Hybrid Imidazole-Pyridine Derivatives: An Approach to Novel Anticancer DNA Intercalators

New imidazole-2-thiones linked to acenaphythylenone as dual DNA intercalators and topoisomerase II inhibitors: structural optimization, docking, and apoptosis studies

In this article, a new series of 2-((3,5-disubstituted-2-thioxo-imidazol-1-yl)imino)acenaphthylen-1(2H)-ones were synthesized. Imidazole-2-thione with acenaphthylen-one gave a hybrid scaffold that integrated key structural elements essential for DNA damage via direct DNA intercalation and inhibition of the topoisomerase II enzyme. All the synthesized compounds were screened to detect their DNA damage using a terbium fluorescent probe. Results demonstrated that 4-phenyl-imidazoles 5b and 5e in addition to 4-(4-chlorophenyl)imidazoles 5h and 5j would induce detectable potent damage in ctDNA. The four most potent compounds as DNA intercalators were further evaluated for their antiproliferative activity against HepG2, MCF-7 and HCT-116 utilizing the MTT assay. The highest anticancer activity was recorded with compounds 5b and 5h against the breast cancer cell line MCF-7 which were 1.5- and 3- folds more active than doxorubicin, respectively. Therefore, imidazole-2-thione tethered acenaphthylenone derivatives can be considered as promising scaffold for the development of effective dual DNA intercalators and topoisomerase II inhibitors.

Efficient prediction of anticancer peptides through deep learning

Background

Cancer remains one of the leading causes of mortality globally, with conventional chemotherapy often resulting in severe side effects and limited effectiveness. Recent advancements in bioinformatics and machine learning, particularly deep learning, offer promising new avenues for cancer treatment through the prediction and identification of anticancer peptides.

Objective

This study aimed to develop and evaluate a deep learning model utilizing a two-dimensional convolutional neural network (2D CNN) to enhance the prediction accuracy of anticancer peptides, addressing the complexities and limitations of current prediction methods.

Methods

A diverse dataset of peptide sequences with annotated anticancer activity labels was compiled from various public databases and experimental studies. The sequences were preprocessed and encoded using one-hot encoding and additional physicochemical properties. The 2D CNN model was trained and optimized using this dataset, with performance evaluated through metrics such as accuracy, precision, recall, F1-score, and area under the receiver operating characteristic curve (AUC-ROC).

Results

The proposed 2D CNN model achieved superior performance compared to existing methods, with an accuracy of 0.87, precision of 0.85, recall of 0.89, F1-score of 0.87, and an AUC-ROC value of 0.91. These results indicate the model's effectiveness in accurately predicting anticancer peptides and capturing intricate spatial patterns within peptide sequences.

Conclusion

The findings demonstrate the potential of deep learning, specifically 2D CNNs, in advancing the prediction of anticancer peptides. The proposed model significantly improves prediction accuracy, offering a valuable tool for identifying effective peptide candidates for cancer treatment.

Future Work

Further research should focus on expanding the dataset, exploring alternative deep learning architectures, and validating the model's predictions through experimental studies. Efforts should also aim at optimizing computational efficiency and translating these predictions into clinical applications.

Benzoquinoline Derivatives: An Attractive Approach to Newly Small Molecules with Anticancer Activity

This study presents the synthesis, structural characterization, and in vitro evaluation of anticancer activity of some newly benzo[f]quinoline derivatives. The synthesis is facile and efficient, involving two steps: quaternization of nitrogen heterocycle followed by a [3+2] dipolar cycloaddition reaction. The synthesized compounds were characterized by FTIR, NMR, and X-ray diffraction on monocrystal in the case of compounds 6c and 7c. An in vitro single-dose anticancer assay of eighteen benzo[f]quinoline compounds, quaternary salts, and cycloadducts, was performed. The results showed that the most active compounds were quaternary salts 3d and 3f with aromatic R substituents. Quaternary salt 3d revealed non-selective activity against all types of cancer cells, while salt 3f exhibited a highly selective activity against leukemia cells. Compound 3d also presented remarkable cytotoxic efficiency against four distinct types of cancer cells-namely, non-small cell lung cancer HOP-92, melanoma LOX IMVI, melanoma SK-MEL-5, and breast cancer MDA-MB-468. Compound 3f was selected for five-dose screening. The study also includes SAR correlations.

Antitumor Activity of PEGylated and TEGylated Phenothiazine Derivatives: Structure–Activity Relationship

The paper aims to investigate the antitumor activity of a series of phenothiazine derivatives in order to establish a structure–antitumor activity relationship. To this end, PEGylated and TEGylated phenothiazine have been functionalized with formyl units and further with sulfonamide units via dynamic imine bonds. Their antitumor activity was monitored in vitro against seven human tumors cell lines and a mouse one compared to a human normal cell line by MTS assay. In order to find the potential influence of different building blocks on antitumor activity, the antioxidant activity, the ability to inhibit farnesyltransferase and the capacity to bind amino acids relevant for tumor cell growth were investigated as well. It was established that different building blocks conferred different functionalities, inducing specific antitumor activity against the tumor cells.

Quinoline-imidazole/benzimidazole derivatives as dual-/multi-targeting hybrids inhibitors with anticancer and antimicrobial activity

Two new classes of hybrid quinoline-imidazole/benzimidazole derivatives (the hybrid QIBS salts and QIBC cycloadducts) were designed and synthesized to evaluate their anticancer and antimicrobial activity. The strategy adopted for synthesis is straight and efficient, in four steps: N-acylation, N-alkylation, quaternization and a Huisgen 3 + 2 cycloaddition. The in vitro single-dose anticancer assay of forty six hybrid quinoline-benzimidazole compounds reveal that one QIBS salt (11h), has an excellent quasi nonselective activity against all type of cancer cell with an excellent PGI in the area of 90-100% and very good lethality. Three others quinoline-imidazole/benzimidazole hybrids (8h, 12h, 12f) has an excellent selective activity against some cancer cell lines: breast cancer MDA-MB-468 and Leukemia HL-60 TB). The five-dose assay screening confirms that compound 11h possesses excellent anti-proliferative activity, with GI₅₀ in the range of nano-molar, against some cancer cell lines: Leukemia HL-60 TB, Leukemia K-526, Leukemia RPMI-8226, Breast cancer MDA-MB-468, Lung cancer HOP-92 and Ovarian cancer IGROV1. The antibacterial assay indicates that three hybrid QIBS salts (12f, 12c, 12d) have an excellent activity against Gram-negative bacteria E. coli (superior to control Gentamicin) while against Gram-positive bacteria S. aureus only one compound 8i (R₂ = -CF3) exhibits a significant activity (superior to control Gentamicin). The MIC assay indicates that two other compounds (11h, 12h) are biologically active to a very low concentration, in the range of nano-molar. We believe that all these excellent assets related to anticancer and antibacterial activities, make from our hybrid quinoline-imidazole/benzimidazole compounds bearing a phenyl group (R₂ = -C₆H₅) in the para (4)-position of the benzoyl moiety a good candidate for future drug developing.

A Review on the Synthesis of Fluorescent Five- and Six-Membered Ring Azaheterocycles

Azaheterocycles rings with five and six members are important tools for the obtaining of fluorescent materials and fluorescent sensors. The relevant advances in the synthesis of azaheterocyclic derivatives and their optical properties investigation, particularly in the last ten years, was our main objective on this review. The review is organized according to the size of the azaheterocycle ring, 5-, 6-membered and fused ring azaheterocycles, as well as our recent contribution on this research field. In each case, the reaction pathways with reaction condition and obtained yield, and evaluation of the optical properties of the obtained products were briefly presented.

Hybrid Azine Derivatives: A Useful Approach for Antimicrobial Therapy

Nowadays, infectious diseases caused by microorganisms are a major threat to human health, mostly because of drug resistance, multi-drug resistance and extensive-drug-resistance phenomena to microbial pathogens. During the last few years, obtaining hybrid azaheterocyclic drugs represents a powerful and attractive approach in modern antimicrobial therapy with very promising results including overcoming microbial drug resistance. The emphasis of this review is to notify the scientific community about the latest recent advances from the last five years in the field of hybrid azine derivatives with antimicrobial activity. The review is divided according to the main series of six-member ring azaheterocycles with one nitrogen atom and their fused analogs. In each case, the main essential data concerning synthesis and antimicrobial activity are presented.

Hybrid Sol-Gel Matrices Doped with Colorimetric/Fluorimetric Imidazole Derivatives

Organic-inorganic hybrids (OIH) are materials that can be easily synthesized by the sol-gel method and combine the advantages of organic and inorganic moieties within a single polymeric matrix. Imidazole derivatives are versatile organic compounds that can change their optical properties with the variation of pH due to the protonation or deprotonation of the nitrogen atoms. This work reports the preparation of different OIHs doped with different contents of two imidazole compounds (3a,b). The obtained materials were characterized structurally by FTIR, and the dielectric properties were studied by electrochemical impedance spectroscopy. The optical properties were studied by UV-Vis absorption and fluorescence spectroscopies. The FTIR analysis showed that the presence of the imidazole does not change the structural properties of the matrices. The normalized resistance values obtained for the doped matrices ranged between 8.57 and 9.32 Ω cm2, all being higher than the undoped matrix. The σ ranged between 9.49 and 10.28 S cm-1, being all higher than the pure OIH samples. Compound 3a showed a maximum absorption peak at 390 nm, which is present in the OIH spectra, proving the presence of the compound. In the case of compound 3b, a maximum absorption wavelength at 412 nm was found, and the compound peak was not clear, which may indicate that an interaction between the compound and the matrix occurred. A synergetic effect between the intrinsic emission of the matrix and the fluorescence of 3a is found on the OIH-doped matrices.

Ultrasound assisted synthesis of hybrid quinoline-imidazole derivatives: a green synthetic approach

A green, straightforward and efficient study for obtaining hybrid quinoline-imidazole derivatives under ultrasound (US) irradiation as well as under conventional thermal heating (TH) has been presented. The reaction pathway involves only two steps: the N-alkylation of imidazole ring and a Huisgen [3 + 2] dipolar cycloaddition reaction of ylides to dimethyl acetylenedicarboxylate (DMAD). For both types of reactions, a green workup procedure under US irradiation has been presented. Under US irradiation, the N-alkylation of nitrogen atoms from the imidazole nucleus has outstanding benefits in terms of reaction time, energy consumption and yields, and can thereby be considered an environmentally friendly method. Forty new hybrid quinoline-imidazole compounds have been synthesized: 18 salts, 8 dihydro-benzopyrrolo imidazolo quinoline, 9 benzopyrrolo-imidazolo quinoline and 5 dihydro-pyrroloquinoxaline quinoline cycloadducts.

Preparation and antitumor application of N-phenylcarbazole/triphenylamine-modified fluorescent half-sandwich iridium(III) Schiff base complexes

Four N-phenylcarbazole/triphenylamine-appended half-sandwich iridium(III) salicylaldehyde Schiff base complexes ([(η⁵-Cp^x)Ir(O^N)Cl]) were prepared and characterized. The complexes exhibited similar antitumor activity to cisplatin and effectively inhibited the migration of tumor cells. Furthermore, the complexes showed favourable hydrolytic activity, while remaining relatively stable in the plasma environment, which facilitated the binding of serum proteins and transport through them. These complexes could decrease the mitochondrial membrane potential, catalyze the oxidation of nicotinamide adenine dinucleotide, induce an increase in intracellular reactive oxygen species (ROS), and eventually result in apoptosis. Aided by their suitable fluorescence property, laser confocal detection showed that the complexes followed an energy-dependent mechanism for their cellular uptake, effectively accumulating in the lysosome and leading to lysosomal damage. In summary, the half-sandwich iridium(III) salicylaldehyde Schiff base complexes could induce lysosomal damage, increase intracellular ROS, and lead to apoptosis, which contributed to their antitumor mechanism of oxidation.

Hybrid Pyridine Bis-Anthracene-Imidazolium Salt: NMR Studies on Zn-Acetate Complexation

We report here the design and synthesis of a new hybrid bis-anthracene-imidazolium salt, having a pyridine scaffold. NMR studies of dimer generation, as well as complexation with zinc acetate were performed.

Fluorescent Azasteroids through Ultrasound Assisted Cycloaddition Reactions

We report here the synthesis and optical spectral properties of several new azasteroid derivatives. The formation of these compounds was explained based on the most probable mechanism. The luminescent heterocycles were synthesized by 1,3-dipolar cycloaddition reactions between benzo[f]quinoline and methylpropiolate or dimethyl acetylenedicarboxylate (DMAD). A selective and efficient way for [3+2]-dipolar cycloaddition of benzo[f]quinolinium ylides under ultrasound (US) irradiation (20 kHz processing frequency) is presented. We report substantially higher yields under US irradiation, whereas the solvent amounts required are at least three-fold less compared to classical heating. The azasteroid derivatives are blue emitters with λ_max of fluorescence around 430–450 nm. A certain influence of the azasteroid substituents concerning absorption and fluorescent properties was observed. Compounds anchored with a bulky pivaloyl group or without a C=O carbonyl group have shown increased fluorescence intensity.

Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery

BACKGROUND

CDK2 participates in the control of eukaryotic cell-cycle progression. Due to the great interest in CDK2 for drug development and the relative easiness in crystallizing this enzyme, we have over 400 structural studies focused on this protein target. This structural data is the basis for the development of computational models to estimate CDK2-ligand binding affinity.

OBJECTIVE

This work focuses on the recent developments in the application of supervised machine learning modeling to develop scoring functions to predict the binding affinity of CDK2.

METHOD

We employed the structures available at the protein data bank and the ligand information accessed from the BindingDB, Binding MOAD, and PDBbind to evaluate the predictive performance of machine learning techniques combined with physical modeling used to calculate binding affinity. We compared this hybrid methodology with classical scoring functions available in docking programs.

RESULTS

Our comparative analysis of previously published models indicated that a model created using a combination of a mass-spring system and cross-validated Elastic Net to predict the binding affinity of CDK2-inhibitor complexes outperformed classical scoring functions available in AutoDock4 and AutoDock Vina.

CONCLUSION

All studies reviewed here suggest that targeted machine learning models are superior to classical scoring functions to calculate binding affinities. Specifically for CDK2, we see that the combination of physical modeling with supervised machine learning techniques exhibits improved predictive performance to calculate the protein-ligand binding affinity. These results find theoretical support in the application of the concept of scoring function space.

Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies

Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.

Synthesis and docking studies of three new diaminochromenes as potential leads for anticancer drugs

In this work, the new diaminochromenes: 2,5-dimono-8-methoxychromeno[4,3,2-de][1,6]naphthyridine-4-carbonitrile (4), 8-ethoxy-2-imino-3,4-dihydro-2H-chromene-3-carbonitrile-4-malononitrile (5), 2,5-diamino-8-ethoxychromene[4,3,2-de][1,6]naphthyridine-4-carbonotrile (6), were synthesized and fully characterized through 600 MHz using ¹H, ¹³C, APT, gHSQC, gHMBC, ROESY-1D and gated decoupling ¹³C. Further docking studies suggested that these compounds are capable of intercalating with the Drew-Dickerson Dodecamer DNA and, therefore, be candidates to work as effective compounds to decrease the cancer radiotherapy.Communicated by Ramaswamy H. Sarma.

Protein Interaction with Dendrimer Monolayers: Energy and Surface Topology

Protein interaction with polymers layers is a keystone in designing bio-nano devices. Polyamidoamines (PAMAMs) are well-known polymers. Zero aromatic core dendrimers (ZAC) are molecules with no proven toxic effect in cultured cells. When coating nanodevices with enzymatic systems, active sites are disturbed by an interaction with the biosystem surface. Computational methods were used in order to simulate, characterize, and quantify protein–polymer interaction. Protein corona, i.e., surface proteins disposed on a viral membrane or nanodevice outer surface, are crucial in interactions with a potential pharmacological target or receptor. Corona symmetry has been observed in the Middle East respiratory syndrome-related coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a protein alpha 1 antitrypsin’s a crystallographic structure was chosen. Protein–mono dendrimer layer systems were generated using in silico methods in order to simulate their interaction. Interactions were quantified using topological and quantum mechanical strategies. Results showed that PAMAM and ZAC interact differently with alpha 1 antitrypsin. Energy and topological surfaces of protein vary accordingly with the dendrimer monolayer. Topological surfaces have a higher sensibility in describing the interactions.

Bis-(imidazole/benzimidazole)-pyridine derivatives: synthesis, structure and antimycobacterial activity

Aim:

Over the last decades, few significant achievements have been made in tuberculosis (TB) therapy. As a result, there is an urgent need for new anti-TB drugs.

Results:

Two new classes of bis-(imidazole/benzimidazole)-pyridine derivatives were designed, synthesized and evaluated for their antimycobacterial activity.

Conclusion:

The synthesis is efficient and straightforward, involving only two successive N-alkylations. The anti-TB assay reveal that our compounds have an excellent anti-TB activity against both replicating and nonreplicating Mtb, are not cytotoxic, exhibited a very good intracellular activity and are active against drug-resistant Mtb strains, some compounds have a bactericidal mechanism. The absorption, distribution, metabolism, excretion and toxicity studies performed for one compound are promising, indicating that it is a good candidate for a future drug.

Pyridine-Imidazlolium Salts: Oxidatively Cleavage of N-C Bond via Nitration

Azaheterocycles derivatives with pyridine-imidazole skeleton are compounds of great value for medicinal chemistry. We report herein the nitration of 1,1′-(pyridine-2,6-diylbis(methylene))bis{3-[2-(4-nitrophenyl)-2-oxoethyl]-1H-imidazol-3-ium} bromide using a typical mixture of nitric and sulphuric acid. The nitration occur with the oxidative cleavage of N–C bond between imidazolium ring and methylene group.

Cube-Rhombellane Related Structures: A Drug Perspective

Rhombellanes represent a new class of structures, of which homeomorphs may be synthesized as real molecules. Cube-rhombellane is a double-shell structure, with vertices of degree 3 and 6, respectively. Several hypothetical structures/molecules were proposed and computed using molecular graph theory and coordination chemistry principles. Some geometries were optimized at the B3LYP/6-31G (d, p) level of theory, followed by harmonic vibrational frequency analysis at the same level of theory, single point data were collected in view of molecular stability evaluation. Some of the bioactive functionalized structures were also proposed and explored by molecular mechanics (MM)-based conformational analysis, to check their internal mobility. Drug-like properties of the proposed molecular structures were compared with some existing nano-molecules (fullerenes, nanotubes). ADME and other physico-chemical characteristics were computed using commercial software. Substructures of the proposed molecules, useful in a future synthesis, were provided by retro combinatorial synthesis (RECAP). Computational results obtained are promising regarding ADME properties, drug-likeness and nano-properties.