Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Pyridazine derivatives. Part 40: Reactivity of 5-alkynylpyridazin-3(2H)-ones toward hydrochloric acid

5-Alkynylpyridazin-3(2H)-ones or 5-(2-chloroalkenyl)pyridazin-3(2H)-ones were isolated during the cleavage of the methoxymethyl group in a series of 5-alkynyl-2-methoxymethylpyridazin-3(2H)-ones by treatment with hydrochloric acid. The efficient and selective cleavage of the methoxymethyl group in these compounds can be performed under mild conditions by employing aluminium chloride.     

The role of steric and electronic interactions in the stereocontrol of the asymmetric 1,3-dipolar reactions of 5-ethoxy-3-p-(S)-tolylsulfinylfuran-2(5H)-ones with diazoalkanes: theoretical calculations and experimental evidences

The addition of diazomethane and diazoethane to (5S,SS)- and (5R,SS)-5-ethoxy-3-p-tolylsulfinylfuran-2(5H)-ones (1a and 1b) and their 4-methylderivatives (2a and 2b) proceeded in almost quantitative yields and complete regioselectivity. The observed pi-facial selectivity is determined by the configurations at both C-5 and the sulfinyl group, the later being the most important. The syn adducts were almost exclusively obtained from 1a and 2a in apolar solvents but the pi-facial selectivity was strongly decreased in more polar solvents. On the other hand, the major adducts from 1b and 2b were the anti ones and such predominance was slightly increased with solvent polarity. The exo-selectivity was complete in all the cases except for the anti approach to compounds 2a (in polar solvents) and 2b. The role of the sulfinyl group in this behavior was inferred by comparison of these results with those obtained in reactions of diazoalkanes with 5-methoxyfuran-2(5H)-one (3). Steric interactions seem to be the main ones responsible for the observed exo selectivity of reactions with diazoethane, but electronic factors, which can be modulated by the solvent, are also significant in the pi-facial selectivity control. DFT computational methods are able to correctly predict the reactivity, regioselectivity, and pi-facial selectivity exhibited by 5-alkoxyfuranones as well as their changes with the solvent polarity. A C-H.O hydrogen bond, involving the oxygen atom of the 5-alkoxy group at dipolarophiles and the endo-hydrogen atom at dipoles, seems to play a key role in the electronic interactions influencing the stereochemical course of these reactions.     

Synthesis,characterization and coordination chemistry of the new tetraazamacrocycle 4,10-dimethyl-1,4,7,10-tetraazacyclododecane-1,7-bis(methanephosphonic acid monoethyl ester) dipotassium salt

A new potentially hexadentate tetraazamacrocycle based on the cyclen skeleton has been synthesized and fully characterized. The macrocycle 4,10-dimethyl-1,4,7,10-tetraazacyclododecane-1,7-bis(methanephosphonic acid monoethyl ester) dipotassium salt (Me2DO2PME) contains mutually trans monoethyl ester phosphonate acid substituents on two nitrogen atoms, and trans methyl substituents on the other two nitrogen atoms. The protonation constants of this macrocycle and the stability constants of its complexes with Cu2+, Zn2+, Gd3+ and Ca2+ ions have been determined by pH potentiometric titrations. The protonation sequence of the macrocycle has been studied by 1H, 31P[1H] and 13C[1H] NMR spectroscopy: the first and second protonation steps take place at the methyl-substituted nitrogen atoms, while the third protonation involves one oxygen from a phosphonate group. Upon protonation, all the CH2 ring protons become magnetically inequivalent on the NMR time scale due to a slow conformational rearrangement, most likely occasioned by the formation of multiple hydrogen bonds within the macrocyclic ring. Me2DOPM forms neutral, mononuclear complexes with all the metals investigated. The presence of hydroxo complexes was observed for Ca2+ and Zn2+ at high pH values. Structural information on the neutral complex [Cu(Me2DO2PME)] has been obtained by a solution X-Band EPR study. It is proposed that Me2DO2PME binds Cu2+ in a distorted octahedral structure using all of its donor atoms, i.e. the four nitrogen atoms and the two phosphonate oxygen atoms. The redox chemistry of [Cu(Me2DO2PME)] in dimethyl sulfoxide and water has been studied by electrochemical measurements. Cyclic voltammetry in DMSO shows the complex to undergo a quasireversible one-electron reduction step leading to an unstable CuI species.     

Theoretical investigations on the solvation process

A model to facilitate the computation of the most stable conformer of associated M · H₂O (M being a polar molecule) which depends upon the electrostatic interaction energy between the two associated molecules is proposed and tested. SCF electrostatic potentials for the M molecule and a suitable point charge distribution for H₂O were employed in the model computations. Energies predicted by the model are found to be in good agreement with those resulting from an ab initio minimal STO basis SCF treatment of some conformations of the H₂O dimer.

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Zusammenfassung Ein Modell zur Durchführung der Berechnung des stabilsten Konformeren eines Assoziationskomplexes M · H₂O, wobei M ein polares Molekül ist, wird vorgeschlagen und untersucht. Es basiert auf der elektrostatischen Wechselwirkung zwischen beiden Partnern, und zwar wird für das Molekül M der elektrostatische Anteil seines SCF-Potentials und für H₂O eine angemessene Punktladungsverteilung zugrunde gelegt. Die resultierenden Energien sind in guter Übereinstimmung mit denen, die sich bei einer ab initio Rechnung mit minimaler STO Basis ergeben.

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Work performed with the financial support of the Consiglio Nazionale delle Ricerche, through its Laboratorio di Chimica Quantistica ed Energetica Molecolare.     

Cu+(H2) and Na+(H2) adducts in exchanged ZSM-5 zeolites

Cu(I) ions in Cu-ZSM-5 form Cu+(H2) complexes, stable at room temperature and sub-atmospheric H2 pressure, which do not have any homogeneous analogue except for matrix-isolated [Cu(eta2-H2)Cl]. Comparison with the unstable Na+(H2) adducts formed in the parent Na-ZSM-5 zeolite allow the conclusion that the Cu(I)/H2 bond is governed by sigma-pi overlap forces.     

UV stabilizers bonded to transition metals: Synthesis and X-ray structure of 2-(2′-hydroxyphenyl)benzotriazole-oxovanadium(IV) and -dioxomolybdenum(VI) complexes

The UV-stabilizer 2-(2′-hydroxy-5′-methylphenyl)benzotriazole (Tinuvin P, LH) has been used as a monoanionic bidentate ligand for complexing oxocations. Displacement of acacH from [VO(acac)₂] and [MoO₂(acac)₂] gave [*VO(acac)₂*(μ-L)] (2) and [cis-O₂Mo(acac)L] (3) respectively, as crystalline compounds. Their structure has been determined by an X-ray analysis showing the structural changes occurring upon coordination. The UV spectrum of Tinuvin P is significantly affected by complexation.     

Investigations of chromium(III), manganese(III), tin(II) and lead(II) dithiocarbamate complexes

Piperidine-, morpholine-4-, N-methylpiperazine-4- and thiornorpholine-4-carbodithioate complexes of chromium(III), manganese(III), tin(II) and lead(II) are prepared and characterized by chemical analyses, spectroscopic methods (I.R. and electronic spectra), magnetic susceptibilities, conductivity measurements and mass spectra. The complexes are of the type M(R₂dtc)n, where n is the oxidation number of the metal ion. Where possible a tentative stereochemistry of the complexes is discussed on the basis of the results obtained. In all the complexes the dithiocarbamate ligands show bidentate behaviour.     

Determination of the amino acid tryptophan and the biogenic amine tryptamine in foods by the heavy atom induced-room temperature phosphorescence methodology

Very simple and selective methods are presented to determine the amino acid tryptophan (Trp) and the biogenic amine tryptamine (Tryp), both compounds with an indole-type molecular structure by the methodology named Heavy Atom Induced-Room Temperature Phosphorescence (HAI-RTP) which constitutes the first time that HAI-RTP has been used to detect compounds with non-naphthalenic structures in their molecules. Different variables affecting the phosphorescence signal (heavy atom perturber and sodium sulfite concentration) were carefully studied. The analytical curves give a linear dynamic range of 15-100 ng ml(-1) and a detection limit of 4 ng ml(-1) for Trp and 94-400 ng ml(-1) and 28 ng ml(-1) for Tryp. The methods have been successfully applied to the analysis of complex food matrices such as the presence of tryptophan in yoghurt and tryptamine in bottled beer. A single alkaline hydrolysis to release Trp from yoghurt proteins and two methods for extracting Tryp from beer samples are proposed and optimised. A total Trp content of 374 mg of Trp per kg of yoghurt was quantified by the standard addition method of calibration and a recovery of 90% was obtained for 250 ng ml(-1) of Tryp in spiked non-alcoholic beer samples.     

Trapped electrons in substoichiometric MoO3 observed by X-ray electron spectroscopy

Substoichiometric amorphous thin films of MoO₃ in both the transparent and absorptive forms have been studied by X-ray electron spectroscopy. The transparent films can be colored blue (absorptive) electrically or by UV irradiation. The electron distribution curve of the blue film exhibits a small band near the Fermi edge which is absent in the transparent sample. This new band is attributed to electrons trapped in positively charged anion vacancies in the substoichiometric MoO₃ lattice. This model provides an interpretation of the electrical conductivity and color of the films.