5-(2-amino-pyrimidin-4-yl)-1H-pyrrole and 2-(2-amino-pyrimidin-4-yl)-1,5,6,7-tetrahydro-pyrrolo[3,2-c]pyridin-4-one derivatives as new classes of selective and orally available Polo-like kinase 1 inhibitors

Accelerating discovery of bioactive ligands with pharmacophore-informed generative models

Deep generative models have advanced drug discovery but often generate compounds with limited structural novelty, providing constrained inspiration for medicinal chemists. To address this, we develop TransPharmer, a generative model that integrates ligand-based interpretable pharmacophore fingerprints with a generative pre-training transformer (GPT)-based framework for de novo molecule generation. TransPharmer excels in unconditioned distribution learning, de novo generation, and scaffold elaboration under pharmacophoric constraints. Its unique exploration mode could enhance scaffold hopping, producing structurally distinct but pharmaceutically related compounds. Its efficacy is validated through two case studies involving the dopamine receptor D2 (DRD2) and polo-like kinase 1 (PLK1). Notably, three out of four synthesized PLK1-targeting compounds show submicromolar activities, with the most potent, IIP0943, exhibiting a potency of 5.1 nM. Featuring a new 4-(benzo[b]thiophen-7-yloxy)pyrimidine scaffold, IIP0943 also has high PLK1 selectivity and submicromolar inhibitory activity in HCT116 cell proliferation. TransPharmer offers a promising tool for discovering structurally novel and bioactive ligands.

Study on Pharmacokinetics and Metabolic Profiles of Novel Potential PLK-1 Inhibitors by UHPLC-MS/MS Combined with UHPLC-Q-Orbitrap/HRMS

PLK-1 (Polo-like kinase-1) plays an essential role in cytokinesis, and its aberrant expression is considered to be keenly associated with a wide range of cancers. It has been selected as an appealing target and small-molecule inhibitors have been developed and studied in clinical trials. Unfortunately, most have been declared as failures due to the poor therapeutic response and off-target toxicity. In the present study, a novel potent PLK-1 inhibitor, compound 7a, was designed and synthetized. 1H NMR, 13C NMR, 19F NMR and mass spectrum were comprehensively used for the compound characterization. The compound exhibited higher potency against PLK-1 kinase, HCT-116 and NCI-H2030 cell lines than the positive control. Molecular docking indicated that the binding mode that the ATP binding site of PLK-1 was occupied by the compound. Then, a UHPLC-MS/MS method was established and validated to explore the pharmacokinetic behavior of the drug candidate. The method had good selectivity, high sensitivity and wide linearity. The exposure increased linearly with the dose, but the oral bioavailability was not satisfactory enough. Then, the metabolism was studied using liver microsomes by UHPLC-Q-Orbitrap/HRMS. Our research first studied the pharmacokinetic metabolic characteristics of 7a and may serve as a novel lead compound for the development of PLK-1 inhibitors.

QSAR-guided pharmacophoric modeling reveals important structural requirements for Polo kinase 1 (Plk1) inhibitors

Targeting Polo-like kinase 1 (Plk1) by molecular inhibitors is being a promising approach for tumor therapy. Nevertheless, insufficient methodical analyses have been done to characterize the interactions inside the Plk1 binding pocket. In this study, an extensive combined ligand and structure-based drug design workflow was conducted to data-mine the structural requirements for Plk1 inhibition. Consequently, the binding modes of 368 previously known Plk1 inhibitors were investigated by pharmacophore generation technique. The resulted pharmacophores were engaged in the context of Genetic function algorithm (GFA) and Multiple linear regression (MLR) analyses to search for a prognostic QSAR model. The most successful QSAR model was with statistical criteria of (r2277 = 0.76, r2adj = 0.76, r2pred = 0.75, Q2 = 0.73). Our QSAR-selected pharmacophores were validated by Receiver Operating Characteristic (ROC) curve analysis. Later on, the best QSAR model and its associated pharmacophoric hypotheses (HypoB-T4-5, HypoI-T2-7, HypoD-T4-3, and HypoC-T3-3) were used to identify new Plk1 inhibitory hits retrieved from the National Cancer Institute (NCI) database. The most potent hits exhibited experimental anti-Plk1 IC50 of 1.49, 3.79. 5.26 and 6.35 μM. Noticeably, our hits, were found to interact with the Plk1 kinase domain through some important amino acid residues namely, Cys67, Lys82, Cys133, Phe183, and Asp194.

Simple and efficient one-pot multi-step strategy for the synthesis of 2-substituted (1,2,5-triarylpyrrolo[3,2-c]pyridin-3-yl)-N-arylacetamide derivatives in water

A novel one-pot multi-step domino strategy for the synthesis of functionalized 2-substituted acetic acids, 2-substituted (1,2,5-triarylpyrrolo[3,2-c]pyridin-3-yl)acetates and 2-substituted-(1,2,5-triarylpyrrolo[3,2-c]pyridin-3-yl)-N-arylacetamides has been established from inexpensive and readily available starting materials. The reaction can be easily performed by employing different substrates via a one-pot multi-step domino reaction. The target products can be easily obtained with satisfactory yields by only simple recrystallization from a mixture of hot 95% ethanol and N,N-dimethylformamide. The reaction features of readily available starting materials, broad substrate scope, bond-forming efficiency, simple one-pot multi-step synthesis as well as green reaction media, make the procedure highly useful for the construction of potential pharmacological heterocyclic molecules.

Pyrrole-Aminopyrimidine Ensembles: Cycloaddition of Guanidine to Acylethynylpyrroles

An efficient method for the synthesis of pharmaceutically prospective pyrrole-aminopyrimidine ensembles (in up to 91% yield) by the cyclocondensation of easily available acylethynylpyrroles with guanidine nitrate has been developed. The reaction proceeds under heating (110-115 °C, 4 h) in the KOH/DMSO system. In the case of 2-benzoylethynylpyrrole, the unexpected addition of the formed pyrrole-aminopyrimidine as N- (NH moiety of the pyrrole ring) and C- (CH of aminopyrimidine) nucleophiles to the triple bond is observed.

Synthesis and HPLC-ECD Study of Cytostatic Condensed O,N-Heterocycles Obtained from 3-Aminoflavanones

Racemic chiral O,N-heterocycles containing 2-arylchroman or 2-aryl-2H-chromene subunit condensed with morpholine, thiazole, or pyrrole moieties at the C-3-C-4 bond were synthesized with various substitution patterns of the aryl group by the cyclization of cis- or trans-3-aminoflavanone analogues. The 3-aminoflavanone precursors were obtained in a Neber rearrangement of oxime tosylates of flavanones, which provided the trans diastereomer as the major product and enabled the isolation of both the cis- and trans-diastereomers. The cis- and trans-aminoflavanones were utilized to prepare three diastereomers of 5-aryl-chromeno[4,3-b][1,⁴]oxazines. Antiproliferative activity of the condensed heterocycles and precursors was evaluated against A2780 and WM35 cancer cell lines. For a 3-(N-chloroacetylamino)-flavan-4-ol derivative, showing structural analogy with acyclic acid ceramidase inhibitors, 0.15 μM, 3.50 μM, and 6.06 μM IC₅₀ values were measured against A2780, WM35, and HaCat cell lines, and apoptotic mechanism was confirmed. Low micromolar IC₅₀ values down to 2.14 μM were identified for the thiazole- and pyrrole-condensed 2H-chromene derivatives. Enantiomers of the condensed heterocycles were separated by HPLC using chiral stationary phase, HPLC-ECD spectra were recorded and TDDFT-ECD calculations were performed to determine the absolute configuration and solution conformation. Characteristic ECD transitions of the separated enantiomers were correlated with the absolute configuration and effect of substitution pattern on the HPLC elution order was determined.

Ammonium Acetate-Promoted One-Pot Tandem Aldol Condensation/Aza-Addition Reactions: Synthesis of 2,3,6,7-Tetrahydro-1H-pyrrolo[3,2-c]pyridin-4(5H)-ones

An efficient tandem intermolecular one-pot aldol condensation/aza-addition reaction of 2-methyl-3-carbamoylpyrroles and aldehydes was developed for the synthesis of 2,3,6,7-tetrahydro-1H-pyrrolo[3,2-c]pyridin-4(5H)-ones. The reaction proceeded using only 3.0 equiv of ammonium acetate promoter in green solvent poly(ethylene glycol)-400 at 100 °C to afford a series of pyrrolo[3,2-c]pyridinone derivatives in good to excellent yields.

Fusion of Structure and Ligand Based Methods for Identification of Novel CDK2 Inhibitors

Cyclin dependent kinases play a central role in cell cycle regulation which makes them a promising target with multifarious therapeutic potential. CDK2 regulates various events of the eukaryotic cell division cycle, and the pharmacological evidence indicates that overexpression of CDK2 causes abnormal cell-cycle regulation, which is directly associated with hyperproliferation of cancer cells. Therefore, CDK2 is regarded as a potential target molecule for anticancer medication. Thus, to decline CDK2 activity by potential lead compounds has proved to be an effective treatment for cancer. The availability of a large number of X-ray crystal structures and known inhibitors of CDK2 provides a gateway to perform efficient computational studies on this target. With the aim to identify new chemical entities from commercial libraries, with increased inhibitory potency for CDK2, ligand and structure based computational drug designing approaches were applied. A druglike library of 50,000 compounds from ChemDiv and ChemBridge databases was screened against CDK2, and 110 compounds were identified using the parallel application of these models. On in vitro evaluation of 40 compounds, seven compounds were found to have more than 50% inhibition at 10 μM. MD studies of the hits revealed the stability of these inhibitors and pivotal role of Glu81 and Leu83 for binding with CDK2. The overall study resulted in the identification of four new chemical entities possessing CDK2 inhibitory activity.

Synthesis and Pharmacochemistry of New Pleiotropic Pyrrolyl Derivatives

Within the framework of our attempts to synthesize pleiotropic anti-inflammatory agents, we have synthesized some chalcones and their corresponding 3,4-pyrrolyl derivatives. Chalcones constitute a class of compounds with high biological impact. They are known for a number of biological activities, including anti-inflammatory and free radical scavenging activities. They inhibit several enzymes implicated in the inflammatory process, such as lipoxygenase, cyclooxygenase (COX) and lysozymes. The synthesized pyrroles have been studied for: (1) their in vitro inhibition of lipoxygenase; (2) their in vitro inhibition of COX; (3) their in vitro inhibition of lipid peroxidation; (4) their interaction with the stable, N-centered, free radical, 2,2-diphenyl-1-picrylhydrazyl (DPPH); (5) their inhibition on interleukin-6 (IL-6); (6) their anti-proteolytic activity; and (7) their in vivo anti-inflammatory activity using carrageenan-induced rat paw edema. Their physicochemical properties were determined to explain the biological results. Lipophilicity was experimentally determined. 2i and 2v were found to be promising multifunctional molecules with high antiproteolytic and anti-inflammatory activities in combination with anti-interleukin-6 activity.