Combining ligand-based and structure-based drug design approaches to study the structure-activity relationships of a β-carboline derivative series

Virtual screening of PEBP1 inhibitors by combining 2D/3D-QSAR analysis, hologram QSAR, homology modeling, molecular docking analysis, and molecular dynamic simulations

Human phosphatidylethanolamine binding protein 1 (hPEBP1) is a novel target affecting many cellular signaling pathways involved in the formation of metastases. It can be used in the treatment of many cases of cancer. For these reasons, pharmaceutical companies use computational approaches, including multi-QSAR (2D, 3D, and hologram QSAR) analysis, homology modeling, molecular docking analysis, and molecular dynamic simulations, to speed up the drug discovery process. In this paper, QSAR modeling was conducted using two quantum chemistry optimization methods (AM1 and DFT levels). As per PLS results, we found that the DFT/B3LYP method presents high predictability according to 2D-QSAR, CoMFA, CoMSIA, and hologram QSAR studies, with Q² of 0.81, 0.67, 0.79, and 0.67, and external power with R²_pred of 0.78, 0.58, 0.66, and 0.56, respectively. This result has been validated by CoMFA/CoMSIA graphics, which suggests that electrostatic fields combined with hydrogen bond donor/acceptor fields are beneficial to the antiproliferative activity. While the hologram QSAR models show the contributions of each fragment in improving the activity. The results from QSAR analyses revealed that ursolic acids with heterocyclic rings could improve the activities. Ramachandran plot validated the modeled PEBP1 protein. Molecular docking and MD simulations revealed that the hydrophobic and hydrogen bond interactions are dominant in the PEBP1's pocket. These results were used to predict in silico structures of three new compounds with potential anticancer activity. Similar molecular docking stability studies and molecular dynamics simulations were conducted.

A comprehensive overview of β-carbolines and its derivatives as anticancer agents

β-Carboline alkaloids are a family of natural and synthetic products with structural diversity and outstanding antitumor activities. This review summarizes research developments of β-carboline and its derivatives as anticancer agents, which focused on both natural and synthetic monomers as well as dimers. In addition, the structure-activity relationship (SAR) analysis of β-carboline monomers and dimers are summarized and mechanism of action of β-carboline and its derivatives are also presented. A few possible research directions, suggestions and clues for future work on the development of novel β-carboline-based anticancer agents with improved expected activities and lesser toxicity are also provided.

In silico modeling studies of N9-substituted harmine derivatives as potential anticancer agents: combination of ligand-based and structure-based approaches

A computational study was carried out to develop quantitative-structure activity relationship (QSAR), pharmacophore, molecular docking and molecular dynamics simulations of a series of N9-substituted harmine derivatives in order to investigate the structural factors involved in the cytotoxic activity and thus design new active derivatives. A valid 3 D-QSAR (R²= 0.89, q²=0.67, R²pred = 0.72) and 2 D-QSAR (R²= 0.81, q²=0.69, R²pred = 0.76) models were obtained correlating the cytotoxic activity with hydrophobic and hydrogen bond acceptor (HBA) features for 3 D-QSAR and SlogP and a_acc descriptors for 2 D-QSAR. Analysis of the selected descriptors for both models highlighted that lipophilicity and hydrogen bonding acceptor atoms remain the crucial properties and those on which cytotoxic activity depends. Also, these findings are in agreement with the characteristics of the generated pharmacophore. Furthermore, molecular docking revealed that the binding energy (-9.74 kcal/mol) and inhibition constant (0.071 µmol) correlate with the activity of the most active compound that forms hydrophobic interactions and two hydrogen bonds with the the dual specificity tyrosine phosphorylation regulated kinase 1 A (DYRK1A). The molecular dynamics simulations revealed that the protein-ligand equilibrium is stable after 100000 fs of trajectories. Based on these results, we designed new N⁹-substituted harmine derivatives with improved properties: predicted cytotoxic activities, estimated binding energies, estimated inhibition constants and interaction modes with amino acid residues of DYRK1A, compared to the best compound in the studied dataset. Additionally, these newly designed inhibitors showed promising results in the preliminary in silico Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) evaluations.Communicated by Ramaswamy H. Sarma.

Review on chemogenomic approaches towards hepatitis C viral targets

Hepatitis C virus (HCV) is the most prevalent viral pathogen that infects more than 185 million people worldwide. HCV infection leads to chronic liver diseases such as liver cirrhosis and hepatocellular carcinoma. Direct-acting antivirals (DAAs) are the recent combination therapy for HCV infection with reduced side effects than prior therapies. Sustained virological response (SVR) acts as a gold standard marker to monitor the success of antiviral treatment. Older treatment therapies attain 50-55% of SVR compared with DAAs which attain around 90-95%. The current review emphasizes the recent chemogenomic updates that have been unfolded through structure-based drug design of HCV drug target proteins (NS3/4A, NS5A, and NS5B) and ligand-based drug design of DAAs in achieving a stable HCV viral treatment strategies.