Comparative study of the binding mode between cytochrome P450 17A1 and prostate cancer drugs in the absence of haem iron

Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding

As an important member of cytochrome P450 (CYP) enzymes, CYP17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones, making it an attractive therapeutic target. The emerging structural information about CYP17A1 and the growing number of inhibitors for these enzymes call for a systematic strategy to delineate and classify mechanisms of ligand transport through tunnels that control catalytic activity. In this work, we applied an integrated computational strategy to different CYP17A1 systems with a panel of ligands to systematically study at the atomic level the mechanism of ligand-binding and tunneling dynamics. Atomistic simulations and binding free energy computations identify the dynamics of dominant tunnels and characterize energetic properties of critical residues responsible for ligand binding. The common transporting pathways including S, 3, and 2c tunnels were identified in CYP17A1 binding systems, while the 2c tunnel is a newly formed pathway upon ligand binding. We employed and integrated several computational approaches including the analysis of functional motions and sequence conservation, atomistic modeling of dynamic residue interaction networks, and perturbation response scanning analysis to dissect ligand tunneling mechanisms. The results revealed the hinge-binding and sliding motions as main functional modes of the tunnel dynamic, and a group of mediating residues as key regulators of tunnel conformational dynamics and allosteric communications. We have also examined and quantified the mutational effects on the tunnel composition, conformational dynamics, and long-range allosteric behavior. The results of this investigation are fully consistent with the experimental data, providing novel rationale to the experiments and offering valuable insights into the relationships between the structure and function of the channel networks and a robust atomistic model of activation mechanisms and allosteric interactions in CYP enzymes.

Two-dimensional infrared spectral explorations into bilayer and monolayer self-assemblies of amphiphilic polypeptides

Poly(2-(3-((2-hydroxyethyl)amino)-3-oxopropyl)ethyleneamido) (PHAOE) is an amphiphilic polypeptide. The self-assembly is significant, but the ultrafast dynamic analyses of the peptide self-assembly are exiguous and worth further exploring. In this investigation, the temporal dynamic characteristics of the aggregates and unaggregated PHAOEs are mined by the two-dimensional infrared (2D IR) spectroscopy. The homogeneous and inhomogeneous diffusion processes of the carbonyl stretching modes of the unaggregated PHAOEs are slower than those of the self-assemblies. The inhomogeneous spectral diffusion proportion of the biopolymer PHAOE in methanol is greater than that in dimethyl sulfoxide (DMSO). The solvation shells surround the aggregates and unaggregated PHAOEs in the protic solvent methanol, but there are not any solvation shells around the aggregates or unaggregated PHAOEs in the dipolar solvent DMSO. The massive hydrogen-bonded monolayer self-assembly has merely an aggregate of PHAOEs and no solvation shell in DMSO. But the hydrogen-bonded bilayer self-assembly has a self-assembled methanol shell and an interior aggregate of PHAOEs in methanol. The self-assemblies of PHAOEs motivate the methanols to self-assemble. The large delocalized amide structure results in the fast spectral diffusion of the carbonyl stretching mode.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization and biological evaluation of novel benzimidazole derivatives

In search of achieving less toxic and more potent chemotherapeutics, three novel heterocyclic benzimidazole derivatives: 2-(1H-benzo[d]imidazol-2-yl)-4-chlorophenol (BM1), 4-chloro-2-(6-methyl-1H-benzo[d]imidazol-2-yl)phenol (BM2) and 4-chloro-2-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (BM3) with DNA-targeting properties, were synthesized and fully characterized by important physicochemical techniques. The DNA binding properties of the compounds were investigated by UV-Visible absorption titrations and thermal denaturation experiments. These molecules exhibited a good binding propensity to fish sperm DNA (FS-DNA), as evident from the high binding constants (K_b) values: 1.9 × 10⁵, 1.39 × 10⁵ and 1.8 × 10⁴ M^‒1 for BM1, BM2 and BM3, respectively. Thermal melting studies of DNA further validated the absorption titration results and best interaction was manifested by BM1 with ΔT_m = 4.96 °C. The experimental DNA binding results were further validated theoretically by molecular docking study. It was confirmed that the molecules (BM1-BM3) bind to DNA via an intercalative and groove binding mode. The investigations showed a correlation between binding constants and energies obtained experimentally and through molecular docking, indicating a binding preference of benzimidazole derivatives with the minor groove of DNA. BM1 was the preferential candidate for DNA binding because of its flat structure, π-π interactions and less steric hindrance. To complement the DNA interaction, antimicrobial assays (antibacterial & antifungal) were performed. It was observed that compound BM2 showed promising activity against all bacterial strains (Micrococcus luteus, Staphylococcus aureus, Enterobacter aerogenes and Escherichia coli) and fungi (Aspergillus flavus, Aspergillus fumigatus and Fusarium solani), while rest of the compounds were active against selective strains. The MIC values of BM2 were found to be in the range of 12.5 ± 2.2-25 ± 1.5 µg/mL. Thus, the compound BM2 was found to be the effective DNA binding antimicrobial agent. Furthermore, the preliminary cytotoxic properties of synthesized compounds were evaluated by brine shrimps lethality assay to check their nontoxic nature towards healthy normal cells.Communicated by Ramaswamy H. Sarma.

Exploration of good and bad structural fingerprints for inhibition of indoleamine-2,3-dioxygenase enzyme in cancer immunotherapy using Monte Carlo optimization and Bayesian classification QSAR modeling

Indoleamine-2,3-dioxygenase 1 (IDO1) is an extrahepatic, heme-containing and tryptophan-catalyzing enzyme responsible for causing blockade of T-cell proliferation and differentiation by depleting tryptophan level in cancerous cells. Therefore, inhibition of IDO1 may be a useful strategy for immunotherapy against cancer. In this study, 448 structurally diverse IDO1 inhibitors with a wide range of activity has been taken into consideration for classification QSAR analysis through Monte Carlo Optimization by using different splits as well as different combinations of SMILES-based, graph-based and hybrid descriptors. The best model from Monte Carlo optimization was interpreted to find out the good and bad structural fingerprints for IDO1 and further justified by using Bayesian classification QSAR modeling. Among the three splits in Monte Carlo optimization, the statistics of the best model was obtained from Split 3: sensitivity = 0.87, specificity = 0.91, accuracy = 0.89 and MCC = 0.78. In Bayesian classification modeling, the ROC scores for training and test set were found to be 0.91 and 0.86, respectively. The combined modeling analysis revealed that the presence of aryl hydrazyl sulphonyl moiety, furazan ring, halogen substitution, nitro group and hetero atoms in aromatic system can be very useful in designing IDO1 inhibitors. All the good and bad structural fingerprints for IDO1 were identified and are justified by correlating these fragments to the inhibition of IDO1 enzyme. These structural fingerprints will guide the researchers in this field to design better inhibitors against IDO1 enzyme for cancer immunotherapy.Communicated by Ramaswamy H. Sarma.

Synthesis and characterization of heterobimetallic SnIV-CuII/ZnII complexes: DFT studies, cleavage potential and cytotoxic activity

Heterobimetallic complexes [Cu(L)Sn(CH₃)₂(H₂O)(Cl)] (3) and [Zn(L)Sn(CH₃)₂(H₂O)(Cl)] (4) have been synthesized from their monometallic analogs [Cu(L)(H₂O)(Cl)] (1) and [Zn(L)(H₂O)(Cl)] (2) of Schiff base ligand (L) which were characterized by various spectroscopic and analytical methods. DFT calculations were carried out to simulate the vibrational spectra to support the anticipated structures. The interaction studies of ligand (L) and complexes (1-4) with CT-DNA were performed by employing UV-vis, and fluorescence spectroscopic techniques which revealed that heterobimetallic complexes 3 and 4 showed higher affinity with DNA due to dual mode of action as compared to monometallic complexes 1 and 2. Further, validation of the interaction studies was accomplished by carrying out molecular docking studies with DNA. Gel assay displayed that both the complexes have ability to cleave DNA efficiently and are specific minor groove binders. Cu^II-Sn^IV complex 3 cleaved pBR322 DNA via oxidative mechanism, while Zn^II-Sn^IV complex 4 followed hydrolytic cleavage pathway. In vitro cytotoxicity evaluation of complex 3 was tested on a different cancer cell lines showing promising antitumor activity.Communicated by Ramaswamy H. Sarma.

Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase

The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q² of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q² of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma.