Current Computer - Aided Drug Design - Volume 16, Issue 2, 2020

Background: Pharmacological and physicochemical classification of bases’ selected analogues of nucleic acids is proposed in the study. Objective: Structural parameters received by the PCM (Polarizable Continuum Model) with several types of calculation methods for the structures in vacuo and in the aquatic environment together with the huge set of extra molecular descriptors obtained by the professional software and literature values of biological activity were used to search the relationships. Methods: Principal Component Analysis (PCA) together with Factor Analysis (FA) and Multiple Linear Regressions (MLR) as the types of the chemometric approach based on semi-empirical ab initio molecular modeling studies were performed. Results: The equations with statistically significant descriptors were proposed to demonstrate both the common and differentiating characteristics of the bases' analogues of nucleic acids based on the quantum chemical calculations and biological activity data. Conclusion: The obtained QSAR models can be used for predicting and explaining the activity of studied molecules.

Background: Sulpiride, which has selective dopaminergic blocking activity, is a substituted benzamide antipsychotic drug playing a prominent role in the treatment of schizophrenia, which more selective and primarily blocks dopamine D2 and D3 receptor. Objective: This study has two main objectives, firstly; the molecular modeling studies (MD and Docking, ADME) were conducted to define the molecular profile of sulpiride and sulpiridereceptor interactions, another to synthesize polymeric nanoparticles with chitosan, having the advantage of slow/controlled drug release, to improve drug solubility and stability, to enhance utility and reduce toxicity. Methods: Molecular dynamic simulation was carried out to determine the conformational change and stability (in water) of the drug and the binding profile of D3 dopamine receptor was determined by molecular docking calculations. The pharmacological properties of the drug were revealed by ADME analysis. The ionic gelation method was used to prepare sulpiride loaded chitosan nanoparticles (CS NPs). The Dynamic Light Scattering (DLS), UV-vis absorption (UV), Scanning Electron Microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy techniques were carried out to characterize the nanoparticles. In vitro cell cytotoxicity experiments examined with MTT assay on mouse fibroblast (L929), human neuroblastoma (SH-SY5Y) and glioblastoma cells (U-87). The statistical evaluations were produced by ANOVA. Results: The residues (ASP-119, PHE-417) of D3 receptor provided a stable docking with the drug, and the important pharmacological values (blood brain barrier, Caco-2 permeability and human oral absorption) were also determined. The average particle size, PdI and zeta potential value of sulpiride- loaded chitosan NPs having a spherical morphology were calculated as 96.93 nm, 0.202 and +7.91 mV. The NPs with 92.8% encapsulation and 28% loading efficiency were found as a slow release profile with 38.49% at the end of the 10th day. Due to the formation of encapsulation, the prominent shifted wave numbers for C-O, S-O, S-N stretching, S-N-H bending of Sulpiride were also identified. Mitochondrial activity of U87, SHSY-5Y and L929 cell line were assayed and evaluated using the SPSS program. Conclusion: To provide more efficient use of Sulpiride having a low bioavailability of the gastrointestinal tract, the nanoparticle formulation with high solubility and bioavailability was designed and synthesized for the first time in this study for the treatment of schizophrenia. In addition to all pharmacological properties of drug, the dopamine blocking activity was also revealed. The toxic effect on different cell lines have also been interpreted.

Background: The catecholamines such as dopamine, norepinephrine, and epinephrine are neurotransmitters that regulate different physiological functions of the central nervous system. Some evidence suggests that the degeneration of dopamine neurons in the substantia nigra contributes to Parkinson’s Disease (PD), which is a neurodegenerative disorder and it is responsible for the major symptoms of PD. It is suggested that replenishment of striatal dopamine through the oral administration of the dopamine precursor, levodopa, can compensate for the lack of endogenously produced dopamine. Some studies have shown competitive inhibition of dopamine receptor such as methamphetamine, and other amphetamine-related derivatives, which block dopamine receptor activity to uptake dopamine. Methods: In this study, 3D structures of amphetamine, methamphetamine, cocaine, methylphenidate, cathinone, MDMA, and mephedrone were obtained from the PubChem database, which has reported some evidence about their inhibitory effect with dopamine receptor. Then, these structures were provided for molecular docking analysis by Autodock Vina software. Eventually, the binding energies between docked dopamine receptor and them were calculated and their interactions were prognosticated. Results: Our results indicated that all chemicals can interact with dopamine receptor molecule in the active site of dopamine and the minimum binding energies belong to Cocaine and Methylphenidate with -7.9 Kcal/mol and -7.2 Kcal/mol, respectively. Conclusion: It might be concluded that amphetamine, methamphetamine, cocaine, methylphenidate, cathinone, MDMA, and mephedrone could act as potential inhibitors of DA receptor for dopamine uptake, which could cause degenerative disorders.

Background: Huntington's disease is characterized by three side effects, including motor disturbances, psychiatric elements, and intellectual weakness. The onset for HD has nonlinear converse associations with the number of repeat sequences of the polyglutamine mutations, so that younger patients have a tendency for longer repeats length. This HD variation is because of the development of a polyglutamine (CAG) repeats in the exon 1 of the Huntingtin protein. Methods: In the present study, a few derivatives utilized as a part of the treatment of HD, are used to create the pharmacophore model and based on the features of the pharmacophore model; an attempt is made to design the de-novo drug for the HD protein. HD protein structure was built and docked with the novel ligand, based on shared feature pharmacophore model, through a ligand-based pharmacophore modeling approach. Results: The novel ligand contains 1 HBAs, 2 HBDs, and 2 aromatic rings. It fulfills all the properties of certain drug-likeness rules, non-toxic in nature. In the docked complex, the common interactive amino acids identified are SER 1035, ALA 1062, MET 1068, LEU 1031, and THR 1036, which confirmed the validity and stability of a ligand molecule to be used as a drug in the treatment of Huntington’s disease. Conclusion: A novel ligand can be used in clinical trials as a drug molecule against the mutations of HD gene and in laboratory procedures for efficacy analysis.

Background: Diabetes is a leading cause of high mortality rate in the world. Recently, SGLT2 inhibitors showed the promising result to treat diabetes and therefore several molecules are approved by the US FDA. Objective: SGLT2 inhibitors were designed based on dioxabicyclo[3.2.1] octane with the aim to search new lead molecule. Methods: The molecular structures were drawn in ChemBiodraw ultra and molecular docking study was performed by AutoDock Vina 1.5.6 software. The LogP and toxicity were predicted online using AlogP and Lazar in-silico respectively. Results: Among all the designed molecules, SK306 showed the maximum binding affinity against the 3dh4 SGLT2 protein of Vibrio parahaemolyticus. LogP values were also calculated in order to determine the lipophilic property of the best binding molecules which show LogP 2.82-3.79 in the range for good absorption and elimination, also predicted to be non-toxic. Conclusion: SGLT2 inhibitors were designed based on the dioxabicyclo [3.2.1] octane resulting in a new lead molecule with high binding affinity; also these molecules were predicted to be noncarcinogenic with low LogP.

Background: Microtubules are dynamic filamentous cytoskeletal structures which play several key roles in cell proliferation and trafficking. They are supposed to contribute in the development of important therapeutic targeting tumor cells. Chalcones are important group of natural compounds abundantly found in fruits & vegetables that are known to possess anticancer activity. We have used QSAR and docking studies to understand the structural requirement of chalcones for understanding the mechanism of microtubule polymerization inhibition. Methods: Three dimensional (3D) QSAR (CoMFA and CoMSIA), pharmacophore mapping and molecular docking studies were performed for the generation of structure activity relationship of combretastatin-like chalcones through statistical models and contour maps. Results: Structure activity relationship revealed that substitution of electrostatic, steric and donor groups may enhance the biological activity of compounds as inhibitors of microtubule polymerization. From the docking study, it was clear that compounds bind at the active site of tubulin protein. Conclusion: The given strategies of modelling could be an encouraging way for designing more potent compounds as well as for the elucidation of protein-ligand interaction.

Introduction: Although the transition of a lead candidate into a drug is currently structured by well-defined milestone, it is still most challenging and offers no guarantee in success to the end. In fact, ligand-based pharmacophore modeling has become a key motive force for retrieving potential leads across several therapeutic areas. Methods: An urgent need towards the development of novel antidepressant agents led us to generate a pharmacophore model from an existing 44 compounds dataset. The best model with one hydrophobic, two ring aromatic, and one positive ionization features was chosen on behalf of the correlation coefficient, sensitivity, specificity, yield of actives and accuracy measures using HypoGen module of Discovery Studio. In house library consisting of 10,000 substituted 1,3,5 triazine derivatives were shortlisted to select four insilico hits. All shortlisted compounds were synthesized and characterized by FTIR, 1H-& 13C-NMR spectroscopy and finally tested for antidepressant-like activity using behavioral models on rats viz. Forced Swim Test (FST) and Elevated Plus Maze (EPM). Results: Two shortlisted compounds with optimal fit values showed a significant decrease in the duration of immobility as compared to standard drug Imipramine in FST while time spent in open arm in enhanced in case of EPM.

Introduction: Intermediate covalent complex of DNA-Topoisomerase II enzyme is the most promising target of the anticancer drugs to induce apoptosis in cancer cells. Currently, anticancer drug and chemotherapy are facing major challenges i.e., drug resistance, chemical instability and, dose-limiting side effect. Therefore, in this study, natural therapeutic agents (series of Ganoderic acids) were used for the molecular docking simulation against Human DNATopoisomerase II beta complex (PDB ID:3QX3). Methods: Molecular docking studies were performed on a 50 series of ganoderic acids reported in the NCBI-PubChem database and FDA approved anti-cancer drugs, to find out binding energy, an interacting residue at the active site of Human DNA-Topoisomerase II beta and compare with the molecular arrangements of the interacting residue of etoposide with the Human DNA topoisomerase II beta. The autodock 4.2 was used for the molecular docking and pharmacokinetic and toxicity studies were performed for the analysis of physicochemical properties and to check the toxicity effects. Discovery studio software was used for the visualization and analysis of docked pose. Results and Conclusion: Ganoderic acids (GS-1, A and DM) were found to be a more suitable competitor inhibitor among the ganoderic acid series with appropriate binding energy, pharmacokinetic profile and no toxicity effects. The interacting residue (Met782, DC-8, DC-11 and DA-12) shared a chemical resemblance with the interacting residue of etoposide present at the active site of human topoisomerase II beta receptor.

Background: Reckoning molecular topological indices of drug structures gives the data about the underlying topology of these drug structures. Novel anticancer drugs have been leading by researchers to produce ideal drugs. Materials and Methods: Pharmacological properties of these new drug agents explored by utilizing simulation strategies. Topological indices additionally have been utilized to research pharmacological properties of some drug structures. Novel alkylating agents based anticancer drug candidates and ve-degree molecular topological indices have been introduced recently. Results and Conclusion: In this study we calculate ve-degree atom-bond connectivity, harmonic, geometric-arithmetic and sum-connectivity molecular topological indices for the newly defined alkylating agents based dual-target anticancer drug candidates.