions of MMP-1. The identified hits were validated using molecular dynamics simulation studies. Electronic structure analysis was performed for two top hit compounds myricetin and quercetin using density function theory (DFT) at B3LYP/6-31**G level to understand their molecular reactivity. Finally, one compound myricetin has emerged as the structurally stable compound with -7.801 kcal/mol and reasonable pose inside the binding site. Molecular dynamics results indicated that myricetin forms a stable interaction with the key amino acid residues such as Glu209, Glu219, Tyr240 and Pro238. In addition, it did not form any binding with the catalytic zinc at its active site. The interaction pattern of myricetin at its substrate binding site exhibited to be potent MMP-1 inhibitor. DFT study also showed that it has more potent inhibitory effect and solubility. These factors altogether show that myricetin could be considered as the best among the compounds evaluated in inhibiting MMP-1 thereby preventing metastasis of breast cancer. Communicated by Ramaswamy H. Sarma.

A novel one-pot method for the stereoselective synthesis of tetrahydropyrimidinones in a low melting mixture

A direct and metal free one-pot method has been developed for the stereoselective synthesis of tetrahydropyrimidinone derivatives from a vinyl arene and formaldehyde using a tartaric acid-dimethylurea (TA : DMU) melt as a green reaction medium. The substrate scope of this method is very general and the tetrahydropyrimidinone (THPM) derivatives are synthesized in good yields with a high degree of diastereoselectivity. In this reaction, the melt plays a triple role as the solvent, catalyst and reagent.

3,4-Dihydropyrimidin-2(1H)-One Analogues: Microwave irradiated Synthesis with Antimicrobial and Antituberculosis Study

Background:

For rapid and sustainable synthesis, microwave irradiation method is serviceable. This present study deals with the preparation of oxadiazole and pyridine bearing 1,2,3,4- tetrahydro pyrimidine derivatives by microwave irradiation.

Objective:

The present study aims to carry out rapid synthesis of chloro-acetamides of oxadiazoles of Biginelli product and amino cyano derivative of pyridine by microwave-assisted heating. Our efforts are focused on the introduction of chemical diversity in the molecular framework in order to synthesize pharmacologically interesting compounds.

Methods::

Microwave irradiation was used for the synthesis of 2-((3-cyano-4-(3,4-dichloro phenyl)- 6-(4-hydroxy-3-methoxyphenyl) pyridin-2-yl) amino)-N-(5-(substituted) -(6-methyl-2-oxo -1,2,3,4- tetrahydro pyrimidin-5-yl)-1,3,4-oxadiazol-2-yl)acetamide by using Biginelli reaction. New structural analogues were confirmed by spectral studies followed by their screening for in vitro antibacterial activity against Staphylococcus aureus, Staphylococcus Pyogenus, Escherichia coli and Pseudomonas aeruginosa bacterial strains and for antifungal activity against Candida albicans, Aspergillus niger and Aspergillus clavatus by micro-broth dilution method. In vitro antimycobacterial activity determined out against (Mycobacterium tuberculosis) H37Rv strain using Lowenstein-Jensen medium.

Results:

As compared to the conventional method, microwave irradiation method is advantageous for the synthesis of 1,2,3,4-tetrahydropyrimidin derivatives. Potent antimicrobial activities and antitubercular activity were found for some of the compounds.

Conclusion:

Microwave irradiation method provided an effective way to discover a novel class of antimicrobial and antituberculosis agents. 1,2,3,4-tetrahydropyrimidin derivatives showed improved antimicrobial and good antituberculosis activity.

Understanding the Lack of Reactivity of 2,4-Dihydroxybenzaldehyde Towards the Biginelli Adduct Using Density Functional Theory Molecular Modeling

The Biginelli reaction is a multicomponent reaction for obtaining dihydropyrimidinthiones quickly, with multiple substitution patterns. The reaction mechanism remains unclear. Three possible pathways proposed for the reaction are the iminium route, an enamine intermediate, and the Knoevenagel pathway. However, when thiourea was used, no theoretical calculations were reported. Thus, based on the literature, the iminium pathway was used to obtain evidence explaining the lack of reactivity of 2,4-dihydroxybenzaldehyde towards the Biginelli adduct, compared with 4-hydroxybenzaldehyde. This computational study, carried out using the B3LYP/6-31++G(d,p) level of theory, showed an increment of 150 kJ/mol in the activation energy of the slowest pathway, due to the presence of a hydroxyl group in position 2 (ortho) of the aromatic aldehyde, decreasing its reactivity. Natural bond orbital (NBO) calculations suggest that the determinant steps are simultaneous, i.e., the polarization of the carbonyl group and its corresponding protonation by the hydrogen of the SH fragment of the thiourea tautomer. The activation enthalpy values suggest that the nucleophile attack takes place later on the compound 2,4-dihydroxybenzaldehyde compared to 4-hydroxybenzaldehyde-TS, confirming that the OH group in position 2 hinders the condensation reaction.

Synthesis and vasodilator activity of 3,4-dihydropyrimidin-2(1H)-ones bearing urea, thiourea, and sulfonylurea moieties

A series of novel 3,4-dihydropyrimidin-2(1H)-ones bearing urea, thiourea, and sulfonylurea moieties were synthesized and pharmacologically evaluated as vasodilator agents. The most interesting vasodilators were the thiourea derivatives 6a and 6b and the urea derivatives 6f–6i and 7f–7h, although the ureas were relatively more active than thioureas. Twenty-fold more active than diazoxide, the urea 6g was the most potent vasodilator (EC50 = 0.983 ± 0.061 μmol/L) and proved to act as a voltage-gated calcium channel blocker. The lack of activity of sulfonylureas, 6k and 7j, could be attributed to their partial ionization at the physiological pH because of their acidic character. It should be interesting to investigate a larger number of compounds, including N-methylated sulfonylureas, to increase the vasodilator activity and to explore other biological models.

Recent developments in the synthesis and applications of dihydropyrimidin-2(1H)-ones and thiones

Dihydropyrimidin-2(1H)-ones/thiones (DHPMs) are important heterocyclic compounds owing to their excellent biological activities and have been widely utilized in pharmaceutical applications. Recently, numerous DHPM derivatives have been prepared. This review covers the synthesis of DHPMs and improved procedures for the preparation of DHPMs from 1995 to 2016.

Structural insights into the binding mode of flavonols with the active site of matrix metalloproteinase-9 through molecular docking and molecular dynamic simulations studies

Cartilage degradation in rheumatoid arthritis is mediated principally by the collagenases and gelatinases. Gelatinase B (also called matrix metalloproteinase 9 - MMP-9), is a valid target molecule which is known to participate in cartilage degradation as well as angiogenesis associated with the disease and inhibition of its activity shall prevent cartilage damage and angiogenesis. The focus of this study is to investigate the possibilities of MMP-9 inhibition by flavonol class of bioflavonoids by studying their crucial binding interactions at the active site of MMP 9 using molecular docking (Glide XP and QPLD) and further improvisation by post-docking MM-GBSA and molecular dynamic (MD) simulations. The results show that flavonols can convincingly bind to active site of MMP-9 as demonstrated by their stable interactions at the S1' specificity pocket and favourable binding energies. Gossypin has emerged as a promising candidate with a docking score of -14.618 kcal/mol, binding energy of -79.97 kcal/mol and a stable MD pattern over 15 ns. In addition, interaction mechanisms with respect to catalytic site zinc are also discussed. Further, the drug-like characters of the ligands were also analysed using ADME analysis.

Biological activity of dihydropyrimidinone (DHPM) derivatives: A systematic review

Dihydropyrimidinones are heterocycles with a pyrimidine moiety in the ring nucleus, which, in recent decades, have aroused interest in medicinal chemistry due to alleged versatile biological activity. In this systematic review, we describe the currently published activities of dihydropyrimidinone derivatives. Between 1990 and December 31st, 2016, 115 articles outlined biological activities or toxicity of DHPM derivatives, 12 of those involved in vivo experiments. The main activities associated with this class of compounds are antitumoral (43 articles), anti-inflammatory (12 articles), antibacterial (20 articles) and calcium channel antagonism/inhibition (14 articles). Antitumoral activity is the main biological property evaluated, since the main representative compound of this class (monastrol) is a known Eg5 kinesin inhibitor. This review depicts a variety of other pharmacological activities associated with DHPM derivatives, but the main findings are essentially in vitro characteristics of the substances. This review presents the current state of the art of DHPM biological activities and demonstrates that there is still a need for further in vivo studies to better delineate the pharmacological potential of this class of substances.