DNA minor groove pharmacophores describing sequence specific properties

Tracking the binding site of anticancer drug fluxoridin with Fe-related proteins to achieve intelligent drug delivery

In cancer cells that need a lot of iron for growth and metastasis, halo-transferrin (TF-containing iron) enters the cell with the help of the transferrin receptor 1 (TFR1) protein. If the anticancer drug can bind to the iron site by interacting with apo-transferrin (iron-free FT), it can enter the cancer cell by the same mechanism. Two iron-related proteins, Bovine liver catalase (BLC) and apo-Transferrin (TF), that are important in cancer patients were selected and their interaction with the anti-cancer drug Floxuridine (FUDR) was investigated. Here, the protective role of FUDR was evaluated by several variables such as drug concentration, interaction time, and temperature-induced degradation of enzyme function. The results showed that the protective effect of the FUDR is greater in high concentrations (in 5 × 10-5 M:1.78 % and 2.59 % after 24 and 48 h). The interaction of the FUDR with both proteins can reduce the intensity of the fluorescence emission by a static mechanism. The binding strength of the FUDR with both proteins was almost similar and with the order of 104 M-1 (Kb = 3.90 ± 0.41 × 104 M-1 for BLC-FUDR and 5.01 ± 0.36 × 104 M-1 for TF-FUDR at 310 K). The thermodynamic calculations (in agreement with the docking results) indicated that FUDR-protein complex formation was exothermic and the main binding forces in the binding process were van der Waals interactions and hydrogen bonds. Both fluorophores tryptophan (Trp) and tyrosine (Tyr) of both proteins had significant roles in fluorescence quenching and the interaction process, the polarity of their microenvironment changed. CD results showed that the secondary structure changes of TF are slightly more than BLC. Molecular docking showed that the binding of the FUDR to TF is very close to the Fe-specific site and is placed in the cavity among the wrapping domain, N-Terminal arm, and β-barrel in BLC.

Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies

We have synthesized the pyrazole-bearing Schiff base derivatives (5a-5e) and (6a-6h) then the structural confirmation was supported by various spectral analyses. The antibacterial activity of all analogs was screened against bacterial strains Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumonieae and Pseudomonas aeruginosa. In comparison to the reference drug ciprofloxacin, the lead analogs 5c and 6c showed potent activity, with MIC values of 64 µg/mL against E. coli and B. subtilis. Compound 5c showed a moderate effect with a MIC value of 128 µg/mL against B. subtilis, P. aeruginosa and K. pneumonieae, while compound 6c was against E. coli and P. aeruginosa. Furthermore, the compounds 5c and 6c displayed groove binding mode towards CT-DNA by absorption, emission, competitive fluorescence studies using EtBr, CD and time-resolved fluorescence studies. Thermodynamic parameters of analogs 5c and 6c with CT-DNA were also calculated at 298, 303 and 308K temperatures by UV-visible spectroscopy. The molecular docking studies give the docking score for all compounds with PDB codes: 1BNA and 2XCT. The MD simulation study of analogs 5c and 6c was also carried out. The pharmacokinetic and ADME properties were calculated for all of the synthesized analogs (5a-5e) and (6a-6h).Communicated by Ramaswamy H. Sarma.

Structural and functional changes of catalase through interaction with Erlotinib hydrochloride. Use of Chou's 5-steps rule to study mechanisms

Erlotinib hydrochloride (Erlo) is used in the treatment of non-small cell lung cancer, pancreatic cancer and other types of cancer. Interaction of small molecules with bio-macromolecules can lead to changes in the structure and function of them which is one of the possible side effects of the drugs. In this study, the interaction of Erlo with bovine liver catalase (BLC) using spectroscopic and computational methods is presented in detail. The enzymatic function of BLC decreased to 58.7% when the concentration of the Erlo was 0.5 × 10^-7 M. Fluorescence results revealed that the combination of BLC with Erlo undergoes static quenching mechanism (K_b = 1.15 × 10⁴ M^-1 at 300 K). The interaction process was spontaneous, exothermic and enthalpy-driven and Van der Waals and hydrogen bonds forces played major roles in the this process. UV-Vis, CD, 3D, and synchronous fluorescence measurements indicated the changes in the microenvironment residues and α-helix contents of BLC in the presence of Erlo. Docking and molecular dynamics presented a stable binding configuration and their results were perfectly consistent with the spectroscopic results. Theoretical calculations and experimental analysis help to fully understand of drug interaction with important biological molecules such as enzymes.

New molecular insights into the tyrosyl-tRNA synthase inhibitors: CoMFA, CoMSIA analyses and molecular docking studies

Drug resistance caused by excessive and indiscriminate antibiotic usage has become a serious public health problem. The need of finding new antibacterial drugs is more urgent than ever before. Tyrosyl-tRNA synthase was proved to be a potent target in combating drug-resistant bacteria. In silico methodologies including molecular docking and 3D-QSAR were employed to investigate a series of newly reported tyrosyl-tRNA synthase inhibitors of furanone derivatives. Both internal and external cross-validation were conducted to obtain high predictive and satisfactory CoMFA model (q 2 = 0.611, r 2pred  = 0.933, r 2m  = 0.954) and CoMSIA model (q 2 = 0.546, r 2pred  = 0.959, r 2m  = 0.923). Docking results, which correspond with CoMFA/CoMSIA contour maps, gave the information for interactive mode exploration. Ten new molecules designed on the basis of QSAR and docking models have been predicted more potent than the most active compound 3-(4-hydroxyphenyl)-4-(2-morpholinoethoxy)furan-2(5H)-one (15) in the literatures. The results expand our understanding of furanones as inhibitors of tyrosyl-tRNA synthase and could be helpful in rationally designing of new analogs with more potent inhibitory activities.

Development of pharmacophore models for small molecules targeting RNA: Application to the RNA repeat expansion in myotonic dystrophy type 1

RNA is an important drug target, but current approaches to identify bioactive small molecules have been engineered primarily for protein targets. Moreover, the identification of small molecules that bind a specific RNA target with sufficient potency remains a challenge. Computer-aided drug design (CADD) and, in particular, ligand-based drug design provide a myriad of tools to identify rapidly new chemical entities for modulating a target based on previous knowledge of active compounds without relying on a ligand complex. Herein we describe pharmacophore virtual screening based on previously reported active molecules that target the toxic RNA that causes myotonic dystrophy type 1 (DM1). DM1-associated defects are caused by sequestration of muscleblind-like 1 protein (MBNL1), an alternative splicing regulator, by expanded CUG repeats (r(CUG)^exp). Several small molecules have been found to disrupt the MBNL1-r(CUG)^exp complex, ameliorating DM1 defects. Our pharmacophore model identified a number of potential lead compounds from which we selected 11 compounds to evaluate. Of the 11 compounds, several improved DM1 defects both in vitro and in cells.

Prediction and evaluation of the lipase inhibitory activities of tea polyphenols with 3D-QSAR models

The extraordinary hypolipidemic effects of polyphenolic compounds from tea have been confirmed in our previous study. To gain compounds with more potent activities, using the conformations of the most active compound revealed by molecular docking, a 3D-QSAR pancreatic lipase inhibitor model with good predictive ability was established and validated by CoMFA and CoMISA methods. With good statistical significance in CoMFA (r²_cv = 0.622, r² = 0.956, F = 261.463, SEE = 0.096) and CoMISA (r²_cv = 0.631, r² = 0.932, F = 75.408, SEE = 0.212) model, we summarized the structure-activity relationship between polyphenolic compounds and pancreatic lipase inhibitory activities and find the bulky substituents in R₂, R₄ and R₅, hydrophilic substituents in R₁ and electron withdrawing groups in R₂ are the key factors to enhance the lipase inhibitory activities. Under the guidance of the 3D-QSAR results, (2R,3R,2′R,3′R)-desgalloyloolongtheanin-3,3′-O-digallate (DOTD), a potent lipase inhibitor with an IC50 of 0.08 μg/ml, was obtained from EGCG oxidative polymerization catalyzed by crude polyphenol oxidase. Furthermore, DOTD was found to inhibit lipid absorption in olive oil-loaded rats, which was related with inhibiting the activities of lipase in the intestinal mucosa and contents.

Insight into the interactions between novel isoquinolin-1,3-dione derivatives and cyclin-dependent kinase 4 combining QSAR and molecular docking

Several small-molecule CDK inhibitors have been identified, but none have been approved for clinical use in the past few years. A new series of 4-[(3-hydroxybenzylamino)-methylene]-4H-isoquinoline-1,3-diones were reported as highly potent and selective CDK4 inhibitors. In order to find more potent CDK4 inhibitors, the interactions between these novel isoquinoline-1,3-diones and cyclin-dependent kinase 4 was explored via in silico methodologies such as 3D-QSAR and docking on eighty-one compounds displaying potent selective activities against cyclin-dependent kinase 4. Internal and external cross-validation techniques were investigated as well as region focusing, bootstraping and leave-group-out. A training set of 66 compounds gave the satisfactory CoMFA model (q² = 0.695, r² = 0.947) and CoMSIA model (q² = 0.641, r² = 0.933). The remaining 15 compounds as a test set also gave good external predictive abilities with r²_pred values of 0.875 and 0.769 for CoMFA and CoMSIA, respectively. The 3D-QSAR models generated here predicted that all five parameters are important for activity toward CDK4. Surflex-dock results, coincident with CoMFA/CoMSIA contour maps, gave the path for binding mode exploration between the inhibitors and CDK4 protein. Based on the QSAR and docking models, twenty new potent molecules have been designed and predicted better than the most active compound 12 in the literatures. The QSAR, docking and interactions analysis expand the structure-activity relationships of constrained isoquinoline-1,3-diones and contribute towards the development of more active CDK4 subtype-selective inhibitors.

Minor groove binders and drugs targeting proteins cover complementary regions in chemical shape space

DNA minor groove binders (MGBs) are known to influence gene expression and are therefore widely studied to explore their therapeutic potential. We identified shape-based virtual screening with ROCS as a highly effective computational approach to enrich known MGBs in top-ranked molecules. Discovery of ten previously unknown MGBs by shape-based screening further confirmed the relevance of ligand shape for minor groove affinity. Based on experimental testing we propose three simple rules (at least two positive charges, four nitrogen atoms, and one aromatic ring) as filters to reach even better enrichment of true positives in ROCS hit lists. Interestingly, shape-based ranking of MGBs versus FDA-approved drugs again leads to high enrichment rates, indicating complementary coverage of chemical shape space and indicating minor groove affinity to be unfavorable for approval of drugs targeting proteins.

In search of second-generation HIV integrase inhibitors: targeting integration beyond strand transfer

Highly active antiretroviral therapy combines antiviral drugs targeting different steps in the HIV replication cycle in order to reduce viral loads in patients to undetectable levels. Since HIV readily develops resistance and can therefore escape the action of existing drugs, novel drugs with novel mechanisms of action must be developed. The integration of the viral genome into the human genome is an essential and critical replication step that is catalyzed by the viral integrase with the help of cellular cofactors. Although HIV-1 integrase has been studied for more than two decades, the first integrase inhibitor, raltegravir, was only recently approved for clinical use. A second compound, elvitegravir, is currently in advanced clinical trials. Both drugs interfere with the strand-transfer reaction of integrase. Due to the complexity and multistep nature of the integration reaction, several other functions of integrase can be exploited for drug discovery. In this review, we will describe these alternative strategies to inhibit integration. They have recently attracted considerable interest for the development of second-generation integrase inhibitors.

Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds

Minor groove-binding ligands are able to control gene expression and are of great interest for therapeutic applications. We extracted hydrogen-bonding geometries from all available structures of minor groove-binder-DNA complexes of two noncovalent binding modes, namely 1:1 (including hairpin and cyclic ligands) and 2:1 ligand/DNA binding. Positions of the ligand atoms involved in hydrogen bonding deviate from idealized hydrogen bond geometries and do not exploit the possibilities indicated by water molecules. Therefore, we suggest the inclusion of shape-based descriptors rather than hydrogen-bond patterns in virtual screening protocols for the identification of innovative minor groove-binding scaffolds.

Netropsin improves survival from endotoxaemia by disrupting HMGA1 binding to the NOS2 promoter

The inducible form of nitric oxide synthase (NOS2) plays an important role in sepsis incurred as a result of infection with Gram-negative bacteria that elaborate endotoxin. The HMGA1 (high-mobility group A1) architectural transcription factor facilitates NOS2 induction by binding a specific AT-rich Oct (octamer) sequence in the core NOS2 promoter via AT-hook motifs. The small-molecule MGB (minor-groove binder) netropsin selectively targets AT-rich DNA sequences and can interfere with transcription factor binding. We therefore hypothesized that netropsin would improve survival from murine endotoxaemia by attenuating NOS2 induction through interference with HMGA1 DNA binding to the core NOS2 promoter. Netropsin improved survival from endotoxaemia in wild-type mice, yet not in NOS2-deficient mice, supporting an important role for NOS2 in the beneficial effects of MGB administration. Netropsin significantly attenuated NOS2 promoter activity in macrophage transient transfection studies and the AT-rich HMGA1 DNA-binding site was critical for this effect. EMSAs (electrophoretic mobility-shift assays) demonstrated that netropsin interferes with HMGA1 NOS2 promoter binding and NMR spectroscopy was undertaken to characterize this disruption. Chemical shift perturbation analysis identified that netropsin effectively competes both HMGA1 DNA-binding AT-hooks from the AT-rich NOS2 promoter sequence. Furthermore, NOESY data identified direct molecular interactions between netropsin and A/T base pairs within the NOS2 promoter HMGA1-binding site. Finally, we determined a structure of the netropsin/NOS2 promoter Oct site complex from molecular modelling and dynamics calculations. These findings represent important steps toward refined structure-based ligand design of novel compounds for therapeutic benefit that can selectively target key regulatory regions within genes that are important for the development of critical illness.

Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex

The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nucleic acid targets within a resolution of approximately 2 A, which is similar to the limit of the crystal structure resolution. However, for the top ranked poses, Autodock and Surflex both dock ellipticine into the correct site but in a different orientation compared to the crystal structure. This appears not only to be partly related to the symmetry of the target nucleic acid, as ellipticine is able to dock from either side of the intercalation site, but also due to the shape of the ligand and docking accuracy. Surflex docks pentamidine in a symmetrically equivalent orientation relative to the crystal structure, while Autodock was able to dock this molecule in the original orientation. In the case of the Surflex docking of pentamidine, the initial rmsd is misleading, given the symmetrical structure of pentamidine. Importantly, the ranking functions of both of these programs are able to return a top pose within approximately 2 A rmsd for daunorubicin, distamycin, and pentamidine and approximately 3 A rmsd for ellipticine compared to their respective crystal structures. Some docking challenges and potential pitfalls are explored, such as the importance of hydrogen treatment on ligands as well as the scoring functions of Autodock and Surflex. Overall for this set of complexes, Surflex is preferred over Autodock for virtual screening, as although the results are comparable, Surflex has significantly faster performance and ease of use under the optimal software conditions tested. These experiments show that molecular docking techniques can be successfully extended to include nucleic acid targets, a finding which has important implications for virtual screening applications and in the design of new small molecules to target therapeutically relevant morphologies of nucleic acids.