Synthetic Strategies of Pyrimidine-Based Scaffolds as Aurora Kinase and Polo-like Kinase Inhibitors

Hit discovery of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines as potential anti-glioblastoma therapeutics: Design, synthesis, biological evaluation, and computational screening

Glioblastoma multiforme (GBM) is a highly-aggressive, dreadful disease with poor prognosis and disappointing clinical success. There is an unmet medical need of molecularly-targeted therapeutics for GBM treatment. In the present work, a series of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines was designed, synthesized, purified, characterized, and evaluated for cytotoxicity against glioblastoma cell line U87-MG. The design process (virtual library enumeration around the core, physicochemical and molecular property prediction/calculation of the designs, filtering the undesirable ones, and the diversity analyses of the lead-like designs), was carefully curated so as to obtain a set of structurally-diverse, novel molecules (total 20), with a particular focus on the relatively unexplored core structure, 6,7-dihydro-5H-cyclopenta[d]pyrimidine. The preliminary screening was done using MTT assay at 10 and 100 μM concentrations of the title compounds F₁ -F₂₀ and positive control cisplatin, which yielded six hits (% inhibition at 10 μM: ~50%)-F₂ , F₃ , F₅ , F₇ , F₁₅ , and F₂₀ , which were taken up for IC₅₀ determination. The top hits F₂ and F₇ (IC₅₀  < 10 μM) were further used for computational studies such as target prediction, followed by their molecular docking in the binding sites of the top-3 predicted targets (epidermal growth factor receptor kinase domain, cyclin-dependent kinase 2 [CDK2]) /cyclin E, and anaplastic lymphoma kinase [ALK]). The docking pose analyses revealed interesting trends. The relatively planar core structure, presence of favorable hinge-binding substructures, basic groups, all added up, and culminated in appreciable cytotoxicity against GBM cell line.

Antiproliferative Activity of (-)-Isopulegol-based 1,3-Oxazine, 1,3-Thiazine and 2,4-Diaminopyrimidine Derivatives

A series of novel heterocyclic structures, namely 1,3‐oxazines, 1,3‐thiazines and 2,4‐diaminopyrimidines, were designed and synthesised. The bioassay tests demonstrated that, among these analogues, 2,4‐diaminopyridine derivatives showed significant antiproliferative activity against different human cancer cell lines (A2780, SiHa, HeLa, MCF‐7 and MDA‐MB‐231). Pyrimidines substituted with N²‐(p‐trifluoromethyl)aniline, in particular, displayed a potent inhibitory effect on the growth of cancer cells. Structure–activity relationships were also studied from the aspects of stereochemistry on the aminodiol moiety as well as exploring the effects of substituents on the pyrimidine scaffold.

SNAr Reactions on 2-Amino-4,6-dichloropyrimidine-5-carbaldehyde

We report the experimental results of unexpected aromatic nucleophilic substitution reaction products on 2-amino-4,6-dichloropyrimidine-5-carbaldehyde. The isolated compounds are products of amination, solvolysis, and condensation processes under mild and environmentally friendly conditions, due to the influence of structural factors of the starting pyrimidine and a high concentration of alkoxide ions. This method allows the building of pyrimidine-based compound precursors of N-heterocyclic systems.

DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6'-Diamino-1,1',3,3'-tetramethyl-5,5'-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]

Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (-7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand-protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. -5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.