Chemical substituent effect on pyridine permeability and mechanistic insight from computational molecular descriptors

Elaborated study of Cu(II) carbosilane metallodendrimers bearing substituted iminopyridine moieties as antitumor agents

Iminopyridine-decorated carbosilane metallodendrimers have recently emerged as a promising strategy in the treatment of cancer diseases. Their unique features such as the nanometric size, the multivalent nature and the structural perfection offer an extraordinary platform to explore structure-to-property relationships. Herein, we showcase the outstanding impact on the antitumor activity of a parameter not explored before: the iminopyridine substituents in meta position. New Cu(II) carbosilane metallodendrimers, bearing methyl or methoxy substituents in the pyridine ring, were synthesized and thoroughly characterized. Electron Paramagnetic Resonance (EPR) was exploited to unveil the properties of the metallodendrimers. This study confirmed the presence of different coordination modes of the Cu(II) ion (Cu-N₂O₂, Cu-N₄ and Cu-O₄), whose ratios were determined by the structural features of the dendritic molecules. These metallodendrimers exhibited IC₅₀ values in the low micromolar range (<6 μM) in tumor cell lines such as HeLa and MCF-7. The subsequent in vitro assays on both healthy (PBMC) and tumor (U937) myeloid cells revealed two key facts which improved the cytotoxicity and selectivity of the metallodrug: First, maximizing the Cu-N₂O₂ coordination mode; second, adequately selecting the pair ring-substituent/metal-counterion. The most promising candidates, G₁(-CH₃)Cl (8) and G₁(-OCH₃)NO₃(17), exhibited a substantial increase in the antitumor activity in U937 tumor cells, compared to the non-substituted counterparts, probably through two different ROS-production pathways.

Artificial Intelligence (AI) to the Rescue: Deploying Machine Learning to Bridge the Biorelevance Gap in Antioxidant Assays

Oxidative stress induced by excessive levels of reactive oxygen species (ROS) underlies several diseases. Therapeutic strategies to combat oxidative damage are, therefore, a subject of intense scientific investigation to prevent and treat such diseases, with the use of phytochemical antioxidants, especially polyphenols, being a major part. Polyphenols, however, exhibit structural diversity that determines different mechanisms of antioxidant action, such as hydrogen atom transfer (HAT) and single-electron transfer (SET). They also suffer from inadequate in vivo bioavailability, with their antioxidant bioactivity governed by permeability, gut-wall and first-pass metabolism, and HAT-based ROS trapping. Unfortunately, no current antioxidant assay captures these multiple dimensions to be sufficiently "biorelevant," because the assays tend to be unidimensional, whereas biorelevance requires integration of several inputs. Finding a method to reliably evaluate the antioxidant capacity of these phytochemicals, therefore, remains an unmet need. To address this deficiency, we propose using artificial intelligence (AI)-based machine learning (ML) to relate a polyphenol's antioxidant action as the output variable to molecular descriptors (factors governing in vivo antioxidant activity) as input variables, in the context of a biomarker selectively produced by lipid peroxidation (a consequence of oxidative stress), for example F2-isoprostanes. Support vector machines, artificial neural networks, and Bayesian probabilistic learning are some key algorithms that could be deployed. Such a model will represent a robust predictive tool in assessing biorelevant antioxidant capacity of polyphenols, and thus facilitate the identification or design of antioxidant molecules. The approach will also help to fulfill the principles of the 3Rs (replacement, reduction, and refinement) in using animals in biomedical research.

Structure-activity relationship studies of naphthol AS-E and its derivatives as anticancer agents by inhibiting CREB-mediated gene transcription

CREB (cyclic AMP-response element binding protein) is a downstream transcription factor of a multitude of signaling pathways emanating from receptor tyrosine kinases or G-protein coupled receptors. CREB is not activated until it is phosphorylated at Ser133 and its subsequent binding to CREB-binding protein (CBP) through kinase-inducible domain (KID) in CREB and KID-interacting (KIX) domain in CBP. Tumor tissues from various organs present higher level of expression and activation of CREB. Thus CREB has been proposed as a promising cancer drug target. We previously described naphthol AS-E (1a) as a small molecule inhibitor of CREB-mediated gene transcription in living cells. Here we report the structure-activity relationship (SAR) studies of 1a by modifying the appendant phenyl ring. All the compounds were evaluated for in vitro inhibition of KIX-KID interaction, cellular inhibition of CREB-mediated gene transcription and inhibition of proliferation of four cancer cell lines (A549, MCF-7, MDA-MB-231 and MDA-MB-468). SAR indicated that a small and electron-withdrawing group was preferred at the para-position for KIX-KID interaction inhibition. Compound 1a was selected for further biological characterization and it was found that 1a down-regulated the expression of endogenous CREB target genes. Expression of a constitutively active CREB mutant, VP16-CREB in MCF-7 cells rendered the cells resistant to 1a, suggesting that CREB was critical in mediating its anticancer activity. Furthermore, 1a was not toxic to normal human cells. Collectively, these data support that 1a represents a structural template for further development into potential cancer therapeutics with a novel mechanism of action.

Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes

Drug permeability is often a limiting step in drug action, requiring chemical optimization of a drug candidate to improve this property. Such optimization is typically performed in the context of a congeneric series, where substituents are varied to optimize the target property. Motivated by this need the present work examines the influence of chemical substituents on passive permeability (log P pass) across parallel artificial membranes (PAMPA) undertaken for three congeneric series of compounds; benzoic acids, pyridines and quinolines. PAMPA showed pyridine and quinoline to have high permeability and chemical substituents to typically reduce the permeability. On the contrary, benzoic acid showed poor permeability and chemical substituents typically increased the permeability. To quantitate these effects with respect to physical properties, models were built to explain and predict the permeability of these classes of compounds based on computed molecular descriptors. Models for the benzoic acid series in the ionized state indicated the solvent accessible surface area, cavity dispersion and the free energy of solvation in hexane as well as in water to dominate permeability. However, when the acid group is treated as neutral, the free energy of solvation in water, the fraction polar surface area, the polar surface area and difference in the free energy of solvation between hexane and water were important; these terms, among others, were also important for the neutral pyridine-quinoline series. Considering that the permeability of the benzoic acid series is about 2 orders of magnitude lower than the pyridines and quinolines and that a shift of approximately two pH units in the p K a of the acid group of benzoic acid will allow for the neutral species of the molecule to dominate under experimental conditions (pH = 6.5), these results suggest that the additional energy barrier associated with permeation of the benzoic acid series is associated with the need to protonate the acidic group, thereby forming the neutral species which may then cross the hydrophobic region of the membrane.

Cinnamic acids and mono-substituted benzoic acids as useful capping groups for the preparation of hNK2 receptor antagonists

NK(2) antagonists have been reported to be potentially useful for the treatment of a number of chronic diseases, such as asthma, irritable bowel syndrome, cystitis, and depression. Starting from an in-house prepared library of capped dipeptides, we have identified a series of molecules with subnanomolar binding affinity for the hNK(2) receptor. These molecules are composed by three well-defined regions: a planar aromatic acyl system as N-terminal capping group, a rigid and quite lipophilic core, and a flexible and relatively hydrophilic C-terminal capping group. Here we report how we were able to manipulate the N-terminal capping group to obtain significant in vivo activity after i.v. and i.d. administration.