Computational analysis of benzyl vinylogous derivatives as potent PDE3B inhibitors

Promising Anticancer Activity of β-Carboline Derivatives: Design, Synthesis, and Pharmacological Evaluation

β-carboline consists of a pyridine ring fused to an indole skeleton; it possesses numerous pharmacological activities, including anticancer. Previously, we reported a satisfactory 2D and 3D QSAR study on β-carboline derivatives. Based on QSAR studies, we designed, synthesized, characterized, and screened fourteen β-carboline derivatives for anticancer activity. Eleven of them demonstrated potent anticancer activity against both liver (HepG2) and adenocarcinoma (A549) cell lines. Compound 1-(N, N-dimethylbenzenamine)-3-(4-(p-tolylmethanimine)-5-thio-1, 2, 4-triazol-3-yl) β-carboline (9) was found to be most potent against both cancer cell lines and equipotent towards standard drug Adriamycin. Compounds 1-(p-tolyl)-3-(4-(p-(iminomethyl)-N, N-dimethylbenzenamine) -5-thio-1, 2, 4-triazol-3-yl) β-carboline (4) and 1-(N, N-dimethylbenzenamine)-3-(4-(m-tolylmethanimine)-5-thio-1, 2, 4-triazol-3-yl) β-carboline (10) were found to be 7 to 10 times less potent as compared to Adriamycin against the HepG2 cell line. Molecular docking was also performed with the Glide docking program to explore the binding mode between the synthesized β-carboline derivatives and the receptor CDK2 [1AQ1] protein.

Caspase-3: A primary target for natural and synthetic compounds for cancer therapy

Caspases, a group of protease enzymes (cysteine proteases), exist as inactive zymogens in the cells and execute apoptosis (programmed cell death). Caspase-3, an executioner caspase, plays an imperative role in apoptosis and becomes a primary target for cancer treatment. A number of analogues of quinazoline, quinazolinone, indoloquinazolines, quinone, naphthoquinones, pyrroloiminoquinones, styrylquinolines, tetheredtetrahydroquinoline, fluoroquinolone, thiosemicarbazones, benzotriazole, pyrimidines, chalcone, and carbazoles have been reported till date, representing caspase-3 mediated apoptosis for cancer therapy. Simultaneously, plant isolates, including lysicamine, podophyllotoxin, and majoranolide, have also been claimed for caspase-3-mediated apoptosis-induced cytotoxicity. Procaspase-activating compound-1 (PAC-1) is the first FDA approved orphan drug, and its synthetic derivative WF-208 also showed fascinating caspase-3 mediated anticancer activity. Till date, a large number of compounds have been reported and patented for their caspase-3-mediated cytotoxicity and now scientist is also focusing to introduce new compounds in market to encompass anticancer activity.

Discovery of Novel 1,2,4-Oxadiazole Derivatives as Potent Caspase-3 Activator for Cancer Treatment

In the present study, a quantitative structure–activity relationship (QSAR) and docking studies were accomplished on a series of 1,2,4-oxadiazoles. The results of QSARs are reliable and have high predictive ability for both the internal (q2 = 0.610) and external (pred_r2 = 0.553) datasets with least standard error (SE; i.e., 0.130) and four principal components, which signifies the reliability of the generated model. Molecular docking was also reported by the GOLD docking program, which showed that the hydrogen bonding may be responsible for the activity, and may be further increased upon adding high electronegative substitutions.

Exploring the Role of Water Molecules in the Ligand Binding Domain of PDE4B and PDE4D: Virtual Screening Based Molecular Docking of Some Active Scaffolds

BACKGROUND

The phosphodiesterase (PDE) is a superfamily represented by four genes: PDE4A, B,C, and D which cause the hydrolysis of phosphodiester bond of cAMP to yield inactive AMP. c-AMP catalyzing enzyme is predominant in inflammatory and immunomodulatory cells. Therapy to treat Chronic Obstructive Pulmonary Disease (COPD) with the use of PDE4 inhibitors is highly envisaged.

OBJECTIVE

A molecular docking experiment with large dataset of diverse scaffolds has been performed on PDE4 inhibitors to analyze the role of amino acid responsible for binding and activation of the secondary transmitters. Apart from the general docking experiment, the main focus was to discover the role of water molecules present in the ligand-binding domain.

METHODS

All the compounds were docked in the PDE4B and PDE4D active cavity to produce the free binding energy scores and spatial disposition/orientation of chemical groups of inhibitors around the cavity. Under uniform condition, the experiments were carried out with and without water molecules in the LBD. The exhaustive study was carried out on the Autodock 4.2 software and explored the role of water molecules present in the binding domain.

RESULTS

In presence of water molecule, Roflumilast has more binding affinity (-8.48 Kcal/mol with PDE4B enzyme and -8.91 Kcal/mol with PDE4D enzyme) and forms two hydrogen bonds with Gln443 and Glu369 and amino acid with PDE4B and PDE4D enzymes respectively. While in absence of water molecule its binding affinity has decreased (-7.3 Kcal/mol with PDE4B enzyme and -5.17 Kcal/mol with PDE4D enzyme) as well as no H-bond interactions were observed. Similar observation was made with clinically tested molecules.

CONCLUSION

In protein-ligand binding interactions, appropriate selection of water molecules facilitated the ligand binding, which eventually enhances the efficiency as well as the efficacy of ligand binding.