Reaching multi‐nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling

We report an enhanced sampling technique that allows to reach the multi‐nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid–vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall‐clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc.     

Determinants for α4β2 vs. α3β4 Subtype Selectivity of Pyrrolidine-Based nAChRs Ligands: A Computational Perspective with Focus on Recent cryo-EM Receptor Structures

The selectivity of α4β2 nAChR agonists over the α3β4 nicotinic receptor subtype, predominant in ganglia, primarily conditions their therapeutic range and it is still a complex and challenging issue for medicinal chemists and pharmacologists. Here, we investigate the determinants for such subtype selectivity in a series of more than forty α4β2 ligands we have previously reported, docking them into the structures of the two human subtypes, recently determined by cryo-electron microscopy. They are all pyrrolidine based analogues of the well-known α4β2 agonist N-methylprolinol pyridyl ether A-84543 and differ in the flexibility and pattern substitution of their aromatic portion. Indeed, the direct or water mediated interaction with hydrophilic residues of the relatively narrower β2 minus side through the elements decorating the aromatic ring and the stabilization of the latter by facing to the not conserved β2-Phe119 result as key distinctive features for the α4β2 affinity. Consistently, these compounds show, despite the structural similarity, very different α4β2 vs. α3β4 selectivities, from modest to very high, which relate to rigidity/extensibility degree of the portion containing the aromatic ring and to substitutions at the latter. Furthermore, the structural rationalization of the rat vs. human differences of α4β2 vs. α3β4 selectivity ratios is here proposed.     

Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking,dynamics simulations,and MMGBSA

Antimicrobial resistance (AMR) threatens millions of people around the world and has been declared a global risk by the World Economic Forum. One of the important AMR mechanisms in Enterobacteriaceae is the production of extended-spectrum β-lactamases. The most common ESBL, CTX-M β-lactamases, is spread to the world by CTX-M-15 and CTX-M-14. Sulbactam, clavulanic acid, and tazobactam are first-generation β-lactamase inhibitors and avibactam is a new non-β-lactam β-lactamase inhibitor. We studied that avibactam, sulbactam, clavulanic acid, tazobactam, and quercetin natural flavonoids were docked to target protein CTXM-15. Subsequently, the complexes were simulated using the molecular dynamics simulations method during 100 ns for determining the final binding positions of ligands. Clavulanic acid left CTX-M-15 and other ligands remained in the binding site after the simulation. The estimated binding energies were calculated during 100 ns simulation by the MMGBSA-MMPBSA method. The estimated free binding energies of avibactam, sulbactam, quercetin, tazobactam, and clavulanic acid were sorted as –33.61 kcal/mol, –16.04 kcal/mol, –14 kcal/mol, –12.68 kcal/mol, and –2.95 kcal/mol. As a result of both final binding positions and free binding energy calculations, Quercetin may be evaluated an alternative candidate and a more potent β-lactamases inhibitor for new antimicrobial combinations to CTX-M-15. The results obtained in silico studies are predicted to be a preliminary study for in vitro studies for quercetin and similar bioactive natural compounds. These studies are notable for the discovery of natural compounds that can be used in the treatment of infections caused by β-lactamase-producing pathogens.     

How Mutations Affecting the Ligand-receptor Interactions:a Combined MD and QM/MM Calculation on CYP2E1 and Its Two Mutants

Cytochrome P450(CYP) 2E1 is a dual function monoxygenase with a crucial role in the metabolism of 6% of drugs on the market at present. The enzyme is of tremendous interest for its association with alcohol consumption, diabetes, obesity and fasting. Despite the abundant experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activity deficiencies have not been rationalized at the atomic level. In this regard, we have investigated the effects of mutation on the structural and energetic characteristics upon single point mutations in CYP2E1, N219D and S366C. The molecular dynamics(MD) simulation combined with quantum mechanics/molecular mechanics(QM/MM) and noncovalent interaction(NCI) analysis was carried out on CYP2E1 and its two mutants. The results highlight the critical role of Phe207, which is responsible for both structural flexibility and energetic variation, shortening the gap between the theory and the experimentally observed results of enzymatic activity decrease. The underlying molecular mechanism of the enzymatic activity deficiencies for mutants may be attributed to the changes of spatial position of Phe207 in the two mutants. This work provides particular explanations to how mutations affect ligand-receptor interactions based on combined MD and QM/MM calculations. Furthermore, the mutational effects on the activity of CYP2E1 obtained in the present study are beneficial to both the experimental and the computational works of CYPs and may allow researchers to achieve desirable changes in enzymatic activity.     

Establishing effective simulation protocols for β‐ and α/β‐peptides. III. Molecular mechanical model for acyclic β‐amino acids

All‐atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic β‐amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using β³‐homo‐Alanine (β³‐hAla) diamide in water with SCC‐DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC‐DFTB/MM results regarding the distribution of key dihedral angles for the β³‐hAla diamide in water. The MM model is further applied to a β‐hepta‐peptide in methanol solution. The calculated NOE values and ³J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non‐natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of β amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that β‐amino‐acid based random copolymers can develop a high degree of amphiphilicity without regular three‐dimensional structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Less is more when simulating unsulfated glycosaminoglycan 3D‐structure: Comparison of GLYCAM06/TIP3P,PM3‐CARB1/TIP3P,and SCC‐DFTB‐D/TIP3P predictions with experiment

The 3D‐structure of extracellular matrix glycosaminoglycans is central to function, but is currently poorly understood. Resolving this will provide insight into their heterogeneous biological roles and help to realize their significant therapeutic potential. Glycosaminoglycan chemical isoforms are too numerous to study experimentally and simulation provides a tractable alternative. However, best practice for accurate calculation of glycosaminoglycan 3D‐structure within biologically relevant nanosecond timescales is uncertain. Here, we evaluate the ability of three potentials to reproduce experimentally observed glycosaminoglycan monosaccharide puckering, disaccharide 3D‐conformation, and characteristic solvent interactions. Temporal dynamics of unsulfated chondroitin, chondroitin‐4‐sulfate, and hyaluronan β(1→3) disaccharides were simulated within TIP3P explicit solvent unrestrained for 20 ns using the GLYCAM06 force‐field and two semi‐empirical quantum mechanics methods, PM3‐CARB1 and SCC‐DFTB‐D (both within a hybrid QM/MM formalism). Comparison of calculated and experimental properties (vicinal couplings, nuclear Overhauser enhancements, and glycosidic linkage geometries) showed that the carbohydrate‐specific parameterization of PM3‐CARB1 imparted quantifiable benefits on monosaccharide puckering and that the SCC‐DFTB‐D method (including an empirical correction for dispersion) best modeled the effects of hexosamine 4‐sulfation. However, paradoxically, the most approximate approach (GLYCAM06/TIP3P) was the best at predicting monosaccharide puckering, 3D‐conformation, and solvent interactions. Our data contribute to the debate and emerging consensus on the relative performance of these levels of theory for biological molecules. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

A novel series of M(II) complexes of 6‐methylpyridine‐2‐carboxylic acid with 4(5)methylimidazole: Synthesis,crystal structures, α‐glucosidase activity,density functional theory calculations and molecular docking

Novel complexes of 6‐methylpyridine‐2‐carboxylic acid and 4(5)methylimidazole, namely [Mn(6‐mpa)₂(4(5)MeI)₂] ( 1 ), [Zn(6‐mpa)₂(4(5)MeI)₂] ( 2 ), [Cd(6‐mpa)₂(4(5)MeI)₂] ( 3 ), [Co(6‐mpa)₂(4(5)MeI)₂] ( 4 ), [Ni(6‐mpa)₂(4(5)MeI)(OAc)] ( 5 ) and [Cu(6‐mpa)₂(4(5)MeI)] ( 6 ), were synthesized for the first time. The structures of complexes 1 – 4 and complexes 5 and 6 were determined using X‐ray diffraction and mass spectrometric techniques, respectively. The experimental spectral analyses for these complexes were performed using Fourier transform infrared and UV–visible techniques. The α‐glucosidase inhibition activity values (IC₅₀) of complexes 1 – 6 were identified in view of genistein reference compound. Moreover, the DFT/HSEh1PBE/6‐311G(d,p)/LanL2DZ level was used to obtain optimal molecular geometry and vibrational wavenumbers for complexes 1 – 6 . Electronic spectral behaviours and major contributions to the electronic transitions were investigated using TD‐DFT/HSEh1PBE/6‐311G(d,p)/LanL2DZ level with conductor‐like polarizable continuum model and SWizard program. Finally, in order to investigate interactions between the synthesized complexes ( 1 – 6 ) and target protein (template structure S. cerevisiae isomaltase), a molecular docking study was carried out.     

Design,Synthesis, and Evaluation of 3‐((4‐(t‐Butyl)‐2‐(2‐benzylidenehydrazinyl)thiazol‐5‐yl)methyl)quinolin‐2(1H)‐ones as Neuraminidase Inhibitors

A series of novel 3‐((4‐(t‐butyl)‐2‐(2‐benzylidenehydrazinyl)thiazol‐5‐yl)methyl)quinolin‐2(1H)‐ones ( 7a – 7z ) were designed, synthesized and evaluated for their ability of inhibiting neuraminidase (NA) of in?uenza H1N1 virus. Some compounds displayed moderate influenza NA inhibitory activity. Compound 7l with the scaffold of 2‐(2‐(2‐methoxybenzylidene)hydrazinyl)thiazole was the best one, exhibiting moderate NA inhibitory activity with IC₅₀ of 44.66 µmol/L. Structure‐activity relationship showed that compounds with methoxy or hydroxy groups at the ortho position, fluorine and nitro groups at the meta position and chlorine and bromine groups at the para position of phenyl ring were more active. Docking study indicated that compound 7l has important interactions with some key residues (including Asp151, Glu119, Arg292, Tyr406, and Asn347) and binds to 430‐cavity adjacent to NA active site.     

Synthesis and Fungicidal Activity of (E)‐5‐[1‐(2‐Oxo‐1‐oxaspiro[4,5]dec/non‐3‐en‐3‐yl)ethylidene]‐2‐aminoimidazolin‐4‐one Derivatives

The novel fungicidal agents, (E )‐5‐[1‐(2‐oxo‐1‐oxaspiro[4,5]dec/non‐3‐en‐3‐yl)ethylidene]‐2‐aminoimidazolin‐ 4‐one derivatives, were designed and synthesized in moderate to excellent yields in four steps using α ‐hydroxyketone and diketene as raw materials and characterized by HR‐ESI‐MS , ¹H NMR and X‐ray diffraction. The preliminary bioassay showed that some of these compounds, such as 5e , 6a , 6e , and 7 h exhibit 87.8%, 91.3%, 89.9% and 87.8% inhibition rates against Sclerotinia scleotiorum , 3b , 3c , 4c and 7 h exhibit 96.4%, 92.5%, 90.3% and 76.9% inhibition rates against Phytophthora capsici at the concentration of 50 µg/mL , respectively. These compounds exhibited significant fungicidal activities against S. scleotiorum and P. capsici with EC₅₀ values of 2.56–11.60 µg/mL , and compounds 6e and 7 h exhibited weak inhibition against the spore germination of S. scleotiorum , while the spore germination of P. capsici was strongly inhibited by compound 7 h solution. Scanning electron microscopy (SEM ) and transmission electron microscopy (TEM ) observation indicated that compound 7 h had a significant impact on the structure and function of the hyphal cell wall of P. capsici mycelium.     

Bioactivity‐integrated ultra‐performance liquid chromatography/quadrupole time‐of‐flight mass spectrometry for the identification of nuclear factor‐κB inhibitors and β2 adrenergic receptor agonists in Chinese medicinal preparation Chuanbeipipa dropping pills

A simple and dual‐target method based on ultra‐performance liquid chromatography/quadrupole time‐of‐flight mass spectrometry combined with dual‐bioactive [nuclear factor‐κB (NF‐κB) and β₂‐adrenergic receptor] luciferase reporter assay systems was developed to rapidly characterize the chemical structure of various bioactive compounds of TCM preparations. Chuanbeipipa dropping pills, a traditional Chinese medicine preparation used for the clinical therapy of chronic obstructive lung disease and cough caused by bronchial catarrh, was analyzed with this method. Potential anti‐inflammatory and spasmolytic constituents were screened using NF‐κB and β₂‐adrenergic receptor activity luciferase reporter assay systems and simultaneously identified according to the time‐of‐flight mass spectrometry data. One β₂‐adrenergic receptor agonist (ephedrine) and two structural types of NF‐κB inhibitors (platycosides derivatives and ursolic acid derivatives) were characterized. Platycodin D3 and E were considered new NF‐κB inhibitors. Further cytokine and chemokine detection confirmed the anti‐inflammatory effects of the potential NF‐κB inhibitors. Compared with conventional fingerprints, activity‐integrated fingerprints that contain both chemical and bioactive details offer a more comprehensive understanding of the chemical makeup of plant materials. This strategy clearly demonstrated that multiple bioactivity‐integrated fingerprinting is a powerful tool for the improved screening and identification of potential multi‐target lead compounds in complex herbal medicines. Copyright © 2013 John Wiley & Sons, Ltd.     

Polymerization of 2‐pentene with Ni(II) α‐diimine complex/M‐MAO catalyst and structure of the polymer

Polymerization of 2‐pentene with [ArN?C(An)C(An)·NAr)NiBr₂ (Ar?2,6‐iPr₂C₆H₃)] ( 1‐Ni) /M‐MAO catalyst was investigated. A reactivity between trans‐2‐pentene and cis‐2‐pentene on the polymerization was quite different, and trans‐2‐pentene polymerized with 1‐Ni /M‐MAO catalyst to give a high molecular weight polymer. On the other hand, the polymerization of cis‐2‐butene with 1‐Ni /M‐MAO catalyst did not give any polymeric products. In the polymerization of mixture of trans‐ and cis‐2‐pentene with 1‐Ni /M‐MAO catalyst, the M_n of the polymer increased with an increase of the polymer yields. However, the relationship between polymer yield and the M_n of the polymer did not give a strict straight line, and the M_w/M_n also increased with increasing polymer yield. This suggests that side reactions were induced during the polymerization. The structures of the polymer obtained from the polymerization of 2‐ pentene with 1‐Ni /M‐MAO catalyst consists of ? CH₂? CH₂? CH(CH₂CH₃)? , ? CH₂? CH₂? CH₂? CH(CH₃)? , ? CH₂? CH(CH₂CH₂CH₃)? , and methylene sequence ? (CH₂)_n? (n ≥ 5) units, which is related to the chain walking mechanism. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2858–2863, 2008     

Syntheses,Crystal Structures,and Photocatalytic Activities of Three Copper Coordination Polymers Based on Bis(1H‐imidazol‐4‐yl)benzene/3‐(2‐Pyridyl)pyrazole

Three copper(II) coordination polymers (CuCPs), namely, [Cu_0.5(1,4‐bib)(SO₄)_0.5]_n ( 1 ), {[Cu(1,3‐bib)₂(H₂O)] · SO₄ · H₂O}_n ( 2 ), and [Cu(bpz)(SO₄)_0.5]_n ( 3 ), were assembled from the reaction of three N‐donors [1,4‐bib = 1,4‐bis(1H‐imidazol‐4‐yl)benzene, 1,3‐bib = 1,3‐bis(1H‐imidazol‐4‐yl)benzene, and Hbpz = 3‐(2‐pyridyl)pyrazole] with copper sulfate under hydrothermal conditions. Their structures were determined by single‐crystal X‐ray diffraction analyses and further characterized by elemental analyses (EA), IR spectroscopy, powder X‐ray diffraction (PXRD), and thermogravimetric analyses (TGA). Structure analyses reveal that complex 1 is a 3D 6‐connected {4¹² · 6³}‐ pcu net, complex 2 is a fourfold 3D 4‐connected 6⁶‐ dia net, whereas complex 3 is a 1D snake‐like chain, which further expanded into 3D supramolecular architectures with the help of C–H ··· O hydrogen bonds. Moreover, the photocatalytic tests demonstrate that the obtained CuCPs are photocatalysts in the degradation of MB with the efficiency is 86.4 % for 1 , 75.3 % for 2 , and 91.3 % for 3 after 2 h, respectively.     

Synthesis and Characterization of Mixed-Ligand Nickel(II) Chelates of β-Diones and α-Diimines. Crystal and Molecular Structure of [Ni(ncup)2Etacet]ClO4

A series of new nickel(II) perchlorate complexes containing an α-diimine(enR) and the anion of a β-dione (1,3-ketoenol or 1,3-ketoester, βH) was prepared and characterized. The composition and the overall structure of the new chelates depend on ligand concentration, on steric and electronic effects induced by substituents within the ligands and the ability of the perchlorate group to coordinate. The IR and electronic excitation spectra of [Ni(enR)₂β]ClO₄ and [Ni(enR)β(O₂ClO₂)] indicate, in conjunction with other physicochemical measurements, bidentate coordination of the ligands and replacement of the (O,O′) perchlorato group by basic solvents. The structure of the new chelates was further supported by an X-ray structure analysis of [Ni(ncup)₂Etacet]ClO₄, where ncup denotes neocuproine and Etacet the anion of the ethyl acetoacetate (orthorhombic, space group Pc2₁n, a = 14.087(5), b = 14.713(5) and c = 15.952(5) Å, Z = 4). The coordination sphere of nickel is a distorted octahedron, arised from the chromophore NiN₄O₂, in which the base is favored by three neocuproine nitrogens and one Etacet oxygen. The apical sites are occupied by the remaining oxygen and nitrogen atoms, one from Etacet and one from neocuproine respectively.     

Synthesis,characterization and catalytic performance of core‐shell structure magnetic Fe3O4/P(GMA‐EGDMA)‐NH2/HPG‐COOH‐Pd catalyst

A strategy has been developed for the synthesis, characterization and catalysis of magnetic Fe₃O₄/P(GMA‐EGDMA)‐NH₂/HPG‐COOH‐Pd core‐shell structure supported catalyst. The P(GMA‐EGDMA) polymer layer was coated on the surface of hollow magnetic Fe₃O₄ microspheres through the effect of KH570. The core‐shell magnetic Fe₃O₄/P(GMA‐EGDMA) modified by ‐NH₂ could be grafted with HPG. Then, the hyperbranched glycidyl (HPG) with terminal ‐OH were modified by ‐COOH and adsorbed Pd nanoparticles. The hyperbranched polymer layer not only protected the Fe₃O₄ magnetic core from acid–base substrate corrosion, but also provided a number of functional groups as binding sites for Pd nanoparticles. The prepared catalyst was characterized by UV–vis, TEM, SEM, FTIR, TGA, ICP‐OES, BET, XRD, DLS and VSM. The catalytic tests showed that the magnetic Fe₃O₄/P(GMA‐EGDMA)‐NH₂/HPG‐COOH‐Pd catalyst had excellent catalytic performance and retained 86% catalytic efficiency after 8 consecutive cycles.     

Study of E/Z isomerization of (arylamino)methylidenefuran‐2(3H)‐ones by 1H, 13C, 15N spectroscopy and DFT calculations in different solvents

The structure and configuration of the series of previously unknown arylaminomethylidenefuran‐2(3H)‐ones have been determined in solution by ¹H, ¹³C, ¹⁵N nuclear magnetic resonance spectroscopy including two‐dimensional experiments such as ¹H─¹H COSY, dqCOSY, ¹H─¹³C HSQC, ¹H─¹³C HMBC. It was found that synthesized substances exist as an equilibrium mixture of E‐ and Z‐enamines in solution. It was established on the basis of density functional theory calculations that the exchange between the two push–pull enamines is a simple rotation around an exocyclic partial double bond that depends on the effect of the solvents. Copyright © 2017 John Wiley & Sons, Ltd.