Comprehensive data on a 2D-QSAR model for Heme Oxygenase isoform 1 inhibitors

Heme oxygenase 1 inhibitor discovery and formulation into nanostructured lipid carriers as potent and selective treatment against triple negative metastatic breast cancer

Heme oxygenase-1 (HO-1) has been identified as a potential new target in anticancer therapy, being overexpressed in different tumors and crucial for cell proliferation. Advances in the development of specific HO-1 inhibitors should support the understanding of controlling HO-1 activity as antitumoral strategies, opening the path for future therapeutic applications. In the present study, small series of new HO-1 inhibitors were synthesized by joining a butylimidazolic pharmacophore together with a hydrophobic moiety spaced by a 2-oxybenzamide central linker. The most active and selective HO-1 inhibitor, VP 21-04, 2-(4-(1H-imidazol-1-yl)butoxy)-N-benzyl-5-iodobenzamide (7b) was identified. This ligand showed strong cytotoxic activity against melanoma and breast cancer cell lines. Encapsulation of VP 21-04 in nanostructured lipid carriers (NLC 21-04) was performed to exploit its therapeutic potential by passive-targeting delivery ameliorating water-solubility and toxicity. Interestingly, NLC 21-04 showed a marked antiproliferative effect in both cancer cell lines, and an improved safety profile with a wider therapeutic window when compared to the free drug. Finally, NLC 21-04 showed a marked tumor growth reduction while being safe in an in ovo tumor model, highlighting the therapeutic potential of the developed nanoparticles against triple negative metastatic breast cancer.

Novel Acetamide-Based HO-1 Inhibitor Counteracts Glioblastoma Progression by Interfering with the Hypoxic-Angiogenic Pathway

Glioblastoma multiforme (GBM) represents the deadliest tumor among brain cancers. It is a solid tumor characterized by uncontrolled cell proliferation generating the hypoxic niches in the cancer core. By inducing the transcription of hypoxic inducible factor (HIF), hypoxia triggers many signaling cascades responsible for cancer progression and aggressiveness, including enhanced expression of vascular endothelial growth factor (VEGF) or antioxidant enzymes, such as heme oxygenase-1 (HO-1). The present work aimed to investigate the link between HO-1 expression and the hypoxic microenvironment of GBM by culturing two human glioblastoma cell lines (U87MG and A172) in the presence of a hypoxic mimetic agent, deferoxamine (DFX). By targeting hypoxia-induced HO-1, we have tested the effect of a novel acetamide-based HO-1 inhibitor (VP18/58) on GBM progression. Results have demonstrated that hypoxic conditions induced upregulation and nuclear expression of HO-1 in a cell-dependent manner related to malignant phenotype. Moreover, our data demonstrated that the HO-1 inhibitor counteracted GBM progression by modulating the HIFα/HO-1/VEGF signaling cascade in cancer cells bearing more malignant phenotypes.

Growing the molecular architecture of imidazole-like ligands in HO-1 complexes

Up-regulation of HO-1 had been frequently reported in different cases and types of human malignancies. Since poor clinical outcomes are reported in these cases, this enzyme's inhibition is considered a valuable and proven anticancer approach. To identify novel HO-1 inhibitors suitable for drug development, we report a structure-guided fragment-based approach to identify new lead compounds. Different parts of the selected molecules were analyzed, and the different series of novel compounds were virtually evaluated. The growing experiments of the classical HO-1 inhibitors structure led us to different hit-compounds. A synthetic pathway for six selected molecules was designed, and the compounds were synthesized. The biological activity revealed that molecules 10 and 12 inhibit the HO-1 activity with an IC₅₀ of 1.01 and 0.90 μM, respectively. This study suggested that our growing approach was successful, and these results are ongoing for further development.

The Monte Carlo Method as a Tool to Build up Predictive QSPR/QSAR

Background:

The Monte Carlo method has a wide application in various scientific researches. For the development of predictive models in a form of the quantitative structure-property / activity relationships (QSPRs/QSARs), the Monte Carlo approach also can be useful. The CORAL software provides the Monte Carlo calculations aimed to build up QSPR/QSAR models for different endpoints.

Methods:

Molecular descriptors are a mathematical function of so-called correlation weights of various molecular features. The numerical values of the correlation weights give the maximal value of a target function. The target function leads to a correlation between endpoint and optimal descriptor for the visible training set. The predictive potential of the model is estimated with the validation set, i.e. compounds that are not involved in the process of building up the model.

Results:

The approach gave quite good models for a large number of various physicochemical, biochemical, ecological, and medicinal endpoints. Bibliography and basic statistical characteristics of several CORAL models are collected in the present review. In addition, the extended version of the approach for more complex systems (nanomaterials and peptides), where behaviour of systems is defined by a group of conditions besides the molecular structure is demonstrated.

Conclusion:

The Monte Carlo technique available via the CORAL software can be a useful and convenient tool for the QSPR/QSAR analysis.

Chromatograpic resolution of phenylethanolic-azole racemic compounds highlighted stereoselective inhibition of heme oxygenase-1 by (R)-enantiomers

Heme oxygenase-1 (HO-1) has been recognized as extensively involved in the development and aggravation of cancer, cell propagation and at in the mechanism of chemoresistance development. Low micromolar HO-1 inhibitors selective towards HO-2 has been recently reported, wherein the azole core and the hydrophobic residues are linked through a phenylethanolic spacer bearing a chiral center. Since less information are known about the stereoselective requirements for HO-1 inhibition, here we report the enantiomeric resolution of 1-(biphenyl-3-yl)-2-(1H-imidazol-1-yl)ethanol (1) and 1-[4-[(4-bromobenzyl)oxy]phenyl]-2-(1H-imidazol-1-yl)ethanol (2), two among the most potent and selective HO-1 inhibitors known thus far when tested as racemates. The absolute configuration was established for 1 by a combination of experimental and in silico derived electronic circular dichroism spectra, while docking approaches were useful in the case of compound 2. Biological evaluation of pure enantiomers highlighted higher HO-1 inhibitory activity of (R)-enantiomers. Docking studies demonstrated the importance of hydrogen bond interaction, more pronounced for the (R)-enantiomers, with a consensus water molecule within the binding pocket. The present study demonstrates that differences in three-dimensional structure amongst compounds 1 and 2 enantiomers affect significantly the selectivity of these HO-1 inhibitors.

New Arylethanolimidazole Derivatives as HO-1 Inhibitors with Cytotoxicity against MCF-7 Breast Cancer Cells

In this paper, a novel series of imidazole-based heme oxygenase-1 (HO-1) inhibitors is reported. These compounds were obtained by modifications of previously described high potent and selective arylethanolimidazoles. In particular, simplification of the central linker and repositioning of the hydrophobic portion were carried out. Results indicate that a hydroxyl group in the central region is crucial for the potency as well as the spatial distribution of the hydrophobic portion. Docking studies revealed a similar interaction of the classical HO-1 inhibitors with the active site of the protein. The most potent and selective compound (5a) was tested for its potential cytotoxic activity against hormone-sensitive and hormone-resistant breast cancer cell lines (MCF-7 and MDA-MB-231).

Non-competitive heme oxygenase-1 activity inhibitor reduces non-small cell lung cancer glutathione content and regulates cell proliferation

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related death mainly due to its high metastatic rate. Impairment of redox homeostasis mechanisms has been previously described in NSCLC and is associated with the disease itself as well as with comorbidities such as smoking. The aim of the present in vitro study was to evaluate the effect of selective and non-competitive inhibition of heme oxygenase-1 (HO-1) on cancer redox homeostasis with particular regards to glutathione (GSH) metabolism related enzymes. NSCLC cell line (A549) was treated with the HO-1 activity inhibitor VP13/47 (10 µM) and we further evaluated cell viability, apoptosis, mitochondrial dysfunction and oxidative stress. Our results showed that VP13/47 significantly reduced HO-1 expression and total HO activity thus, resulting in a significant reduction of cell viability, proliferation and increased apoptosis, mitochondrial dysfunction and oxidative stress. Consistently with increased oxidative stress, we also showed that reduced GSH was significantly decreased and such effect was also accompanied by a significant downregulation of the enzymes involved in its biosynthesis. Taken all together our results show that selective HO-1 inhibition significantly impairs NSCLC progression and may represent a possible pharmacological strategy for new chemotherapy agents.

Ginseng and heme oxygenase-1: The link between an old herb and a new protective system

Ginseng is an ancient herb, belonging to Asian traditional medicine, that has been considered as a restorative to enhance vitality for centuries. It has been demonstrated that the antioxidant action of ginseng may be mediated through activation of different cellular signaling pathways involving the heme oxygenase (HO) system. Several compounds derived from ginseng have been studied for their potential role in brain, heart and liver protection, and the Nrf2 pathway seems to be the most affected by these natural molecules to exert this effect. Ginseng is also popularly used in cancer patients therapy for the demonstrated capability to defend tissues from chemotherapy-induced damage. Reported results suggest that the effect of ginseng is primarily associated with ROS scavenging, mainly exerted through the activation of Nrf2 pathway, and the consequent induction of HO-1 levels. This review aims to discuss the connection between the antioxidant properties of ginseng and the activation of the HO system, as well as to outline novel therapeutic applications of this medicinal plant to human health.

Heme Oxygenase-2 (HO-2) as a therapeutic target: Activators and inhibitors

Heme oxygenase (HO) enzymes are involved in heme catabolism and several physiological functions. Among the different HO isoforms, HO-2 stands out for its neuroprotective properties and modulatory activity in male reproduction. However, unlike the HO-1 ligands, the potential therapeutic applications of HO-2 inhibitors/activators have not been extensively explored yet. Moreover, the physiological role of HO-2 is still unclear, mostly due to the lack of highly selective HO-2 chemical probes. To boost the interest on this intriguing target, the present review updates the knowledge on the structure-activity relationships of HO-2 inhibitors and activators, as well as their potential therapeutic applications. To the best of our knowledge, among HO-2 inhibitors, clemizole derivatives are the most selective HO-2 inhibitors reported so far (IC₅₀ HO-1 >100 μM, IC₅₀ HO-2 = 3.4 μM), while the HO-2 nonselective inhibitors described herein possess IC₅₀ HO-2 values ≤ 10 μM. Furthermore, the development of HO-2 activators, such as menadione analogues, helped to understand the critical moieties required for HO-2 activation. Recent advances in the potential therapeutic applications of HO-2 inhibitors/activators cover the fields of neurodegenerative, cardiovascular, inflammatory, and reproductive diseases further stimulating the interest towards this target.

QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models

Quantitative structure-activity relationships (QSAR) modeling is a well-known computational technique with wide applications in fields such as drug design, toxicity predictions, nanomaterials, etc. However, QSAR researchers still face certain problems to develop robust classification-based QSAR models, especially while handling response data pertaining to diverse experimental and/or theoretical conditions. In the present work, we have developed an open source standalone software "QSAR-Co" (available to download at https://sites.google.com/view/qsar-co ) to setup classification-based QSAR models that allow mining the response data coming from multiple conditions. The software comprises two modules: (1) the Model development module and (2) the Screen/Predict module. This user-friendly software provides several functionalities required for developing a robust multitasking or multitarget classification-based QSAR model using linear discriminant analysis or random forest techniques, with appropriate validation, following the principles set by the Organisation for Economic Co-operation and Development (OECD) for applying QSAR models in regulatory assessments.

The study of the index of ideality of correlation as a new criterion of predictive potential of QSPR/QSAR-models

Acetylcholinesterase (AChE) inhibitors, dihydrofolate reductase inhibitors (DHFR), Toxicity in Tetrahymena pyriformis (TP), Acute Toxicity in fathead minnow (TFat), Water solubility (WS), and Acute Aquatic Toxicity in Daphnia magna (DM) are examined as endpoints to establish quantitative structure - property/activity relationships (QSPRs/QSARs). The Index of Ideality of Correlation (IIC) is a measure of predictive potential. The IIC has been studied in a few recent works. The comparison of models for the six endpoints above confirms that the index can be a useful tool for building up and validation of QSPR/QSAR models. All examined endpoints are important from an ecologic point of view. The diversity of examined endpoints confirms that the IIC is real criterion of the predictive potential of a model.

Fourfold Filtered Statistical/Computational Approach for the Identification of Imidazole Compounds as HO-1 Inhibitors from Natural Products

Over-regulation of Heme oxygenase 1 (HO-1) has been recently identified in many types of human cancer, and in these cases, poor clinical outcomes are normally reported. Indeed, the inhibition of HO-1 is being considered as an anticancer approach. Imidazole scaffold is normally present in most of the classical HO-1 inhibitors and seems indispensable to the inhibitory activity due to its strong interaction with the Fe(II) of the heme group. In this paper, we searched for new potentially HO-1 inhibitors among three different databases: Marine Natural Products (MNP), ZINC Natural Products (ZNP) and Super Natural II (SN2). 484,527 compounds were retrieved from the databases and filtered through four statistical/computational filters (2D descriptors, 2D-QSAR pharmacophoric model, 3D-QSAR pharmacophoric model, and docking). Different imidazole-based compounds were suggested by our methodology to be potentially active in inhibiting the HO-1, and the results have been rationalized by the bioactivity of the filtered molecules reported in the literature.

Progress in the development of selective heme oxygenase-1 inhibitors and their potential therapeutic application

Heme oxygenases (HOs) are a family of enzymes involved in the selective catabolism of free circulating heme. While HO-2 is constitutively expressed, HO-1 is strongly overexpressed under stressful stimuli (e.g., oxidative stress). Under these conditions, HO-1 exerts its strong cytoprotective activities and plays a crucial role in stimulating cell survival by removing the pro-oxidant heme and by producing carbon monoxide and biliverdin (promptly reduced to bilirubin). Unfortunately, the broad spectrum of HO-1 cytoprotective effects has been well experimentally documented both in normal and tumor cells, where the enzyme can be overexpressed, making it an exciting target in the management of some type of tumors. Development of non-competitive HO-1 inhibitors dates back in 2002 with the discovery of Azalanstat. Since then, many efforts have been devoted to the identification of selective HO-1 and HO-2 inhibitors and to unravel the molecular determinants responsible for selectivity. Molecular modeling studies supported the identification of chemical features involved in the recognition and inhibition of these enzymes. Herein, medicinal chemistry aspects and in silico studies related to the development of HO inhibitors will be discussed. The purpose of this review is to highlight recent advances in the development of new selective HO-1 and HO-2 inhibitors and covers the last six years (2013-2018).

Environmentally friendly polychlorinated naphthalenes (PCNs) derivatives designed using 3D-QSAR and screened using molecular docking, density functional theory and health-based risk assessment

A complete design and screening system for environmental-friendly polychlorinated naphthalene (PCN) derivatives was established through three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, density functional theory (DFT) methods and health-based risk assessment based on dynamic multimedia fugacity model. Two types of 3D-QSAR models were established for PCNs using the experimental biological toxicity (logEC₅₀) of 14 PCNs to carry out a modification to lower the logEC₅₀ of CN-70. Consequently, 67 new monosubstituted and disubstituted derivatives with a lower biological toxicity than CN-70 were designed. Furthermore, 21 new CN-70 derivatives were selected through the evaluation of their persistent organic pollutant properties (biological toxicity, bio-concentration, long-range transport potential, biodegradability) and practicability (stability, insulativity, flame retardancy) using 3D-QSAR, molecular docking and DFT methods. Finally, the non-carcinogenic and carcinogenic risks of 19 new CN-70 derivatives in different exposure pathways were reduced, and 5 derivatives with a significant decrease both in biological toxicity (amplitude reduction: 12.73%-32.51%) and risk (amplitude reduction: 32.18%-59.19%) were selected as environmental-friendly PCN derivatives, which had been screened using the health-based risk assessment system associated with dynamic multimedia fugacity model. This study provides a theoretical basis for the design of environmental-friendly flame retardants and insulating materials.

Modification of Hexachlorobenzene to Molecules with Lower Long-Range Transport Potentials Using 3D-QSAR Models with a Full Factor Experimental Design

In this study, the hexachlorobenzene molecule was modified by three-dimensional quantitative structure-activity relationship (3D-QSAR) models and a full factor experimental design to obtain new hexachlorobenzene molecules with low migration ability. The 3D-QSAR models (comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)) were constructed by SYBLY-X 2.0 software, using experimental data of octanol-air partition coefficients (K_OA) for 12 chlorobenzenes (CBs) congeners as the dependent variable, and the structural parameters of CBs as independent variables, respectively. A target molecule (hexachlorobenzene; HCB: its long-distance migration capability leads to pollution of the marine environment in Antarctic and Arctic) was modified using the 3D-QSAR contour maps associated with resolution V of the 2^10-3 full-factorial experimental design method, and 11 modified HCB molecules were produced with a single chlorine atom (-Cl₂) and three chlorine atoms (-Cl₁, -Cl₃, and -Cl₅) replaced with electropositive groups (-COOH, -CN, -CF₃, -COF, -NO₂, -F, -CHF₂, -ONO₂, and -SiF₃) to increase the logK_OA. The new molecules had essentially similar biological enrichment functions and toxicities as HCB but were found to be more easily degraded. A 2D-QSAR model and molecular docking technology indicated that both dipole moments and highest occupied orbital energies of the substituents markedly affected migration and degradation of the new molecules. The abilities of the compounds to undergo long distance migration were assessed. The modified HCB molecules (i.e. 2-CN-HCB, 2-CF₃-HCB, 1-F-3-COOH-5-NO₂-HCB, 1-NO₂-3-CN-5-CHF₂-HCB and 1-CN-3-F-5-NO₂-HCB) moved from a long-range transport potential of the modified molecules to a relatively low mobility class, and the transport potentials of the remaining modified HCB molecules (i.e. 2-COOH-HCB, 2-COF-HCB, 1-COF-3-ONO₂-5-NO2-HCB, 1-F-3-CN-5-SiF₃-HCB, 1-F-3-COOH-5-SiF₃-HCB and 1-CN-3-SiF₃-5-ONO₂-HCB) also significantly decreased. These results provide a basic theoretical basis for designing environmentally benign molecules based on HCB.

A Structure- and Ligand-Based Virtual Screening of a Database of "Small" Marine Natural Products for the Identification of "Blue" Sigma-2 Receptor Ligands

Sigma receptors are a fascinating receptor protein class whose ligands are actually under clinical evaluation for the modulation of opioid analgesia and their use as positron emission tomography radiotracers. In particular, peculiar biological and therapeutic functions are associated with the sigma-2 (σ₂) receptor. The σ₂ receptor ligands determine tumor cell death through apoptotic and non-apoptotic pathways, and the overexpression of σ₂ receptors in several tumor cell lines has been well documented, with significantly higher levels in proliferating tumor cells compared to quiescent ones. This acknowledged feature has found practical application in the development of cancer cell tracers and for ligand-targeting therapy. In this context, the development of new ligands that target the σ₂ receptors is beneficial for those diseases in which this protein is involved. In this paper, we conducted a search of new potential σ₂ receptor ligands among a database of 1517 “small” marine natural products constructed by the union of the Seaweed Metabolite and the Chemical Entities of Biological Interest (ChEBI) Databases. The structures were passed through two filters that were constituted by our developed two-dimensional (2D) and three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) statistical models, and successively docked upon a σ₂ receptor homology model that we built according to the FASTA sequence of the σ₂/TMEM97 (SGMR2_HUMAN) receptor.

Development of new HO-1 inhibitors by a thorough scaffold-hopping analysis

HO-1 inhibition is considered a valuable anticancer approach. In fact, up-regulation of HO-1 had been repeatedly reported in many types of human malignancies, and in these clinical cases, poor outcomes are reported. To identify novel HO-1 inhibitors suitable for drug development, a scaffold-hopping strategy calculation was utilized to design novel derivatives. Different parts of the selected molecule were analyzed and the different series of novel compounds were virtually evaluated. The calculation for the linker moiety of the classical HO-1 inhibitors structure led us to compounds 5 and 6. A synthetic pathway for the two molecules was designed and the compounds were synthesized. The biological activity revealed an HO-1 inhibition of 0.9 and 54 μM for molecules 5 and 6 respectively. This study suggested that our scaffold-hopping approach was successful and these results are ongoing for further development.

Novel Structural Insight into Inhibitors of Heme Oxygenase-1 (HO-1) by New Imidazole-Based Compounds: Biochemical and In Vitro Anticancer Activity Evaluation

In this paper, the design, synthesis, and molecular modeling of a new azole-based HO-1 inhibitors was reported, using compound 1 as a lead compound, in which an imidazole moiety is linked to a hydrophobic group by means of an ethanolic spacer. The tested compounds showed a good inhibitor activity and possessed IC₅₀ values in the micromolar range. These results were obtained by targeting the hydrophobic western region. Molecular modeling studies confirmed a consolidated binding mode in which the nitrogen of the imidazolyl moiety coordinated the heme ferrous iron, meanwhile the hydrophobic groups were located in the western region of HO-1 binding pocket. Moreover, the new compounds were screened for in silico ADME-Tox properties to predict drug-like behavior with convincing results. Finally, the in vitro antitumor activity profile of compound 1 was investigated in different cancer cell lines and nanomicellar formulation was synthesized with the aim of improving compound's 1 water solubility. Finally, compound 1 was tested in melanoma cells in combination with doxorubicin showing interesting synergic activity.

Mutagenicity, anticancer activity and blood brain barrier: similarity and dissimilarity of molecular alerts

The aim of the present work is an attempt to define computable measure of similarity between different endpoints. The similarity of structural alerts of different biochemical endpoints can be used to solve tasks of medicinal chemistry. Optimal descriptors are a tool to build up models for different endpoints. The optimal descriptor is calculated with simplified molecular input-line entry system (SMILES). A group of elements (single symbol or pair of symbols) can represent any SMILES. Each element of SMILES can be represented by so-called correlation weight i.e. coefficient that should be used to calculate descriptor. Numerical data on the correlation weights are calculated by the Monte Carlo method, i.e. by optimization procedure, which gives maximal correlation coefficient between the optimal descriptor and endpoint for the training set. Statistically stable correlation weights observed in several runs of the optimization can be examined as structural alerts, which are promoters of the increase or the decrease of a biochemical activity of a substance. Having data on several runs of the optimization correlation weights, one can extract list of promoters of increase and list of promoters of decrease for an endpoint. The study of similarity and dissimilarity of the above lists has been carried out for the following pairs of endpoints: (i) mutagenicity and anticancer activity; (ii) mutagenicity and blood brain barrier; and (iii) blood brain barrier and anticancer activity. The computational experiment confirms that similarity and dissimilarity for pairs of endpoints can be measured.