Determination of absolute configuration in 4-aryl-3, 4-dihydro-2(1H)-pyrimidones by high performance liquid chromatography and CD spectroscopy

Exploring Biginelli-based scaffolds as A2B adenosine receptor antagonists: Unveiling novel structure-activity relationship trends, lead compounds, and potent colorectal anticancer agents

Antagonists of the A2B adenosine receptor have recently emerged as targeted anticancer agents and immune checkpoint inhibitors within the realm of cancer immunotherapy. This study presents a comprehensive evaluation of novel Biginelli-assembled pyrimidine chemotypes, including mono-, bi-, and tricyclic derivatives, as A2BAR antagonists. We conducted a comprehensive examination of the adenosinergic profile (both binding and functional) of a large compound library consisting of 168 compounds. This approach unveiled original lead compounds and enabled the identification of novel structure-activity relationship (SAR) trends, which were supported by extensive computational studies, including quantum mechanical calculations and free energy perturbation (FEP) analysis. In total, 25 molecules showed attractive affinity (Ki < 100 nM) and outstanding selectivity for A2BAR. From these, five molecules corresponding to the new benzothiazole scaffold were below the Ki < 10 nM threshold, in addition to a novel dual A2A/A2B antagonist. The most potent compounds, and the dual antagonist, showed enantiospecific recognition in the A2BAR. Two A2BAR selective antagonists and the dual A2AAR/A2BAR antagonist reported in this study were assessed for their impact on colorectal cancer cell lines. The results revealed a significant and dose-dependent reduction in cell proliferation. Notably, the A2BAR antagonists exhibited remarkable specificity, as they did not impede the proliferation of non-tumoral cell lines. These findings support the efficacy and potential that A2BAR antagonists as valuable candidates for cancer therapy, but also that they can effectively complement strategies involving A2AAR antagonism in the context of immune checkpoint inhibition.

Exploring the Effect of Halogenation in a Series of Potent and Selective A2B Adenosine Receptor Antagonists

The modulation of the A_2B adenosine receptor is a promising strategy in cancer (immuno) therapy, with A_2BAR antagonists emerging as immune checkpoint inhibitors. Herein, we report a systematic assessment of the impact of (di- and mono-)halogenation at positions 7 and/or 8 on both A_2BAR affinity and pharmacokinetic properties of a collection of A_2BAR antagonists and its study with structure-based free energy perturbation simulations. Monohalogenation at position 8 produced potent A_2BAR ligands irrespective of the nature of the halogen. In contrast, halogenation at position 7 and dihalogenation produced a halogen-size-dependent decay in affinity. Eight novel A_2BAR ligands exhibited remarkable affinity (K_i < 10 nM), exquisite subtype selectivity, and enantioselective recognition, with some eutomers eliciting sub-nanomolar affinity. The pharmacokinetic profile of representative derivatives showed enhanced solubility and microsomal stability. Finally, two compounds showed the capacity of reversing the antiproliferative effect of adenosine in activated primary human peripheral blood mononuclear cells.

Identification of V6.51L as a selectivity hotspot in stereoselective A2B adenosine receptor antagonist recognition

The four adenosine receptors (ARs) A₁AR, A_2AAR, A_2BAR_, and A₃AR are G protein-coupled receptors (GPCRs) for which an exceptional amount of experimental and structural data is available. Still, limited success has been achieved in getting new chemical modulators on the market. As such, there is a clear interest in the design of novel selective chemical entities for this family of receptors. In this work, we investigate the selective recognition of ISAM-140, a recently reported A_2BAR reference antagonist. A combination of semipreparative chiral HPLC, circular dichroism and X-ray crystallography was used to separate and unequivocally assign the configuration of each enantiomer. Subsequently affinity evaluation for both A_2A and A_2B receptors demonstrate the stereospecific and selective recognition of (S)-ISAM140 to the A_2BAR. The molecular modeling suggested that the structural determinants of this selectivity profile would be residue V250^6.51 in A_2BAR, which is a leucine in all other ARs including the closely related A_2AAR. This was herein confirmed by radioligand binding assays and rigorous free energy perturbation (FEP) calculations performed on the L249V^6.51 mutant A_2AAR receptor. Taken together, this study provides further insights in the binding mode of these A_2BAR antagonists, paving the way for future ligand optimization.

3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A2B Adenosine Receptor: Optimization, Structure-Activity Relationship Studies, and Enantiospecific Recognition

We present and thoroughly characterize a large collection of 3,4-dihydropyrimidin-2(1H)-ones as A_2BAR antagonists, an emerging strategy in cancer (immuno) therapy. Most compounds selectively bind A_2BAR, with a number of potent and selective antagonists further confirmed by functional cyclic adenosine monophosphate experiments. The series was analyzed with one of the most exhaustive free energy perturbation studies on a GPCR, obtaining an accurate model of the structure-activity relationship of this chemotype. The stereospecific binding modeled for this scaffold was confirmed by resolving the two most potent ligands [(±)-47, and (±)-38 K_i = 10.20 and 23.6 nM, respectively] into their two enantiomers, isolating the affinity on the corresponding (S)-eutomers (K_i = 6.30 and 11.10 nM, respectively). The assessment of the effect in representative cytochromes (CYP3A4 and CYP2D6) demonstrated insignificant inhibitory activity, while in vitro experiments in three prostate cancer cells demonstrated that this pair of compounds exhibits a pronounced antimetastatic effect.

Nitrogen-Walk Approach to Explore Bioisosteric Replacements in a Series of Potent A2B Adenosine Receptor Antagonists

A systematic exploration of bioisosteric replacements for furan and thiophene cores in a series of potent A_2BAR antagonists has been carried out using the nitrogen-walk approach. A collection of 42 novel alkyl 4-substituted-2-methyl-1,4-dihydrobenzo[4,5]imidazo[1,2-a]pyrimidine-3-carboxylates, which contain 18 different pentagonal heterocyclic frameworks at position 4, was synthesized and evaluated. This study enabled the identification of new ligands that combine remarkable affinity (K_i < 30 nM) and exquisite selectivity. The structure-activity relationship (SAR) trends identified were substantiated by a molecular modeling study, based on a receptor-driven docking model and including a systematic free energy perturbation (FEP) study. Preliminary evaluation of the CYP3A4 and CYP2D6 inhibitory activity in optimized ligands evidenced weak and negligible activity, respectively. The stereospecific interaction between hA_2BAR and the eutomer of the most attractive novel antagonist (S)-18g (K_i = 3.66 nM) was validated.

Advantages of electronic circular dichroism detection for the stereochemical analysis and characterization of drugs and natural products by liquid chromatography

The need for analytical methods for the determination of the enantiomeric excess of chiral compounds increased significantly in the last decades, and enantioselective separation techniques resulted particularly efficient to this purpose. Moreover, when detection systems based on chiroptical properties (optical rotation or circular dichroism) are employed in high-performance liquid chromatography (HPLC), the stereochemistry of a chiral analyte can be fully determined. Indeed, the coupling of HPLC with chiroptical detection systems allows the simultaneous assessment of the absolute configuration of stereoisomers and the evaluation of the enantiomeric/diastereomeric excess of samples. These features are particularly important in the study of drugs and natural products provided with biological activity, because the assignment of their absolute stereochemistry is essential to establish reliable structure-activity relationships. The following review aims to discuss the analytical advantages arising from the employment of electronic circular dichroism (ECD) detection systems in stereochemical analysis by HPLC upon chiral and non-chiral stationary phases and their use for the stereochemical characterization of chiral drugs and natural compounds. The different methods for the correlation between absolute stereochemistry and chiroptical properties are critically discussed. Relevant HPLC applications of ECD detection systems are then reported, and their analytical advantages are highlighted. For instance, the importance of the concentration-independent anisotropy factor (g-factor; g=Δɛ/ɛ) for the determination of the stereoisomeric composition of samples upon non-chiral stationary phases is underlined, since its sensitivity makes ECD detection very well suited for the enantioselective analysis of large libraries of chiral compounds in relatively short times.

An efficacious protocol for C-4 substituted 3,4-dihydropyrimidinones. Synthesis and calcium channel binding studies

Ethyl 1,2-dihydro-1,6-dimethyl/6-methyl-2-oxopyrimidine-5-carboxylates react with C-nucleophiles as well as anion of enantiopure chiral auxiliary (1R,2S,5R)-(-)-methyl (S)-p-toluenesulfinate to afford C-4 substituted and enantiopure congeners of medicinally potent Biginelli dihydropyrimidinones. The calcium channel blocking activity of some of the compounds was evaluated and compared with nifedipine for their ability to relax a membrane depolarization induced contraction.

Identification and characterization of 4-aryl-3,4-dihydropyrimidin-2(1H)-ones as inhibitors of the fatty acid transporter FATP4

Several potent, cell permeable 4-aryl-dihydropyrimidinones have been identified as inhibitors of FATP4. Lipophilic ester substituents at the 5-position and substitution at the para-position (optimal groups being -NO(2) and CF(3)) of the 4-aryl group led to active compounds. In two cases racemates were resolved and the S enantiomers shown to have higher potencies.

Highly Enantioseletive Biginelli Reaction Using a New Chiral Ytterbium Catalyst: Asymmetric Synthesis of Dihydropyrimidines

The highly enantioselective three-component Biginelli condensation catalyzed by a recyclable chiral ytterbium triflate with a novel hexadentate amine phenol ligand containing a pyridyl group has been developed. A wide range of optically active dihydropyrimidines with remarkable pharmacological interest was obtained in high yields with good to excellent enantioselectivities under mild conditions.

Enantioseparation of racemic 4-aryl-3,4-dihydro-2(1H)-pyrimidones on chiral stationary phases based on 3,5-dimethylanilides of N-(4-alkylamino-3,5-dinitro)benzoyl L-alpha-amino acids

Three novel chiral packing materials for high-performance liquid chromatography were prepared by covalently binding of (2S)-N-(3,5-dimethylphenyl)-2-[(4-chloro-3,5-dinitrophenyl)carbonylamino]propan-amide (7), (2S)-N-(3,5-dimethylphenyl)-2-[(4-chloro-3,5-dinitrophenyl)carbonylamino]-4-methylpentanamide (8), and (2S)-N-(3,5-dimethylphenyl)-2-[(4-chloro-3,5-dinitrophenyl)carbonyl-amino]-2-phenylacetamide (9) to aminopropyl silica. The resulting chiral stationary phases (CSPs 1-3) proved effective for the resolution of racemic 4-aryl-3,4-dihydro-2(1H)-pyrimidone derivatives (TR 1-14). The mechanism of their enantioselection, supported by the elution order of (S)-TR 13 and (R)-TR 13 and molecular modeling of the complex of the slower running (S)-TR 13 with CSP 1 is discussed.

Three-component Biginelli cyclocondensation reaction using C-glycosylated substrates. Preparation of a collection of dihydropyrimidinone glycoconjugates and the synthesis of C-glycosylated monastrol analogues

The aldehyde-ketoester-urea cyclocondensation reaction has been revisited using C-glycosylated reagents with the aim of exploring a potential entry to a library of dihydropyrimidinone glycoconjugates. A collection of 13 mono- and bis-C-glycosylated dihydropyrimidinones has been prepared by a parallel synthesis approach using the three-component promoter CuCl/AcOH/BF(3) x Et(2)O. The sugar residues have been installed at either N1, C4, or C6 in the monoglycosylated derivatives and at both the C4 and C6 in the bisglycosylated products. The mono- and bisglycosylated products at C4 and C6 were obtained as mixtures of diastereoisomers with good to excellent selectivities due to the asymmetric induction by the sugar residue in the formation of the C4 stereocenter of the dihydropyrimidinone ring. Individual stereoisomers were isolated as pure compounds and their structures assigned with the aid of X-ray crystallography and chiroptical properties. As a demonstration of this new concept in the Biginelli reaction, the synthesis of two C4 epimer monastrol analogues bearing the ribofuranosyl moiety at C6 has been described.

Absolute configuration in 4-alkyl- and 4-aryl-3,4-dihydro-2(1H)-pyrimidones: a combined theoretical and experimental investigation

Structural features (orientation of the carboxyl group, ring puckering), electronic absorption, and circular dichroism spectra of 4-alkyl- and 4-aryl-dihydropyrimidones 1-5 are calculated by semiempirical (AM1, INDO/S), ab initio (HF/6-31G, CIS/6-31G, RPA/6-31G), and density functional theory (B3LYP/6-31G) methods. These calculations allow an assignment of the absolute configuration by comparison of simulated and experimental CD spectra. Although the ab initio methods greatly overestimate electronic transition energies, the general appearance of the experimental CD spectra is quite nicely reproduced by these calculations. Thus, comparison of experimental with calculated CD spectra is a reliable tool for the assignment of the absolute configuration. For 4-methyl derivatives 1, the first enantiopure DHPM examples with no additional aromatic substituent, the stereochemistry at C4 provided by the theoretical results is confirmed by X-ray structure determination of the diastereomeric salt 6. Additional support is the consistent HPLC elution order found for all investigated DHPMs on a cellulose-derived chiral stationary phase.

Recent advances in the Biginelli dihydropyrimidine synthesis. New tricks from an old dog

In 1893, P. Biginelli reported the synthesis of functionalized 3, 4-dihydropyrimidin-2(1H)-ones (DHPMs) via three-component condensation reaction of an aromatic aldehyde, urea, and ethyl acetoacetate. In the past decade, this long-neglected multicomponent reaction has experienced a remarkable revival, mainly due to the interesting pharmacological properties associated with this dihydropyrimidine scaffold. In this Account, we highlight recent developments in the Biginelli reaction in areas such as solid-phase synthesis, combinatorial chemistry, and natural product synthesis.