Comparative antibacterial analysis of the anthraquinone compounds based on the AIM theory, molecular docking, and dynamics simulation analysis

[1]  Guosong Chen,et al.  Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. , 2022, Journal of the American Chemical Society.

[2]  M. Wójcik,et al.  Intermolecular hydrogen bonds interactions in water clusters of ammonium sulfamate: FTIR, X-ray diffraction, AIM, DFT, RDG, ELF, NBO analysis , 2021, Journal of Molecular Liquids.

[3]  G. T. Feliciano,et al.  Atomic and Electronic Structure of Pilus from Geobacter sulfurreducens through QM/MM Calculations: Evidence for Hole Transfer in Aromatic Residues. , 2021, The journal of physical chemistry. B.

[4]  D. Klostermeier,et al.  What makes a type IIA topoisomerase a gyrase or a Topo IV? , 2021, Nucleic acids research.

[5]  D. Gong,et al.  Binding mechanism of 4-octylphenol with human serum albumin: Spectroscopic investigations, molecular docking and dynamics simulation. , 2021, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[6]  Xiche Hu,et al.  Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors , 2021, Molecules.

[7]  D. Klostermeier Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors , 2021, Molecules.

[8]  C. Stevenson,et al.  Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds , 2021, Nature communications.

[9]  Y. Mabkhot,et al.  Synthesis, crystal structure, hirshfeld surface analysis, DFT calculations, anti-diabetic activity and molecular docking studies of (E)-N’-(5-bromo-2-hydroxybenzylidene) isonicotinohydrazide , 2020, Journal of Molecular Structure.

[10]  Xiaoming Cui,et al.  Effects of Rhein-8-O-β-D-glucopyranoside on the Biofilm Formation of Streptococcus mutans , 2020, Current microbiology.

[11]  I. Turel,et al.  Synthesis, Characterization, Catalytic Activity, and DFT Calculations of Zn(II) Hydrazone Complexes , 2020, Molecules.

[12]  T. Roisnel,et al.  Synthesis, experimental, theoretical study and molecular docking of 1-ethylpiperazine-1,4-diium bis(nitrate) , 2020 .

[13]  A. Kazachenko,et al.  Intermolecular hydrogen bond interactions in the thiourea/water complexes (Thio-(H2O)n) (n = 1, …, 5): X-ray, DFT, NBO, AIM, and RDG analyses , 2020, Journal of Molecular Modeling.

[14]  A. Amro,et al.  New antimicrobial and cytotoxic benzofuran glucoside from Senecio glaucus L , 2020, Natural product research.

[15]  D. Sriram,et al.  Design, synthesis and biological evaluation of novel Pseudomonas aeruginosa DNA gyrase B inhibitors. , 2020, Bioorganic chemistry.

[16]  H. Tandon,et al.  A model of atomic compressibility and its application in QSAR domain for toxicological property prediction , 2019, Journal of Molecular Modeling.

[17]  Naihong Chen,et al.  Physcion and physcion 8-O-β-glucopyranoside: A review of their pharmacology, toxicities and pharmacokinetics. , 2019, Chemico-biological interactions.

[18]  T. Roisnel,et al.  A proton transfer compound template phenylethylamine: Synthesis, a collective experimental and theoretical investigations , 2019, Journal of Molecular Structure.

[19]  S. Muthu,et al.  Computational evaluation of the reactivity and pharmaceutical potential of an organic amine: A DFT, molecular dynamics simulations and molecular docking approach , 2019, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy.

[20]  J. Ilaš,et al.  Synthesis and Evaluation of N‐Phenylpyrrolamides as DNA Gyrase B Inhibitors , 2018, ChemMedChem.

[21]  J. Hohmann,et al.  Antibacterial screening of Rumex species native to the Carpathian Basin and bioactivity-guided isolation of compounds from Rumex aquaticus. , 2017, Fitoterapia.

[22]  K. Park,et al.  Potent bacterial neuraminidase inhibitors, anthraquinone glucosides from Polygonum cuspidatum and their inhibitory mechanism. , 2016, Journal of ethnopharmacology.

[23]  L. Domingo Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry , 2016, Molecules.

[24]  Kunming Qin,et al.  Profiling and analysis of multiple compounds in rhubarb decoction after processing by wine steaming using UHPLC-Q-TOF-MS coupled with multiple statistical strategies. , 2016, Journal of separation science.

[25]  Ralf Blossey,et al.  Molecular docking as a popular tool in drug design, an in silico travel , 2016, Advances and applications in bioinformatics and chemistry : AABC.

[26]  Yan Song,et al.  A theoretical study of the electronic structure and charge transport properties of thieno[2,3-b]benzothiophene based derivatives. , 2016, Physical chemistry chemical physics : PCCP.

[27]  S. Andujar,et al.  Conformational transition of Aβ42 inhibited by a mimetic peptide. A molecular modeling study using QM/MM calculations and QTAIM analysis , 2016 .

[28]  Ruiqin Q. Zhang,et al.  Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory , 2016, Journal of Molecular Modeling.

[29]  M. A. Azam,et al.  Dual targeting DNA gyrase B (GyrB) and topoisomerse IV (ParE) inhibitors: A review. , 2015, Bioorganic chemistry.

[30]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[31]  N. Prabavathi,et al.  Quantum chemical calculations on elucidation of molecular structure and spectroscopic insights on 2-amino-4-methoxy-6-methylpyrimidine and 2-amino-5-bromo-6-methyl-4-pyrimidinol--a comparative study. , 2015, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[32]  P. Kumaradhas,et al.  A combined molecular docking and charge density analysis is a new approach for medicinal research to understand drug-receptor interaction: curcumin-AChE model. , 2015, Chemico-biological interactions.

[33]  A. Becke Perspective: Fifty years of density-functional theory in chemical physics. , 2014, The Journal of chemical physics.

[34]  Arlan da Silva Gonçalves,et al.  Reactivation steps by 2-PAM of tabun-inhibited human acetylcholinesterase: reducing the computational cost in hybrid QM/MM methods , 2014, Journal of biomolecular structure & dynamics.

[35]  T. Tomašič,et al.  Prospects for developing new antibacterials targeting bacterial type IIA topoisomerases. , 2013, Current topics in medicinal chemistry.

[36]  P. Kumaradhas,et al.  Molecular flexibility and the electrostatic moments of curcumin and its derivatives in the active site of p300: a theoretical charge density study. , 2013, Chemico-biological interactions.

[37]  P. Kumaradhas,et al.  Exploring the conformation, charge density distribution and the electrostatic properties of galanthamine molecule in the active site of AChE using DFT and AIM theory , 2013 .

[38]  P. Kumaradhas,et al.  Exploring the charge density distribution and the electrical characteristics of Oligo phenylene ethylene molecular nanowire using quantum chemical and charge density analysis , 2012 .

[39]  Tian Lu,et al.  Quantitative analysis of molecular surface based on improved Marching Tetrahedra algorithm. , 2012, Journal of molecular graphics & modelling.

[40]  V. Baboo,et al.  Molecular structure, spectral studies, intra and intermolecular interactions analyses in a novel ethyl 4-[3-(2-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate and its dimer: A combined DFT and AIM approach. , 2012, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[41]  M. Shamsipur,et al.  Combined fluorescence spectroscopy and molecular modeling studies on the interaction between harmalol and human serum albumin. , 2012, Journal of pharmaceutical and biomedical analysis.

[42]  P. Kumaradhas,et al.  Understanding the charge density distribution and the electrostatic properties of hexadecane molecular nanowire under electric field using DFT and AIM theory , 2012 .

[43]  D. Turk,et al.  Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA gyrase inhibitors. , 2012, Journal of medicinal chemistry.

[44]  Tian Lu,et al.  Multiwfn: A multifunctional wavefunction analyzer , 2012, J. Comput. Chem..

[45]  B. Martin,et al.  Benzobisoxazole cruciforms: heterocyclic fluorophores with spatially separated frontier molecular orbitals. , 2011, The Journal of organic chemistry.

[46]  Peter Politzer,et al.  The electrostatic potential: an overview , 2011 .

[47]  W. Kong,et al.  The diarrhoeogenic and antidiarrhoeal bidirectional effects of rhubarb and its potential mechanism. , 2011, Journal of ethnopharmacology.

[48]  H. Eslami,et al.  Molecular dynamics simulation with weak coupling to heat and material baths. , 2010, The Journal of chemical physics.

[49]  C. Jin,et al.  Microcalorimetric assay on the antimicrobial property of five hydroxyanthraquinone derivatives in rhubarb (Rheum palmatum L.) to Bifidobacterium adolescentis. , 2010, Phytomedicine : international journal of phytotherapy and phytopharmacology.

[50]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[51]  E. Davidson,et al.  Koopmans' theorem in the restricted open-shell Hartree-Fock method. 1. A variational approach. , 2009, The journal of physical chemistry. A.

[52]  C. Suresh,et al.  Theoretical studies on the carcinogenic activity of diol epoxide derivatives of PAH: proton affinity and aromaticity as decisive descriptors. , 2008, Organic & biomolecular chemistry.

[53]  Yan Sun,et al.  Identification of Natural Compounds with Anti-Hepatitis B Virus Activity from Rheum palmatum L. Ethanol Extract , 2007, Chemotherapy.

[54]  R. Brüschweiler,et al.  Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks:  Application to the AMBER99SB Force Field. , 2007, Journal of chemical theory and computation.

[55]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[56]  J. Murray,et al.  Electrostatic Potentials: Chemical Applications , 2002 .

[57]  L. Nilsson,et al.  Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .

[58]  J. Champoux DNA topoisomerases: structure, function, and mechanism. , 2001, Annual review of biochemistry.

[59]  R. Bader Atoms in molecules : a quantum theory , 1990 .

[60]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[61]  M. Gellert,et al.  DNA gyrase: an enzyme that introduces superhelical turns into DNA. , 1976, Proceedings of the National Academy of Sciences of the United States of America.