LINGO-DL: a text-based approach for molecular similarity searching

Journal of Computer-Aided Molecular Design - The line notations of chemical structures are more compact than those of graphs and connection tables, so they can be useful for storing and...     

Supramolecular structure,spectroscopic, thermal studies and antimicrobial activities of Schiff base complexes

Metal(II) complexes of 4-(((2-hydroxynaphthalen-1-yl)methylene)amino)-1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one (HL) were prepared, and their compositions and physicochemical properties were characterized on the basis of elemental analysis, with¹HNMR, UV–Vis, IR, mass spectroscopy and thermogravimetric analysis. All results confirm that the novel complexes have a 1:1 (M:HL) stoichiometric formulae [M(HL)Cl₂] (M = Cu(II)(1), Cd(II)(5)), [Cu(L)(O₂NO)(OH₂)₂](2), [Cu(HL)(OSO₃)(OH₂)₃]2H₂O(3), [Co(HL)Cl₂(OH₂)₂]3H₂O(4), and the ligand behaves as a neutral/monobasic bidentate/tridentate forming a five/six-membered chelating ring towards the metal ions, bonding through azomethine nitrogen, exocyclic carbonyl oxygen, and/or deprotonated phenolic oxygen atoms. The XRD studies show that both the ligand and Cu(II) complex (1) show polycrystalline with monoclinic crystal structure. The molar conductivities show that all the complexes are non-electrolytes. On the basis of electronic spectral data and magnetic susceptibility measurements, a suitable geometry has been proposed. The trend in g values (g _ll > g _⊥ > 2.0023) suggest that the unpaired electron on copper has a \(d_{{x^{2} - y^{2} }}\) character, and the complex (1) has a square planar, while complexes (2) and (3) have a tetragonal distorted octahedral geometry. The molecular and electronic structures of the ligand (HL) and its complexes (1–5) have been discussed. Molecular docking was used to predict the binding between HL ligand and the receptors of the crystal structure of Escherichia coli (E. coli) (3t88) and the crystal structure of Staphylococcus aureus (S. aureus) (3q8u). The activation thermodynamic parameters, such as activation energy (E _a), enthalpy (ΔH), entropy (ΔS), and Gibbs free energy change of the decomposition (ΔG) are calculated using Coats–Redfern and Horowitz–Metzger methods. The ligand and its metal complexes (1–5) showed antimicrobial activity against bacterial species such as Gram positive bacteria (Bacillus cereus and S. aureus), Gram negative bacteria (E. coli and Klebsiella pneumoniae) and fungi (Aspergillus niger and Alternaria alternata); the complexes exhibited higher activity than the ligand.     

Solving Euclidean Distance Matrix Completion Problems Via Semidefinite Programming

Given a partial symmetric matrix A with only certain elements specified, the Euclidean distance matrix completion problem (EDMCP) is to find the unspecified elements of A that make A a Euclidean distance matrix (EDM). In this paper, we follow the successful approach in [20] and solve the EDMCP by generalizing the completion problem to allow for approximate completions. In particular, we introduce a primal-dual interior-point algorithm that solves an equivalent (quadratic objective function) semidefinite programming problem (SDP). Numerical results are included which illustrate the efficiency and robustness of our approach. Our randomly generated problems consistently resulted in low dimensional solutions when no completion existed.     

Anti-virulence strategy against Brucella suis: synthesis, biological evaluation and molecular modeling of selective histidinol dehydrogenase inhibitors

In the facultative intracellular pathogen Brucella suis, histidinol dehydrogenase (HDH) activity, catalyzing the last step in histidine biosynthesis, is essential for intramacrophagic replication. The inhibition of this virulence factor by substituted benzylic ketones was a proof of concept that disarming bacteria leads to inhibition of intracellular bacterial growth in macrophage infection. This work describes the design, synthesis and evaluation of 19 new potential HDH inhibitors, using a combination of classical approaches and docking studies. The IC(50)-values of these inhibitors on HDH activity were in the nanomolar range, and several of them showed a 70-100% inhibition of Brucella growth in minimal medium. One selected compound yielded a strong inhibitory effect on intracellular replication of B. suis in human macrophages at concentrations as low as 5 μM, with an overall survival of intramacrophagic bacteria reduced by a factor 10(3). Docking studies with two inhibitors showed a good fitting in the catalytic pocket and also interaction with the second lipophilic pocket binding the cofactor NAD(+). Experimental data confirmed competition between inhibitors and NAD(+) at this site. Hence, these inhibitors can be considered as promising tools in the development of novel anti-virulence drugs.     

New fragment weighting scheme for the Bayesian inference network in ligand-based virtual screening

Many of the conventional similarity methods assume that molecular fragments that do not relate to biological activity carry the same weight as the important ones. One possible approach to this problem is to use the Bayesian inference network (BIN), which models molecules and reference structures as probabilistic inference networks. The relationships between molecules and reference structures in the Bayesian network are encoded using a set of conditional probability distributions, which can be estimated by the fragment weighting function, a function of the frequencies of the fragments in the molecule or the reference structure as well as throughout the collection. The weighting function combines one or more fragment weighting schemes. In this paper, we have investigated five different weighting functions and present a new fragment weighting scheme. Later on, these functions were modified to combine the new weighting scheme. Simulated virtual screening experiments with the MDL Drug Data Report (23) and maximum unbiased validation data sets show that the use of new weighting scheme can provide significantly more effective screening when compared with the use of current weighting schemes.     

Synthesis and physico-chemical properties of some Ni(II) complexes with isatin-hydrazones

New Ni(II) complexes with bioactive bishydrazones ligands based on (pyridine-2-carboxaldhyde)-3-isatin, (2-acetylpyridine)-3-isatin, and (2-benzoylpyridine)-3-isatin have been synthesized and characterized by elemental analysis, conductivity measurements, IR and UV-Vis spectroscopy, and thermal analysis. The complexes stoichiometry and formation constants have been determined. The results suggest that isatinbishydrazones act as neutral tridentate ligands with ONN sites coordinating to the metal ion via isatin C=O, azomethine CR=N, and pyridine C=N groups to give [Ni(L)H₂O]Cl₂·2H₂O, (L = neutral tridentate isatin hydrazone ligand). Kinetics and thermodynamic parameters of the complexes thermal decomposition have been elucidated from the thermal data using Coats and Redfern method, which has confirmed the first order kinetics.     

Retracted: Acid‐Catalyzed Aquation of Ni(II)‐Hydrazone Complexes: Kinetics and Solvent Effect

Complexes of the type [Ni(L)(H₂O)]Cl₂·nH₂O, where L = 2‐pyridyl‐3‐isatinbishydrazone ligands, have been synthesized and characterized on the bases of elemental analysis, molar conductance, IR, electronic spectra, and thermal analysis (TGA and DTA). Acid‐catalyzed aquation of the Ni(II) isatin‐bishydrazone complexes was followed spectrophotometrically in various water–methanol and water–acetone mixtures at temperature 298 K. Kinetic behavior of the acid aquation is a linear rate law, indicating that the acid‐catalyzed aquation of these complexes in water–methanol and water–acetone mixtures follows a rate law with k_obs = k₂[H⁺]. The effect of the mole fraction of the ganic solvent, i.e., methanol and acetone, on the acid aquation has been analyzed; the decrease in the rate constant values with increasing of the methanol or acetone ratios is attributable to the effect of the co‐organic solvent on the initial states of the acid aquation by the destabilization of the H⁺ ion.