Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein–ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein–ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.     

Investigating cyclic peptides inhibiting CD2–CD58 interactions through molecular dynamics and molecular docking methods

The CD2–CD58 protein–protein interaction is known to favor the recognition of antigen presenting cells by T cells. The structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6, P7, and RTD-c, are studied through molecular dynamics (MD) simulations and molecular docking calculations. The ligands are built so as to mimic the C and F β-strands of protein CD2, connected via turn inducers. The MD analyses focus on the location of the ligands with respect to the experimental binding site and on the direct and water-mediated hydrogen bonds (H bonds) they form with CD58. Ligand P6, with a sequence close to the experimental β-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 H bonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2–CD58 crystal structure and suggests various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2–CD58 structure.     

Can we use docking and scoring for hit-to-lead optimization?

Docking and scoring is currently one of the tools used for hit finding and hit-to-lead optimization when structural information about the target is known. Docking scores have been found useful for optimizing ligand binding to reproduce experimentally observed binding modes. The question is, can docking and scoring be used reliably for hit-to-lead optimization? To illustrate the challenges of scoring for hit-to-lead optimization, the relationship of docking scores with experimentally determined IC₅₀ values measured in-house were tested. The influences of the particular target, crystal structure, and the precision of the scoring function on the ability to differentiate between actives and inactives were analyzed by calculating the area under the curve of receiver operator characteristic curves for docking scores. It was found that for the test sets considered, MW and sometimes ClogP were as useful as GlideScores and no significant difference was observed between SP and XP scores for differentiating between actives and inactives. Interpretation by an expert is still required to successfully utilize docking and scoring in hit-to-lead optimization.     

Thermal stimuli-responsive behavior of pyrene end-functionalized PDMS through tunable Π–Π interactions

Pyrene end-functionalized, telechelic poly(dimethyl siloxane) (PDMS) materials were synthesized and their response to different thermal stimuli was evaluated. The incorporation of pyrene end groups introduces strong π–π interactions that facilitated a broad range of thermally responsive properties, in some circumstances forming pyrene nanocrystals that serve as physical crosslinks leading to elastic materials. By synthesizing different chain lengths, samples exhibiting a 7 orders of magnitude change in storage modulus in response to thermal stimuli were produced by modifying only the end-groups (0.6 wt % of all polymer segments). Repeated thermal cycling during rheological experiments revealed that π–π interaction and crystallization/melting kinetics of pyrene chain-ends plays a key role in their thermal responsiveness. The properties of these materials were tuned by adding free pyrene, neat PDMS, or graphene oxide (GO) nanoparticles, making them attractive for many applications (e.g., tunable damping materials, heat/light sensors, conductive gels, or light repositionable adhesives). For example, nanocomposites containing 1 wt % GO caused the melting temperature for pyrene crystal domains to more than double, and even induced pyrene end-group crystallization in samples that did not exhibit crystals in neat form. It is hypothesized that these features originate from π–π interactions between pyrene ends and GO surfaces. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 159–168     

Design, synthesis and molecular docking studies of novel triazole antifungal compounds

Based on the active site of Candida albicans lanosterol 14α-demethylase (CACYP51), novel triazole compounds structurally different from the current triazole drugs were designed and synthesized. In vitro antifungal activities showed that compounds 10,11, 16 and 20 exhibited strong activities. In addition, compounds 10,11 and 16 also displayed certain activities against fluconazole-resistant fungi.     

Can azulene-like molecules function as substitution-free molecular rectifiers?

The feasibility of employing azulene-like molecules as a new type of high performance substitution-free molecular rectifier has been explored using NEGF-DFT calculation. The electronic transport behaviors of metal-molecule-metal junctions consisting of various azulene-like dithiol molecules are investigated, which reveals that the azulene-like molecules exhibit high conductance and bias-dependent rectification effects. Among all the substitution-free azulene-like structures, cyclohepta[b]cyclopenta[g]naphthalene exhibits the highest rectification ratio, revealing that the all fused aromatic ring structure and an appropriate separation between the pentagon and heptagon rings are essential for achieving both high conductance and high rectification ratio. The rectification ratio can be increased by substituting the pentagon ring with electron-withdrawing group and/or the heptagon ring with electron donating groups. Further increase of the rectification ratio may also be obtained by lithium adsorption on the pentagon ring. This work reveals that azulene-like molecules may be used as a new class of highly conductive unimolecular rectifiers.     

Identification of good and bad fragments of tricyclic triazinone analogues as potential PKC-θ inhibitors through SMILES–based QSAR and molecular docking

Structural Chemistry - Based on the mechanism of action of PKC-θ, the inhibition of this enzyme is considered a potential target for the treatment of autoimmune diseases such as rheumatoid...     

Applying flexible molecular docking to simulate protein retention behavior in hydrophobic interaction chromatography

Interaction between proteins and stationary phase in hydrophobic interaction chromatography (HIC) is differentiated into two thermodynamic processes involving direct nonbonding/conformation interac- tion and surface hydrophobic effect of proteins, hence quantitatively giving rise to a binary linear rela- tion between HIC retention time (RT) at concentrated salting liquid and ligand-protein binding free en- ergy. Then, possible binding manners for 27 proteins of known crystal structures with hydrophobic ligands are simulated and analyzed via ICM flexible molecular docking and genetic algorithm, with re- sults greatly consistent with experimental values. By investigation, it is confirmed local hydrophobic effects of proteins and nonbinding/conformation interaction between ligand and protein both notably influence HIC chromatogram retention behaviors, mainly focusing on exposed portions on the protein surface.     

Green synthesis,antibacterial, antiviral and molecular docking studies of α-aminophosphonates

Abstract

An efficient method for the synthesis of α-aminophosphonate derivatives has been developed with different functional groups under catalyst and solvent free conditions at room temperature in both conventional and ultrasonication methods. Ultrasonication method offers excellent yields within shorter reaction times. All the title compounds 4a–l were tested for their antibacterial, antiviral activity using Gram-positive bacteria (Staphylococcus aureus, and Bacillus subtilis), Gram-negative bacteria (Klebsiella pneumoniae and Escherichia coli) and NDV infected embryonated eggs (in ovo) and NDV infected BHK-21 cell lines (in vitro) respectively. Besides, molecular docking studies were also carried out to the title compounds against Hemagglutinin-neuramidase enzyme to determine the therapeutic binding efficacy of the ligands synthesized. The results indicated that, among the title compounds, compounds such as 4f, 4l, 4k, 4b, 4i and 4h have shown high content of antibacterial and antiviral activity than the rest of the compounds and the level activity was high when compared to the standard, ribavirin. Based on the results, it is concluded that, the reported α-aminophosphonates will open new vistas and stands as a new generation of antiviral and antibacterial drug candidates in future.     

Synthesis and molecular docking of some new bis-thiadiazoles as anti-hypertensive α-blocking agents

Abstract

Twelve bis-thiadiazole derivatives were synthesized in high yield via the reaction of 2,2′-terephthaloyl bis(N-phenylhydrazine carbothioamide) with a variety of hydrazonoyl chlorides in ethanol containing catalytic amounts of TEA. All the newly synthesized compounds were characterized by physical and chemical tools (FT-IR, ¹H NMR, ¹³C NMR, and Mass spectrometry). Moreover, all the novel synthesized derivatives were screened for their antihypertensive α-blocking efficacy against to assess their pharmaceutical significance. The encouraging promising results obtained from antihypertensive α-blocking activity studies on the newly synthesized derivatives make the synthesis of a new series of these compounds and studying of their pharmaceutical importance an active area for more and more investigations. The molecular docking of the most active derivative 15?b against the human dopamine D3 receptor was performed by the Molecular Operating Environment (MOE 2014. 0901) program.     

Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure–activity relationships and molecular docking

One of the most promising anticancer and recent antimalarial targets is the heterodimeric zinc-containing protein farnesyltransferase (FT). In this work, we studied a highly diverse series of 192 Abbott-initiated imidazole-containing compounds and their FT inhibitory activities using 3D-QSAR and docking, in order to gain understanding of the interaction of these inhibitors with FT to aid development of a rational strategy for further lead optimization. We report several highly significant and predictive CoMFA and CoMSIA models. The best model, composed of CoMFA steric and electrostatic fields combined with CoMSIA hydrophobic and H-bond acceptor fields, had r ² = 0.878, q ² = 0.630, and r _pred² = 0.614. Docking studies on the statistical outliers revealed that some of them had a different binding mode in the FT active site based on steric bulk and available active site space, explaining why the predicted activities differed from the experimental activities. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?

Due to the large number of different docking programs and scoring functions available, researchers are faced with the problem of selecting the most suitable one when starting a structure-based drug discovery project. To guide the decision process, several studies comparing different docking and scoring approaches have been published. In the context of comparing scoring function performance, it is common practice to use a predefined, computer-generated set of ligand poses (decoys) and to reevaluate their score using the set of scoring functions to be compared. But are predefined decoy sets able to unambiguously evaluate and rank different scoring functions with respect to pose prediction performance? This question arose when the pose prediction performance of our piecewise linear potential derived scoring functions (Korb et al. in J Chem Inf Model 49:84–96, 2009) was assessed on a standard decoy set (Cheng et al. in J Chem Inf Model 49:1079–1093, 2009). While they showed excellent pose identification performance when they were used for rescoring of the predefined decoy conformations, a pronounced degradation in performance could be observed when they were directly applied in docking calculations using the same test set. This implies that on a discrete set of ligand poses only the rescoring performance can be evaluated. For comparing the pose prediction performance in a more rigorous manner, the search space of each scoring function has to be sampled extensively as done in the docking calculations performed here. We were able to identify relative strengths and weaknesses of three scoring functions (ChemPLP, GoldScore, and Astex Statistical Potential) by analyzing the performance for subsets of the complexes grouped by different properties of the active site. However, reasons for the overall poor performance of all three functions on this test set compared to other test sets of similar size could not be identified.     

One-pot synthesis of Claisen–Schmidt reaction through (E)-chalcone derivatives: Spectral studies in human serum albumin protein binding and molecular docking investigation

An efficient and environmentally benign one-pot multicomponent synthesis of E-chalcones was developed using a mild and reusable new boron nitride-sulphonic acid catalyst. The catalyst was prepared by activating the boron nitride surface with nitric acid, followed by a simple reaction with 3-mercaptopropyl trimethoxysilane. The catalyst was characterized and morphological properties were studied by Fourier transform infrared, X-ray diffraction, transmission electron spectroscopy, scanning electron microscopy, Brunauer–Emmett–Teller theory, and Raman spectroscopy techniques. The solid acid catalyst was recycled five times in a Claisen–Schmidt reaction to synthesize new chalcone derivatives, and X-ray crystallography was used to elucidate the structure of (E)-1-(anthracen-9-yl)-3-(2-(4-methylpiperazin-1-yl)quinolin-3-yl)prop-2-en-1-one. A fluorescence quench titration method was used to assess its binding ability with human serum albumin (HSA), while molecular docking was also performed to get a more detailed insight into their interaction at the binding site of HSA.     

Nano silver particles catalyzed synthesis,molecular docking and bioactivity of α-thiazolyl aminomethylene bisphosphonates

Abstract

A new series of α-thiazolyl aminomethylene bisphosphonates were synthesized by a three component reaction of 4-aryl substituted thiazol-2-amine with different dialkyl/aryl phosphites and triethyl orthoformate in the presence of Ag NPs (nano particles) as a catalyst under solvent free conditions. All the synthesized target compounds were characterized by ¹H, ¹³C, ³¹P, mass and elemental analysis. The target compounds were screened for their in vitro antioxidant, antibacterial and antifungal activity. Molecular docking studies were also performed. The results revealed that among the synthesized compounds tetramethyl(((4-(4-methoxyphenyl)thiazol-2-yl)amino) methylene)bis(phosphonate) (5d), tetramethyl(((4-(4-fluorophenyl)thiazol-2-yl)amino) methylene) bis(phosphonate) (5h), and tetramethyl(((4-(4-bromophenyl)thiazol-2-yl)amino)methylene) bis (phosphonate) (5j) showed remarkably higher antioxidant activity by DPPH and H₂O₂ than the standard ascorbic acid. Compounds tetramethyl(((4-phenyl thiazol-2-yl)amino) methylene) bis(phosphonate) (5a), 5d, 5h and tetraethyl(((4-(4-bromophenyl)thiazol-2-yl) amino)methylene)bis (phosphonate) (5k) showed good antibacterial activity. 5a, 5d, and 5h also showed rather higher antifungal activity than the standard flucanozole. Computational docking methods have been used to predict how several aminomethylene bisphosphonate derivatives compete against the inhibitor BPH-1330 at the crystal enzyme structure of the 4H3A protein active site and how R and R₁ influence their binding ability.     

Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies

Garcinia kola (GK) produces notable effects against neurodegenerative conditions, including experimentally-induced Alzheimer’s disease (AD). These remarkable effects are basically attributable to kolaviron (KV), a bioflavonoid constituent of this seed. Specifically, it has been reported that in AD models, KV produces interesting neuroprotective effects, being able to diminish associated neurotoxicity, via modulation of antioxidative, inflammatory and other disease modifying processes. Intriguingly, the effect of KV on amyloid-beta (Aβ) aggregation and disruption of preformed Aβ fibrils have not been studied. In this study, we have described a thorough computational study on the mechanism of action of KV as an Aβ fibrils disruptor at molecular level. We used comprehensive in silico docking evaluations and extended molecular dynamics simulation to mimic KV/Aβ fibrils system. Results indicate that KV was able to move within the Aβ fibrils, binding with important residues and components in the Aβ peptide identified to be vital for stabilizing preformed fibrils. KV destabilized the assembled Aβ fibrils, indicating the ability KV as a potential anti-amyloidogenic agent. Furthermore, this work highlighted the possibility of identifying new multifunctional phytocompounds as potent AD drugs.     

Biology-oriented drug synthesis of nitrofurazone derivatives: Their α-glucosidase inhibitory activity and molecular docking studies

In the present study, twenty (20) structural variants of nitrofurazone were synthesized based on BIODS (Biology-oriented drug synthesis) approach. The structure elucidation of the synthetic molecules (1–20) was carried out using different spectroscopic techniques, and their α-glucosidase inhibitory activity was also determined. The synthetic molecules 1–20 exhibited good α-glucosidase inhibition than the parent, nitrofurazone. Four compounds 2, 4, 6, and 7 showed potential inhibition against α-glucosidase with IC₅₀ values ranging between 0.63 ± 0.25–1.29 ± 0.46 µM as compared to the standard acarbose (IC₅₀ = 2.05 ± 0.41 µM). Nevertheless, compounds 15 (IC₅₀ = 0.74 ± 0.12 µM), and 19 (IC₅₀ = 0.54 ± 0.3 µM) also displayed good α-glucosidase inhibition and compound 19 was the most active compound of the series. Kinetic study of the active compounds 7 and 19 was also carried out to confirm the mode of inhibition. The binding interactions of the most active compounds within the active site of enzyme were determined by molecular docking. Moreover, molecular dynamic simulation of compound 19 was also performed in order to determine the stability of the overall complex (α-glucosidase + c19) in an explicit watery environment. The synthetic molecules were predicted as non-cytotoxic, however, seven compounds 1, 3, 4, 9, 10, 11, and 12 were predicted as carcinogenic.     

The chemist’s concept of molecular structure

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.

Water Soluble Nickel – metformin ternary complexes: Thermal,DNA binding and molecular docking studies

The Nickel (II) complexes [Ni(Cl)₂(metf)(o-phen)] (1), [Ni(Cl)₂(metf)(opda)] (2) , [Ni(Cl)₂(metf)(en)] (3) , [Ni(Cl)₂(metf)(2,2'-bipy)] (4) , (metf = metformin, o-phen = ortho-phenanthroline, opda = ortho-phenylenediamine, en = ethylenediamine, 2–2′ bipy = 2–2′ bipyridyl) were synthesized and characterized using LC–MS, elemental analysis, molar conductance measurements, TGA-DTA, IR spectroscopy, magnetic moment measurements and electronic spectroscopy. The central Ni²⁺ was found to be in octahedral geometry. The DNA interaction of these complexes have been studied by UV–visible absorption studies, fluorescence emission technique and viscosity measurement. The complexes showed absorption hyperchromism in UV–visible spectra with calf thymus DNA. The binding constants from UV–visible absorption studies were 7.42 × 10⁴, 0.74 × 10⁴, 3.19 × 10⁴, 5.9 × 10⁴ M⁻¹ for 1 , 2 , 3 and 4 , respectively and Stern-Volmer quenching constants from fluorescence studies were 0.16, 0.41, 0.23, 0.18, respectively. Viscosity measurements revealed that the binding of the complexes with DNA could be surface binding, mainly due to groove binding. The highest DNA cleavage activity of the complexes is recorded for complex 1 . The complexes were docked in to B-DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP* GP*TP*CP*GP*GP*T)-3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software. C Docker Intectraction energy of 1 , 2 , 3 and 4 complexes is 32.027, 31.427, 35.393 and 30.521 respectively. The highest docking score is seen for complex 3 .     

In vitro antioxidant activities of five β-carboline alkaloids,molecular docking,and dynamic simulations

Structural Chemistry - Experimental and computational studies were performed to determine the antioxidant activities of harmine, harmaline, harmalol, harmane, and...