Combination of pharmacophore modeling and 3D-QSAR analysis of potential glyoxalase-I inhibitors as anticancer agents

A combined in silico approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives

Inhibition of human mitochondrial peptide deformylase (HsPDF) plays a major role in reducing growth, proliferation, and cellular cancer survival. In this work, a series of 32 actinonin derivatives for HsPDF (PDB: 3G5K) inhibitor's anticancer activity was computationally analyzed for the first time, using an in silico study considering 2D-QSAR modeling, and molecular docking studies, and validated by molecular dynamics and ADMET properties. The results of multilinear regression (MLR) and artificial neural networks (ANN) statistical analysis reveal a good correlation between pIC50 activity and the seven (7) descriptors. The developed models were highly significant with cross-validation, the Y-randomization test and their applicability range. In addition, all considered data sets show that the AC30 compound, exhibits the best binding affinity (docking score = -212.074 kcal/mol and H-bonding energy = -15.879 kcal/mol). Furthermore, molecular dynamics simulations were performed at 500 ns, confirming the stability of the studied complexes under physiological conditions and validating the molecular docking results. Five selected actinonin derivatives (AC1, AC8, AC15, AC18 and AC30), exhibiting best docking score, were rationalized as potential leads for HsPDF inhibition, in well agreement with experimental outcomes. Furthermore, based on the in silico study, new six molecules (AC32, AC33, AC34, AC35, AC36 and AC37) were suggested as HsPDF inhibition candidates, which would be combined with in-vitro and in-vivo studies to perspective validation of their anticancer activity. Indeed, the ADMET predictions indicate that these six new ligands have demonstrated a fairly good drug-likeness profile.

Investigation of novel ligand targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery: complete pharmacophore approach

The Bromodomain (BRD4) and extra-terminal (BET) protein family are reversible; lysine-acetylated epigenetic readers identified as key important epigenetic regulators for protein recognition in posttranslational modifications for targeting cancer for its role in super-enhancers and transcription of oncogene expression in cancer and other forms of cancer and various diseases. Firstly, JQ-1a small potent BET inhibitors, targeting BET proteins were currently in clinical trials to ablate cancer. The identified compounds were taken from the library of preexisting therapeutically potent molecules. The objective of the present study is to identify the potential small molecule inhibitors against BRD4 through in-silico approach for the treatment of cancer. In present study, designed an in-silico screening of small molecules through ligand-based pharmacophore studies against bromodomain-containing protein 4 (BRD-4) protein and used for virtual screening through Database and their binding affinity and interaction of identified molecules were predicted through molecular docking, molecular dynamics simulations for 12 fixed time period, Molecular mechanics (MMGBSA) binding free energy calculations, ADME with drug-likeness properties including violations of lipinski's rule of 5, Jorgensens rule of 3 and other parameters were studied. The docking results indicate from the reported database screened molecules were validated with docking score -7.92 to -4.27Kcal/mol for BRD4-BD1 and the best model identified 21 hits. Among these two drugs were filtered and scrutinized for their ability based on binding modes and common interaction, MMGBSA of the highest affinity -54.53 Kcal/mol of BRD4-BD1 and ADME properties of selected molecules were predicted for its various parameters, dynamics studies evaluating its binding stability using Maestro software. In Conclusion, two BRD4 inhibitors were found to bind strongly in the similar binding sites as JQ-1, highlighting the role of BRD4-BD1. These compounds were identified as promising new options for regulating epigenetics and understanding the structural needs of BRD4 protein, further research in these areas could lead to the development of more effective and targeted cancer drugs.Communicated by Ramaswamy H. Sarma.

Design, Synthesis and Biological Evaluation of 1,4-Benzenesulfonamide Derivatives as Glyoxalase I Inhibitors

Background

Glyoxalase system is one of the defense cellular mechanisms that protect cells against endogenous harmful metabolites, mainly methylglyoxal (MG), through conversion of cytotoxic methylglyoxal into the non-toxic lactic acid. Glyoxalase system comprises of two enzymes glyoxalase I, glyoxalase II, and a catalytic amount of reduced glutathione. Cancerous cells overexpress glyoxalase I, making it a target for cancer therapy. Many studies have been conducted to identify potent Glx-I inhibitors.

Methods

Aiming to discover and develop novel Glx-I inhibitors, a series of 1,4-benzenesulfonamide derivatives were designed, synthesized, and biologically evaluated in vitro against human Glx-I enzyme. Seventeen compounds were designed based on the hit compound that was obtained from searching the National Cancer Institute (NCI) database. The synthesis of the target compounds (13-29) was accomplished utilizing an azo coupling reaction of aniline derivatives and activated substituted aromatic compounds. To understand the binding mode of the active compounds at the active site of Glx-I, docking studies were performed.

Results

Structure activity relationship (SAR) studies were accomplished which led to the identification of several compounds that showed potent inhibitory activity with IC50 values below 10 μM. Among the compounds tested, compounds (E)-2-hydroxy-5-((4-sulfamoylphenyl)diazenyl)benzoic acid (26) and (E)-4-((8-hydroxyquinolin-5-yl)diazenyl) benzenesulfonamide (28) displayed potent Glx-I inhibitory activity with IC50 values of 0.39 μM and 1.36 µM, respectively. Docking studies of compounds 26 and 28 were carried out to illustrate the binding mode of the molecules into the Glx-I active site.

Conclusion

Our results show that compounds 26 and 28 displayed potent Glx-I inhibitory activity and can bind the Glx-I well. These findings should lead us to discover new classes of compounds with better Glx-I inhibition.

Fumarato and Phthalato Bridged Dinuclear Metal-Organic Cu(II) and Mn(II) Compounds involving Infinite Fumarate-water Assemblies and Unusual Structure-guiding H-bonded Synthons: Antiproliferative Evaluation and Theoretical Studies

Two new dinuclear coordination compounds viz. [Cu2(µ-fum)(phen)2(H2O)6](fum)•6H2O (1) and [Mn2(µ-phth)2(phen)4]•2H2O (2) (phen = 1,10-phenanthroline, fum = fumarate and phth = phthalate) have been synthesized and characterized by elemental analysis, single...

Identification of the first "two digit nano-molar" inhibitors of the human glyoxalase-I enzyme as potential anticancer agents

BACKGROUND

Glyoxalase-I (Glo-I) enzyme is recognized as an indispensable druggable target in cancer treatment. Its inhibition will lead to the accumulation of toxic aldehyde metabolites and cell death. Paramount efforts were spent to discover potential competitive inhibitors to eradicate cancer.

OBJECTIVE

Based on our previously work on this target for discovering potent inhibitors of this enzyme, herein, we address the discovery of the most potent Glo-I inhibitors reported in literature with two digits nano-molar activity.

METHODS

Molecular docking and in vitro assay were performed to discover these inhibitors and explore the active site's binding pattern. A detailed SAR scheme was generated, which identifies the significant functionalities responsible for the observed activity.

RESULTS

Compound 1 with an IC50 of 16.5 nM exhibited the highest activity, catechol moiety as an essential zinc chelating functionality. It has been shown by using molecular modeling techniques that the catechol moiety is responsible for the chelation zinc atom at the active site, an essential feature for enzyme inhibition.

CONCLUSION

Catechol derivatives are successful zinc chelators in the Glo-I enzyme while showing exceptional activity against the enzyme to the nanomolar level.

Supramolecular assemblies involving biologically relevant antiparallel π-stacking and unconventional solvent driven structural topology in maleato and fumarato bridged Zn(ii) coordination polymers: antiproliferative evaluation and theoretical studies

In vitro anticancer activities have been explored in solvent driven maleato and fumarato bridged Zn(ii) coordination polymers involving energetically significant antiparallel π-stacking and enclathrated guest MeOH/H₂O moieties.

Design, synthesis and biological evaluation of novel glyoxalase I inhibitors possessing diazenylbenzenesulfonamide moiety as potential anticancer agents

The enzyme glyoxalase-I (Glo-I) is an essential therapeutic target in cancer treatment. Significant efforts have been made to discover competitive inhibitors of Glo-I as potential anticancer agents. Herein, we report the synthesis of a series of diazenylbenzenesulfonamide derivatives, their in vitro evaluation against Glo-I and the resulting structure-activity relationships. Among the compounds tested, compounds 9h and 9j exhibited the highest activity with IC50 1.28 µM and 1.13 µM, respectively. Docking studies to explore the binding mode of the compounds identified key moieties that may contribute to the observed activities. The active compounds will serve as suitable leads for further chemical optimization.

Adipato bridged novel hexanuclear Cu(ii) and polymeric Co(ii) coordination compounds involving cooperative supramolecular assemblies and encapsulated guest water clusters in a square grid host: antiproliferative evaluation and theoretical studies

Novel adipato bridged Cu(ii) and Co(ii) complexes synthesized by considering cytotoxicity, apoptosis, ROS generation, molecular docking and pharmacophore features.

Investigation of Binding Characteristics of Phosphoinositide-dependent Kinase-1 (PDK1) Co-crystallized Ligands Through Virtual Pharmacophore Modeling Leading to Novel Anti-PDK1 Hits

BACKGROUND

3-Phosphoinositide Dependent Protein Kinase-1 (PDK1) is being lately considered as an attractive and forthcoming anticancer target. A Protein Data Bank (PDB) cocrystallized crystal provides not only rigid theoretical data but also a realistic molecular recognition data that can be explored and used to discover new hits.

OBJECTIVE

This incited us to investigate the co-crystallized ligands' contacts inside the PDK1 binding pocket via a structure-based receptor-ligand pharmacophore generation technique in Discovery Studio 4.5 (DS 4.5).

METHODS

Accordingly, 35 crystals for PDK1 were collected and studied. Every single receptorligand interaction was validated and the significant ones were converted into their corresponding pharmacophoric features. The generated pharmacophores were scored by the Receiver Operating Characteristic (ROC) curve analysis.

RESULTS

Consequently, 169 pharmacophores were generated and sorted, 11 pharmacophores acquired good ROC-AUC results of 0.8 and a selectivity value above 8. Pharmacophore 1UU3_2_01 was used in particular as a searching filter to screen NCI database because of its acceptable validity criteria and its distinctive positive ionizable feature. Several low micromolar PDK1 inhibitors were revealed. The most potent hit illustrated anti-PDK1 IC50 values of 200 nM with 70% inhibition against SW480 cell lines.

CONCLUSION

Eventually, the active hits were docked inside the PDK1 binding pocket and the recognition points between the active hits and the receptor were analyzed that led to the discovery of new scaffolds as potential PDK1 inhibitors.