Review Writing on Synthesis of Pyrimidine and Its Biological Activity

Verbitskiy et al. reported the microwave-assisted synthesis of 4-(5-nitrofuran-2-yl)-5-arylamino-substituted pyrimidines. The reaction involved the arylamination of 5-bromo-4-(furan-2-yl)pyrimidine with various anilines in the presence of 20 mol% Pd(OAc)? as a catalyst, employing the Buchwald–Hartwig amination protocol. The transformation was efficiently carried out under microwave irradiation at 250 W and 150 °C for 10 minutes. The corresponding synthetic pathway is illustrated. (Verbitskiy et al., 2009, J. Org. Chem., 74(21), 7595–7598.)

Rahatgaonkar et al. reported an efficient microwave-assisted method for the synthesis of substituted 4,5-diphenyl imidazolyl pyrimidine hybrids. The reaction was performed using ethyl 1-formyl-1,2,3,6-tetrahydro-4-methyl-6-phenyl-2-oxo/thioxopyrimidine-5-carboxylates (25 mmol) and benzil (25 mmol) in the presence of ammonium acetate and acidic alumina. Under microwave irradiation for just 8 minutes, the reaction proceeded smoothly to afford the desired hybrids in excellent yields, highlighting the advantage of microwave techniques in achieving rapid and high-yielding transformations. (Rahatgaonkar et al., 2015, Int. J. Pharm. Chem. Res., 7(2), 89–94.)

Mechanism of action:

v) From 1,3-diaminopropane:

vi) From hetro aryl iodide:

vii)     Synthesis of pyrimidine from C-C-C and N-C-N fragments:

xi) Synthesis of pyrano [2,3-d]pyrimidine compounds using nano CuO-Ag as a catalyst :

xiv) Synthesis of pyrimidine-fused heterocycle derivatives :

From the historical point of view, there are three general synthetic methods for the synthesis of pyrimidine-fused derivatives in the literature.^18,19 In the Bischler’s strategy the synthesis of PFH is achieved from ortho-acetamidobenzaldehyde derivatives.¹⁸ The second method is the Riedel’s synthesis, which PFH compounds can be obtained via reductive cyclization of bisformamido derivatives of ortho-nitrobenzaldehydes.¹⁹ The so-called Niementowski’s synthesis involves preparation of fused pyrimidines from the anthranilic acid derivatives.¹⁸ In modern organic synthesis these compounds have been synthesized using multicomponent reactions (MCRs).²⁰ MCRs are attractive synthetic strategies, as complex products are formed in a single step and the diversity can be achieved simply by varying the reaction components.²⁰ Thus, functionally-substituted starting materials can be used to synthesize the desired biologically active compounds.²¹ The syntheses of new PFH analogues remain challenging, especially when optimizing their activities. Hence, MCRs represent useful procedures for this goal, because by simply changing the starting material, a large number of pyrimidinefused analogues with convenient optimization and range of biological activities can be synthesized. The following multicomponent reaction was used to synthesis PFH ligands L1–L7 . It is noteworthy that the products are precipitated after production and so they are isolated from reaction mixture by simple filtration with high purity. In this protocol barbituric acid was treated with amines and aldehydes. By changing the amine and aldehyde components a set of PFHs were synthesized. In the selection of aldehyde components, it was decided to use only two aldehydes isovanillin and 3indole carboxaldehyde, because they have been used as a chemical source in synthesis of many biological active compounds.^22,23 For the synthesis of ligands L1–L3, 4-bromo-aniline was used as an amine component, because this chemical moiety previously showed a-Gls inhibitory activity in the structure of ligand C2 (Fig. 1). In the synthesis of ligands L4–L7 a series of bi-functionalized aromatic amines was applied to produce a set of PFH with free NH₂ group in their structures. L4–L7 was synthesized according to our previous ligands as they have been demonstrated significant inhibitory activity against a-Gls. Moreover, it is noteworthy to mention that the free amino groups in their structures can possibly improve their ability for hydrogen bonding interaction. In this class of compounds, one equivalent of amine component was used. However, in one case in order to synthesize a new derivative based on ligand L5, 0.5 equiv of amine component was used in the reaction (Scheme 2). This green and efficient reaction was performed in refluxing EtOH in the presence of catalytic amount of tungstophosphoric acid (TPA) as catalyst.²⁴. The synthesized compounds L1–L8 were also characterized, using different spectroscopic techniques such as ¹H NMR, ¹³C NMR, infrared (IR), and mass spectroscopy. The data clearly revealed that these molecules were produced successfully. As the purity of synthetic compounds examined using elemental analysis, they were highly pure (>97%). (Tariq et al., 2019, J. Heterocyclic Chem., 56(8), 2289–2297.)

xv) Design synthesis of pyrimidine derivatives:

A variety of novel pyrimidine derivatives were synthesized through multistep reactions starting from thioxopyrimidine core structures. Initially, thioxopyrimidine was condensed with chloroacetic acid and aromatic aldehydes in the presence of acetic acid/anhydride and sodium acetate to afford thiazolopyrimidine derivatives. In another approach, cyanouracil was reacted with 2-chloro-N-substituted phenylacetamide in DMF and potassium carbonate to yield acetamide-substituted pyrimidines. The resulting compounds were further modified by N-alkylation with tosyl chloride or ethyl chloroacetate to form tosyl and ester derivatives, respectively. Hydrazinolysis of ester derivatives produced hydrazino intermediates, which served as key precursors for a wide range of further transformations. These hydrazino compounds were converted into Schiff bases, acetylated, or reacted with cyclic ketones and acid chlorides to form fused triazolo-, tetrazolo-, and thiazolopyrimidine derivatives. Cyclization reactions with carbon disulfide led to triazolopyrimidines via nucleophilic addition and H?S elimination. All synthesized compounds were characterized using IR, ¹H-NMR, mass spectrometry, and elemental analysis. The developed molecules showed promising antibacterial and antifungal activity, particularly compounds 7 and 9. Several derivatives also demonstrated potent antiproliferative effects against HePG-2 and MCF-7 cancer cell lines. Compound 7, in particular, exhibited higher cytotoxicity than 5-fluorouracil. Molecular docking revealed strong binding interactions with thymidylate synthase enzyme, confirming their therapeutic potential. (Sharma et al., 2015, Bioorg. Med. Chem. Lett., 25(22), 5203–5208.)

4. Biological Activity of Pyrimidine and Its Derivatives:

i) Antimicrobial Activity

i-a) Broad-Spectrum Antibacterial and Antifungal Action

Pyrimidine derivatives synthesized excellent antimicrobial activity against both gram-positive and gram-negative bacteria such as Staphylococcus aureus (SA), Escherichia coli (EC), and fungal strains like Candida albicans. For example, the derivatives III-A, III-B, and III-C synthesized via microwave-assisted reactions exhibited well-defined zones of inhibition in disk diffusion assays comparable to ciprofloxacin, suggesting strong bacteriostatic effects. Substituent effects are crucial: halogen-substituted benzaldehydes (e.g., chloro or nitro groups) significantly increased antimicrobial efficacy by enhancing cell wall permeability and disrupting bacterial metabolic pathways. Schiff base derivatives containing hydrazinyl moieties and fused triazolopyrimidines also demonstrated improved microbial inhibition, attributed to hydrogen bonding with bacterial DNA and enzyme systems.

i-b) Mechanism of Action

These compounds likely target:

• Bacterial enzymes (e.g., dihydrofolate reductase),
• Cell wall synthesis pathways,
• DNA replication enzymes, disrupting nucleic acid synthesis.

SAR analysis reveals that the presence of a cyano or carbonyl group on the pyrimidine ring enhances electron delocalization, increasing the compound's interaction with bacterial biomolecules. (Behalo, 2018, J. Heterocycl. Chem., 55; Wu et al., 2021, Front. Chem., 9, 695628.)

ii) Anticancer Activity

ii-a) Established Pyrimidine Anticancer Agents

Clinically established drugs such as 5-fluorouracil (5-FU), tegafur, and gemcitabine are pyrimidine analogs that act by inhibiting DNA synthesis. These agents incorporate into DNA or inhibit thymidylate synthase, leading to apoptosis.

ii-b) Novel Anticancer Derivatives

Across the papers, novel derivatives such as thiazolopyrimidines, imidazolylpyrimidines, and fused triazolopyrimidines were synthesized and evaluated for cytotoxicity on cancer cell lines like HePG-2 (hepatic carcinoma) and MCF-7 (breast cancer). Compound 7, for example, showed higher cytotoxicity than 5-FU, making it a promising lead for anticancer drug development.

Mechanism: These molecules interact with DNA-binding enzymes (e.g., topoisomerases) or act as kinase inhibitors. Molecular docking studies confirmed strong affinity to targets such as thymidylate synthase and DNA polymerases.

ii-c) Structure-Activity Correlation

• Aryl substitution at C-4/C-6: Enhances DNA binding.
• Fused ring systems: Improve lipophilicity and membrane permeability.

 (Sharma et al., 2015, Bioorg. Med. Chem. Lett., 25(22), 5203–5208; Kimura et al., 2006, Anticancer Res., 26, 91–97.)

iii) Antiviral Activity

iii-a) HIV and CMV Treatment

Several pyrimidine analogs serve as nucleoside reverse transcriptase inhibitors (NRTIs) in antiviral therapy:

• AZT (Zidovudine)
• Stavudine (d4T)
• DDC(Didanosine)
  These act by terminating DNA chain elongation during viral replication.

Cidofovir, another pyrimidine-based drug, is used to treat cytomegalovirus (CMV) infections.

iii-b) Emerging Derivatives and New Mechanisms

Recent studies introduced selenium-based pyrimidine analogs and HEPT derivatives, which selectively inhibit HIV-1 reverse transcriptase. Some fused systems show dual activity against both HIV-1 and HIV-2, indicating potential as next-generation NNRTIs. ( Deep et al., 2018, Curr. Bioact. Compd., 14; Elkanzi, 2020, Orient. J. Chem., 36(6), 1001–1015.)

iv) Anti-inflammatory and Analgesic Activity

iv-a) Pyrimidines as COX Inhibitors

Inflammation and pain are regulated by prostaglandins synthesized via the cyclooxygenase (COX) pathway. Pyrimidine derivatives like pyrazolopyrimidines and imidazolo[1,2-c]pyrimidines inhibit COX-2 selectively, reducing inflammatory response with minimal gastrointestinal effects.

Examples:

• Acetamine, bentamine, and fursultiamine—thiamine derivatives with anti-inflammatory roles.
• 2-phenylpyrazolo[1,5-a]pyrimidine—demonstrated efficacy in carrageenan-induced rat paw edema.

Mechanism:

• Downregulation of inflammatory cytokines (TNF-α, IL-6)
• Inhibition of COX-2 and iNOS expression

(Rashid et al., 2021, RSC Adv., 11, 6060–6098.)

v)  Antioxidant Activity

Pyrimidines with phenolic or electron-rich aromatic substitutions exhibit significant free radical scavenging activity. The DPPH and ABTS assays used in the studies showed that several Schiff base-modified pyrimidines were as effective as ascorbic acid.

Key SAR features:

• Hydroxyl and methoxy groups donate electrons to neutralize radicals.
• Imine linkages enhance conjugation and electron delocalization.

Such antioxidant properties make pyrimidines promising in managing oxidative stress-related diseases like neurodegeneration and atherosclerosis. (Abdollahi-Basir et al., 2018, J. Mol. Liq., 249, 1221–1227.)

vi)  Antitubercular and Antimalarial Activity

vi-a) Mycobacterial Inhibition

Certain triazolopyrimidines and fused derivatives inhibited the growth of Mycobacterium tuberculosis H37Rv. Substituted derivatives targeting dihydrofolate reductase were particularly effective.

vi-b) Antimalarial Efficacy

Pyrimethamine and trimethoprim, known antimalarials, work by inhibiting folate biosynthesis in Plasmodium species. Newly synthesized analogs with electron-withdrawing groups exhibited increased potency and better selectivity indices.

SAR Observations:

• Chloro and fluoro substitution improved membrane penetration.
• Fused systems resisted metabolic degradation.

(Kumbhar et al., 2023, Biol. Forum – Int. J., 15(4), 963–976.)

vii) Antifungal and Antibiofilm Properties

Fungal infections like candidiasis are difficult to manage due to biofilm formation and resistance. Pyrimidine derivatives synthesized via green methods using deep eutectic solvents showed up to 90% inhibition of Candida albicans biofilm.

Compounds like 3,4-dihydropyrimidin-2(1H)-thione inhibit:

• Fungal ergosterol synthesis
• Cell wall integrity pathways

Advantages:

• Dual action against planktonic and sessile fungi
• Reduced risk of resistance development

(Al-Hazmi, 2024, Pol. J. Environ. Stud., 33(5), 5549–5556; Abdollahi-Basir et al., 2018, J. Mol. Liq.)

viii) CNS and Cardiovascular Applications

viii-a)  CNS Modulation

Some pyrimidines like thimylal (general anesthetic) and saxitoxin (potent sodium channel blocker) affect neurotransmission, although toxicity limits their clinical use.

Potential roles:

• Anticonvulsants, Anxiolytics, Sedatives.

viii-b) Cardiovascular Agents

Fused pyrimidine analogs such as quinazoline-pyrimidines act as α1-adrenergic antagonists, helping treat:

• Hypertension (e.g., prazosin, terazosin)
• Benign prostatic hyperplasia

(Elkanzi, 2020, Orient. J. Chem., 36(6), 1001–1015; Dayan et al., 2019, Polyhedron)

5. Future Prospects

Pyrimidine and its derivatives remain one of the most versatile scaffolds in medicinal and synthetic chemistry. Despite extensive research, there is still considerable scope for innovation and application in this field. Future work can be directed along the following lines:

1. Green and Sustainable Synthesis
   • Development of eco-friendly catalytic systems, such as biocatalysts, ionic liquids, or deep eutectic solvents, can further reduce the environmental footprint.
   • Microwave- and ultrasound-assisted protocols should be optimized for scalability in industrial settings.
2. Structure–Activity Relationship (SAR) Exploration
   • More systematic SAR studies are required to fine-tune pharmacophore design.
   • Incorporation of pyrimidine rings with heteroaryl, thiazole, or triazole moieties may enhance antimicrobial, anticancer, and antiviral activities.
3. Drug Discovery and Repurposing
   • Pyrimidine derivatives should be explored as dual- or multi-target agents, particularly in complex diseases such as cancer, viral infections (including emerging pathogens), and neurodegenerative disorders.
   • Drug repurposing strategies can identify new applications for known pyrimidine-based drugs.
4. Nanotechnology and Delivery Systems
   • Functionalization of pyrimidine derivatives for nanoparticle-based drug delivery can improve bioavailability and targeted release.
   • Hybrid materials (e.g., pyrimidine–metal complexes) should be explored for theranostic (therapy + diagnosis) applications.
5. Agrochemical and Environmental Applications
   • Beyond medicinal use, pyrimidine frameworks show promise in designing novel herbicides, insecticides, and fungicides with higher selectivity and lower toxicity.
   • Environmentally benign pyrimidine derivatives could serve as sustainable alternatives in crop protection.
6. Computational and AI-Guided Design
   • Molecular docking, QSAR, and machine learning tools can accelerate the identification of promising pyrimidine leads.
   • Integration of computational predictions with experimental validation will shorten drug development timelines.

6. CONCLUSION

Pyrimidine and its derivatives have emerged as a cornerstone in heterocyclic chemistry, owing to their structural diversity, synthetic accessibility, and wide-ranging biological activities. Various synthetic strategies—such as the Biginelli reaction, microwave-assisted synthesis, multi-component condensation, and green methodologies using natural catalysts or deep eutectic solvents—have enabled the efficient construction of a broad array of functionalized pyrimidine scaffolds. These methods not only improve reaction yields and atom economy but also align with sustainable chemistry principles, making them highly relevant in modern pharmaceutical synthesis. The biological evaluation of synthesized pyrimidine derivatives reveals significant activity across diverse pharmacological domains. Many compounds exhibited potent antimicrobial, anticancer, antiviral, anti-inflammatory, antioxidant, antifungal, antitubercular, and antimalarial effects, often comparable or superior to standard drugs. Structure–activity relationship (SAR) studies confirm that the nature and position of substituents on the pyrimidine ring system strongly influence these activities, offering valuable insights for rational drug design. Overall, the combination of versatile synthesis and impactful biological activity establishes pyrimidine derivatives as promising leads in drug discovery and development. Continued research into their design, optimization, and mechanism of action will further expand their therapeutic potential across unmet medical needs.

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