Combined 3D-QSAR modeling and molecular docking study on azacycles CCR5 antagonists

In search of HIV entry inhibitors using molecular docking, ADME and toxicity studies of some Thiazolidinone-Pyrazine derivatives against CXCR4 co-receptor

BACKGROUND

Entry inhibitors prevent binding of human immunodeficiency virus protein to the chemokine receptor CXCR4 and are used along with conventional anti-HIV therapy. They aid in restoring immunity and can prevent the development of HIV-TB co-infection.

AIM

In the present study various thiazolidinone-pyrazine derivatives earlier studied for NNRT inhibition activity were gauged for their entry inhibitor potential.

OBJECTIVE

Objective of the study is to perform molecular docking, ADME, toxicity studies of some Thiazolidinone-Pyrazine Derivatives as entry inhibitors targeting CXCR4 co-receptors.

METHODS

In-silico docking studies were performed using AutoDock Vina software and compounds were further studied for ADME and toxicity using SwissADME and pkCSM software respectively.

RESULTS

Taking into consideration the docking results, pharmacokinetic behaviour and toxicity profile four molecules (compound 1, 9, 11 and 16) have shown potential as entry inhibitors.

CONCLUSION

These compounds have shown potential as both NNRTI and entry inhibitors and hence can be used in management of immune compromised diseases like TB-HIV coinfection.

QSAR and Docking Studies of DATA Analogues as HIV-1 Reverse Transcriptase Inhibitors

Background:

Acquired Immunodeficiency Syndrome (AIDS) caused by Human Immunodeficiency Virus (HIV) has seriously threatened human health, so development of new, selective and safe non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) remains a high priority for medical research. Diaryltriazine (DATA) have been identified as a new class of potent nonnucleoside HIV-1 Reverse Transcriptase (RT) inhibitors. The study deals with Topomer CoMFA (Comparative Molecular Field Analysis) and molecular docking to explore the important features of DATA analogues for exerting potent HIV-1 RT inhibitors activity.

Methods:

In this work, 40 DATA analogues were studied using a combination of molecular modeling techniques including Three-Dimensional Quantitative Structure–Activity Relationship (3D-QSAR), molecular docking, and Topomer CoMFA were used to build 3D-QSAR models.

Results:

The results show that the Topomer CoMFA analysis has the cross-validation q2 = 0.800, SDCV = 0.45, the non-cross-validated r2 = 0.958, SD = 0.21, and the correlation coefficient of external validation Q2 ext = 0.965 showed that the model is reasonable and credible, and has a good predictive ability. Then binding mode pattern of the compounds to the binding site of enzyme was confirmed and the mechanism of drug and acceptor was studied by docking studies, the results showed that the drug and GLU138, LYS101, THR139 sites have an obvious function, these researches have provided an useful information for designing more effective HIV-1IN inhibitors.

Conclusion:

A series of 40 DATAs analogues was subjected to a 3D-QSAR study. Using Topomer CoMFA 3D-QSAR method built model, and the model has shown a good predictive and statistical validation. Substituent with low electronic density in the R5 and R3 positions and substituent with high electronic density in the R2 and C2 positions will increase the biological activity, small substituent on R4 positions and naphthyloxy as the spacer group C6 substituent hydrophobic will increase biological activity. This effect is supported by Topomer CoMFA contour map and docking results of HIV-1RT inhibition active site, the results of the 3D-QSAR and docking analyses have provided a guide for the synthesis of new putative inhibitors for HIV-1RT to improved inhibitory activity.

Combined pharmacophore modeling, 3D-QSAR, homology modeling and docking studies on CYP11B1 inhibitors

The mitochondrial cytochrome P450 enzymes inhibitor steroid 11β-hydroxylase (CYP11B1) can decrease the production of cortisol. Therefore, these inhibitors have an effect in the treatment of Cushing’s syndrome. A pharmacophore model generated by Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets (GALAHAD) was used to align the compounds and perform comparative molecular field analysis (CoMFA) with Q² = 0.658, R² = 0.959. The pharmacophore model contained six hydrophobic regions and one acceptor atom, and electropositive and bulky substituents would be tolerated at the A and B sites, respectively. A three-dimensional quantitative structure-activity relationship (3D-QSAR) study based on the alignment with the atom root mean square (RMS) was applied using comparative molecular field analysis (CoMFA) with Q² = 0.666, R² = 0.978, and comparative molecular similarity indices analysis (CoMSIA) with Q² = 0.721, R² = 0.972. These results proved that all the models have good predictability of the bioactivities of inhibitors. Furthermore, the QSAR models indicated that a hydrogen bond acceptor substituent would be disfavored at the A and B groups, while hydrophobic groups would be favored at the B site. The three-dimensional (3D) model of the CYP11B1 was generated based on the crystal structure of the CYP11B2 (PDB code 4DVQ). In order to probe the ligand-binding modes, Surflex-dock was employed to dock CYP11B1 inhibitory compounds into the active site of the receptor. The docking result showed that the imidazolidine ring of CYP11B1 inhibitors form H bonds with the amino group of residue Arg155 and Arg519, which suggested that an electronegative substituent at these positions could enhance the activities of compounds. All the models generated by GALAHAD QSAR and Docking methods provide guidance about how to design novel and potential drugs for Cushing’s syndrome treatment.

Biological evaluation and 3D-QSAR studies of curcumin analogues as aldehyde dehydrogenase 1 inhibitors

Aldehyde dehydrogenase 1 (ALDH1) is reported as a biomarker for identifying some cancer stem cells, and down-regulation or inhibition of the enzyme can be effective in anti-drug resistance and a potent therapeutic for some tumours. In this paper, the inhibitory activity, mechanism mode, molecular docking and 3D-QSAR (three-dimensional quantitative structure activity relationship) of curcumin analogues (CAs) against ALDH1 were studied. Results demonstrated that curcumin and CAs possessed potent inhibitory activity against ALDH1, and the CAs compound with ortho di-hydroxyl groups showed the most potent inhibitory activity. This study indicates that CAs may represent a new class of ALDH1 inhibitor.