YETI: An interactive molecular mechanics program for small-molecule protein complexes

YETI, an interactive molecular mechanics program for drug-design applications on small-molecule protein complexes, is described. To model short-range interactions in better agreement with experimental data, its force-field energy expression includes directional potential functions for H-bonds, salt linkages, and metal ligand interactions. The program works on an internal coordinate concept and uses a conjugate-gradient minimizer. YETI is available for distribution through the author. The program has been used to model details of small-molecule binding to the enzyme human carbonic anhydrase I. The impact of the directional potential functions on the geometry of H-bonds and metal-ligand interactions is discussed.     

Ruthenium half-sandwich complexes as protein kinase inhibitors: derivatization of the pyridocarbazole pharmacophore ligand

A general route to ruthenium pyridocarbazole half-sandwich complexes is presented and applied to the synthesis of sixteen new compounds, many of which have modulated protein kinase inhibition properties. For example, the incorporation of a fluorine into the pyridine moiety increases the binding affinity for glycogen synthase kinase 3 by almost one order of magnitude. These data are supplemented with cyclic voltammetry experiments and a protein co-crystallographic study.     

Design of a functional protein for molecular recognition: specificity of ligand binding in a metal-assembled protein cavity probed by 19f NMR

A metal-assembled homotrimeric coiled coil based on the GCN4-p1 sequence has been designed that noncovalently binds hexafluorobenzene and other similar ligands in a hydrophobic cavity, created by making the core substitution Asn16Ala ([Fe(bpyGCN4-N16A)3]2+). The KD of binding of hexafluorobenzene with [Fe(bpyGCN4-N16A)3]2+ was observed to be 1.1(9) x 10(-4) M by diffusion NMR experiments. A control coiled coil with the core substitution Asn16Val ([Fe(bpyGCN4-N16V)3]2+) exhibited a significantly weaker association with hexafluorobenzene, providing evidence that even in the absence of structural data, benzene-like ligands bind in the cavity created by the Asn16Ala substitution. 19F NMR was employed to observe hexafluorobenzene binding and to monitor titrations with competing hydrophobic and polar ligands similar in size and shape to hexafluorobenzene. All hydrophobic ligands bound with greater affinity than the polar ligands in the hydrophobic core, although the cavity seems to be somewhat flexible in terms of the sizes of molecules it can accommodate. Thus 19F NMR has proved to be a useful spectral tool to probe molecular recognition in a hydrophobic cavity of a metal-assembled coiled coil.     

A novel approach to 2-arylated quinolines: electrocyclization of alkynyl imines via vinylidene complexes

[reaction: see text] Alkynyl imines underwent [4 + 2] electrocyclization in the presence of 20 mol % W(CO)(5)(THF) to give 2-arylated quinolines in good yields. A deuterium labeling study suggests that the reaction proceeds via a tungsten vinylidene complex.     

The structural basis for the specificity of pyridinylimidazole inhibitors of p38 MAP kinase

Background: The p38 mitogen-activated protein (MAP) kinase regulates signal transduction in response to environmental stress. Pyridinylimidazole compounds are specific inhibitors of p38 MAP kinase that block the production of the cytokines interleukin-1 β and tumor necrosis factor α, and they are effective in animal models of arthritis, bone resorption and endotoxin shock. These compounds have been useful probes for studying the physiological functions of the p38-mediated MAP kinase pathway.Results: We report the crystal structure of a novel pyridinylimidazole compound complexed with p38 MAP kinase, and we demonstrate that this compound binds to the same site on the kinase as does ATP. Mutagenesis showed that a single residue difference between p38 MAP kinase and other MAP kinases is sufficient to confer selectivity among pyridinylimidazole compounds.Conclusions: Our results reveal how pyridinylimidazole compounds are potent and selective inhibitors of p38 MAP kinase but not other MAP kinases. It should now be possible to design other specific inhibitors of activated p38 MAP kinase using the structure of the nonphosphorylated enzyme.     

Discovery of novel inhibitors of anti-apoptotic Bcl-2 proteins derived from Bim BH3 domain

The BH3 mimetics targeting the interaction between the BH3-only proteins and their prosurvival Bcl-2 family proteins have shown enormous potential as cancer therapeutics. Herein, seven analogues targeting anti-apoptotic Bcl-2 proteins derived from the Bim BH3 domain via sequence simplification and/or modification are described. The in vitro binding affinity on anti-apoptotic Bcl-2 proteins and cell killing activity were evaluated. The results showed that analogues could significantly bind to target proteins and exhibited anti-cancer effect against three cancer cell lines. Of particular interest were the analogue SM-5 (K_D=9.48 nmol/L for Bcl-2) and SM-6 (K_D=0.08 nmol/L for Bcl-x_L), which exhibited improved binding affinity compared with the lead Bim (K_D=16.90 nmol/L for Bcl-2 and 22.2 nmol/L for Bcl-x_L, respectively). These results indicated that the peptide sequence containing the four hydrophobic side chains occupying pockets within the BH3-recognition cleft of anti-apoptotic Bcl-2 proteins might be the minimum sequence required for the bioactivity and the active core region of Bim. Promising inhibitors of anti-apoptotic Bcl-2 proteins with high bioactivity might be designed based on the active core.     

Loading peptidyl-coenzyme A onto peptidyl carrier proteins: a novel approach in characterizing macrocyclization by thioesterase domains

Here we report a new experimental approach to characterize recombinant nonribosomal peptide cyclases that do not show activity with conventional N-acetylcysteamine (SNAC) substrates. To explore the great potential of these domains for the catalysis of cell-free cyclization reactions, the new strategy takes advantage of the direct interaction between the natural substrate where the peptide chain is attached to the phosphopantetheine arm of the peptidyl carrier protein (PCP) and the peptide cyclase. A prerequisite for this reaction is the promiscuity of the Bacillus subtilis phosphopantetheinyl transferase Sfp for loading chemically synthesized peptidyl-coenzyme A substrates instead of the smaller natural substrate coenzyme A (CoASH) onto apoPCP. With this novel method we were able to characterize the regioselectivity of branched-chain cyclization catalyzed by the fengycin cyclase, which displays no activity with peptidyl-SNAC substrates.     

A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

A kinetics study of ligand substitution reaction on dinuclear platinum complexes: Stochastic versus deterministic approach

The kinetics on a basic ligand substitution reaction on dinuclear platinum complexes [Pt(PEt₃)₂PhPt(PEt₃)₂]²⁺ and [Pt(PEt₃)₂PhCOPhPt(PEt₃)₂]²⁺ , with the ligands pyridine and 3-chloropyridine, is studied. This is a fundamental step in a self-assembly, and the time evolution has been observed with a new experimental technique, QASAP (quantitative analysis of self-assembly process), which is recently developed by Hiraoka's group. As a result of numerical calculations based on master equation, we succeed in specifying the reaction rate constants with a simple reaction model. In addition, the time evolutions of all the intermediate components produced and consumed in chemical reaction are revealed, including those unobserved in the experiments. The convergence behavior of the existence ratios of specific chemical species calculated with the stochastic algorithm method is compared with those obtained from deterministic formalism based on rate equations, revealing a clear dependence on the number of constituent molecules. © 2018 Wiley Periodicals, Inc.     

Computational basis for the design of PLK-2 inhibitors

Structural Chemistry - PLK-2 is a serine/threonine protein kinase and plays a crucial role in cell cycle regulation; due to its pivotal function, this enzyme is approved as cancer drug target. We...     

A novel approach for the synthesis of the peripheral benzodiazepine receptor ligand, PK11195

A new synthesis of the peripheral benzodiazepine receptor ligand, PK11195 has been developed in only six-steps using a Heck-type reaction and a Suzuki coupling to effect the key transformations. The flexibility of this new approach is demonstrated by the synthesis of an iodo-analogue of PK11195 prepared from the corresponding bromide using a copper catalysed aromatic Finkelstein reaction.     

Near infrared spectroscopy: A novel technique for classifying and characterizing polysulfone membranes

The industrial manufacture of membranes is well established at the present time. More than any other process, the production of ultrafiltration membranes by immersion or evaporation (phase inversion) precipitation techniques is one of the most common. In many cases, the macroscopic properties of the membranes are similar from one membrane to another and it is impossible to distinguish them, while they differ notably from the microscopic point of view. The aim of this work is to develop a method for the classification of polysulfone ultrafiltration membranes prepared either by immersion or evaporation. It also presents a classification of those membranes by thickness. For these purposes, near infrared spectroscopy (NIR) combined with chemometric techniques are attempted here for the first time in the area of membrane research. The NIR technique permits fast analytical measurement of membrane samples, together with the possibility of characterization in on-line mode, without destruction or invasion of the samples. This appears to be an excellent routine analysis for purposes of membrane classification. The membranes were prepared in our Universitat Autònoma de Barcelona (UAB) laboratory and, after obtaining the NIR spectra, principal component analysis (PCA) was used to describe the system. The second stage involved the application of a pattern recognition method: supervised independent modeling of class analogy (SIMCA) in order to classify unknown samples. Finally, the ultrafiltration membranes were classified in terms of the membrane preparation technique (immersion or evaporation). In addition, membranes prepared by immersion were classified by thickness.     

Receptor-based virtual ligand screening for the identification of novel CDC25 phosphatase inhibitors

CDC25 phosphatases play critical roles in cell cycle regulation and are attractive targets for anticancer therapies. Several small non-peptide molecules are known to inhibit CDC25, but many of them appear to form a covalent bond with the enzyme or act through oxidation of the thiolate group of the catalytic cysteine. Structure-based virtual ligand screening computations were performed with FRED, Surflex, and LigandFit, a compound collection of over 310,000 druglike molecules and the crystal structure of CDC25B in order to identify novel classes of ligands. In vitro experiments carried out on a selected list of 1500 molecules led to the discovery of 99 compounds able to inhibit CDC25B activity at 100 microM. Further docking computations were applied, allowing us to propose a binding mode for the most potent molecule (IC50 = 13 microM). Our best compounds represent promising new classes of CDC25 inhibitors that also exhibit antiproliferative properties.     

A multilayer screening approach toward the discovery of novel Pf-DHFR inhibitors

A small yet diverse xanthone library was build and computationally docked against wild type Pf-DHFR by Molegro Virtual Docker (MolDock). For analysis of results an integrated approach based on re-ranking, scaling (based on heavy atom counts), pose clustering and visual inspection was implemented. Standard methods such as self-docking (for docking), EF analysis, average rank determinations (for size normalization), and cluster quality indices (for pose clustering) were used for validation of results. Three compounds X5, X113A and X164B displayed contact footprints similar to the known inhibitors with good scores. Finally, 16 compounds were extracted from ZINC data base by similarity based screening, docking score and drug/lead likeness. Out of these 16 compounds, 11 displayed very close contact footprints to experimentally known inhibitors, indicating there potential utility in further drug discovery efforts.     

Porphyrazines as molecular scaffolds: flexible syntheses of novel multimetallic complexes

Reductive deselenation of selenodiazole-fused porphyrazines, followed by acylation of the resultant labile porphyrazinediamines, was used to prepare macrocycles bearing two Collins ligands, two oxamido residues, or two quinoline-2-carboxamido units. Peripheral coordination of copper(II) to the di-(quinoline-2-carboxamido)-porphyrazine gave a metal-linked face-to-face porphyrazine dimer array. Sequential derivatization of the two amino groups in the porphyrazinediamines was used to prepare mixed peripheral ligand systems including a dimetallic picolinamido-Schiff base porphyrazine. Such systems exhibit strong metal-metal spin coupling and are anticipated to be of value in the synthesis of novel electronic and magnetic materials.     

Crystal structures of molecular complexes of 2-chloro-11,11,12,12-tetracyanoanthraquinodimethane with benzene (1:1) and pyrene(2:1): A novel type of charge transfer complexes

X-Ray crystal studies of the titled molecular complexes have revealed the arrangement of parallel overlap between one of the benzene rings of the heavily deformed TCNAQ moiety and donor benzene and pyrene molecules, presumably attributable to the complex formation with weak charge transfer interactions.     

Electronic characteristics of an extensive series of ruthenium complexes with the non-innocent o-benzoquinonediimine ligand: A pedagogical approach

Density functional theory (DFT) calculations are carried out on an extensive series of ruthenium complexes with the non-innocent (redox active) o-benzoquinonediimine (bqdi) ligand, namely [Ru(WXYZ)(bqdi)]ⁿ⁺ where WXYZ are a range of spectator ligands including ammonia, phosphines, 2,2′-bipyridine, 2,2′,2″-terpyridine, carbon monoxide, water, halide, acetonitrile, triazacyclononane, nitrosyl, cyclam, etc. In addition, a smaller series, Ru(acac)₂(R-bqdi) is explored, where acac = 2,4-pentanedionate, and R = H, Cl, Me, NO₂ and N-SO₂Me. A range of properties including Mulliken and Natural population analysis (NPA) charges, Mayer bond orders (Ru–N, CN, CC, etc.), net σ-donation and net π-back donation, and percentage Ru 4dπ in the LUMO, are derived and correlated with experimental properties including oxidation and reduction potentials and ligand electrochemical parameters, E_L(L). The various properties are understood in terms of the primary involvement of π-back donation to the π*-LUMO of bqdi. Net π-back donation is derived from the contribution of the π*-LUMO (and higher virtual orbitals) of bqdi, to filled molecular orbitals of the complex. The question of whether these species should be considered exclusively as being represented as [Ru^IIL₄(bqdi)] or [Ru^IIIL₄(sqdi)] (sqdi = o-benzosemiquinonediimine) is briefly considered and evidence presented for the former electronic structure. This is written as a pedagogical treatise rather than a detailed research discussion of the electronic properties of these molecules.