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Andrea Tafi

Publications and source records attributed to Andrea Tafi.

At least 19 recordsLinked to original sources
PubMed2006

Gas-phase enantioselectivity of chiral amido[4]resorcinarene receptors.

Diastereomeric proton-bound [1(L)HA]+ complexes between selected amino acids (A=phenylglycine (Phg), tryptophan (Trp), tyrosine methyl ester (TyrOMe), threonine (Thr), and allothreonine (AThr)) and a chiral amido[4]resorcinarene receptor (1(L)) display a significant enantioselectivity when undergoing loss of the amino acid guest A by way of the enantiomers of 2-aminobutanes (B) in the gas phase. The enantioselectivity of the B-to-A displacement is ascribed to a combination of thermodynamic and kinetic factors related to the structure and the stability of the diastereomeric [1(L)HA]+ complexes and of the reaction transition states. The results of the present and previous studies allow classification of the [1(L)HA]+ complexes in three main categories wherein: i) guest A does not present any additional functionalities besides the amino acid one (alanine (Ala), Phg, and phenylalanine (Phe)); ii) guest A presents an additional alcohol function (serine (Ser), Thr, and AThr); and iii) guest A contains several additional functionalities on its aromatic ring (tyrosine (Tyr), TyrOMe, Trp, and 3,4-dihydroxyphenylalanine (DOPA)). Each category exhibits a specific enantioselectivity depending upon the predominant [1(L)HA]+ structures and the orientation of the 2-aminobutane reactant in the relevant adducts observed. The results may contribute to the understanding of the exceptional selectivity and catalytic properties of enzyme mimics towards unsolvated biomolecules.

Amino Acids↗
PubMed2006

Pharmacophore based receptor modeling: the case of adenosine A3 receptor antagonists. An approach to the optimization of protein models.

To design and synthesize new potent and selective antagonists of the human A(3) adenosine receptor, pharmacophoric hypotheses were generated with the software Catalyst for a comprehensive set of compounds retrieved from previous literature. Three of these pharmacophores were used to drive the optimization of a molecular model of the receptor built by homology modeling. The alignment of the ligands proposed by Catalyst was then used to manually dock a set of known A(3) antagonists into the binding site, and as a result, the model was able to explain the different binding mode of very active compounds with respect to less active ones and to reproduce, with good accuracy, free energies of binding. The docking highlighted that the nonconserved residue Tyr254 could play an important role for A(3) selectivity, suggesting that a mutagenesis study on this residue could be of interest in this respect. The reliability of the whole approach was successfully tested by rational design and synthesis of new compounds.

Adenosine A3 Receptor Antagonists↗
PubMed2005

AMBER force field implementation of the boronate function to simulate the inhibition of beta-lactamases by alkyl and aryl boronic acids.

Boronic acids are a very appealing class of serine proteases inhibitors whose rational design suffers, in spite of their therapeutic potential, from the lack of boron-related parameters in force fields commonly used for proteins. We introduced bonded, non-bonded and point charges in the MacroModel/Amber force field, as well as GB/SA solvation parameters, to model boronic acids as tetrahedral adducts formed after protease's serine Ogamma coordination. With the aim to check the implemented force field, flexible docking studies were performed on three crystallographic complexes of beta-lactamases with boronic acids that output the crystallographic conformation of the complexes as the global minimum energy structure. Although the used approach was basic, nevertheless the resultant force field seems to be efficient and suitable for the structure-based design of new boronic inhibitors of beta-lactamases.

Boronic Acids↗
PubMed2005

Antifungal agents. 11. N-substituted derivatives of 1-[(aryl)(4-aryl-1H-pyrrol-3-yl)methyl]-1H-imidazole: synthesis, anti-Candida activity, and QSAR studies.

1-[(Aryl)(4-aryl-1H-pyrrol-3-yl)methyl]-1H-imidazoles were recently reported by our group as potent anti-Candida agents belonging to the antifungal azole class. In the present paper the synthesis, anti-Candida activities, and QSAR studies on a novel series of N-substituted 1-[(aryl)(4-aryl-1H-pyrrol-3-yl)methyl]-1H-imidazole derivatives are reported. The newly synthesized azoles were tested against 12 strains of Candida albicans together with bifonazole, miconazole, itraconazole, fluconazole, and compounds 1a, 1b, 3a, 3b, and 3c used as reference drugs. In general, tested derivatives showed good antifungal activities, and the most potent compound was 1d (MIC(90) = 0.032 microg/mL), which was from 4- to 250-fold more potent than reference drugs. Catalyst software was applied to develop a quantitative pharmacophore model to be used for the rational design of new antifungal azoles. Some key interactions, as well as excluded volumes, further to the coordination bond of azole antifungals with the demethylase enzyme, are highlighted.

Antifungal Agents↗
PubMed2005

Antimycobacterial compounds. Optimization of the BM 212 structure, the lead compound for a new pyrrole derivative class.

Our work on antitubercular agents led to the identification of BM 212 as a lead compound among a series of pyrrole derivatives with good in vitro activity against mycobacteria and candidae. Further studies led us to synthesize additional pyrroles bearing the thiomorpholinomethyl moiety and different aryl substituents at N1 and C5. Some of them revealed very active, prompting us to design the new pyrrole derivatives 5-20 in the hope of increasing the activity and better understanding the influence of ortho halogens on the antimycobacterial activity. Microbiological data showed interesting in vitro activity toward Mycobacterium tuberculosis and atypical mycobacteria.

Antitubercular Agents↗
PubMed2004

Chiral recognition by resorcin[4]arene receptors: intrinsic kinetics and dynamics.

Molecular recognition of representative amino acids (A) by a chiral amido[4]resorcinarene receptor (1(L)) was investigated in the gas phase by ESI-FT-ICR mass spectrometry. The ligand displacement reaction between noncovalent diastereomeric [1(L).H.A](+) complexes and the 2-aminobutane enantiomers (B) exhibits a distinct enantioselectivity with regard to both the leaving amino acid A and the amine reactant B. The emerging selectivity picture, discussed in the light of molecular mechanics and molecular dynamics calculations, points to chiral recognition by 1(L), as determined by the effects of the host asymmetric frame on the structure, stability, and rearrangement dynamics of the diastereomeric [1(L).H.A](+) complexes and the orientation of the amine reactant B in encounters with [1(L).H.A](+). The results contribute to the development of a dynamic model of chiral recognition of biomolecules by enzyme mimics in the unsolvated state.

Amino Acids↗
PubMed2004

Antimycobacterial compounds. New pyrrole derivatives of BM212.

We have identified BM212 as a lead compound among a series of pyrrole derivatives with good in vitro activity against mycobacteria and candidae. First studies led us to synthesize some pyrrole compounds in which the thiomorpholine fragment was present. Some compounds revealed very active and these findings prompted us to prepare new pyrrole derivatives 2-15 in the hope of increasing the activity. The microbiological data showed interesting in vitro activity against Mycobacterium tuberculosis and atypical mycobacteria.

Antitubercular Agents↗
PubMed2004

Chalcone dimethylallyltransferase from Morus nigra cell cultures. Substrate specificity studies.

A new prenyltransferase (PT) enzyme derived from the microsomal fractions of cell cultures of Morus nigra was shown to be able to prenylate exclusively chalcones with a 2',4'-dihydroxy substitution and the isoflavone genistein. Computational studies were performed to shed some light on the relationship between the structure of the substrate and the enzymatic activity. PT requires divalent cations, particularly Mg(2+), to be effective. The apparent K(m) values for gamma,gamma-dimethylallyldiphosphate and 2',4'-dihydroxychalcone were 63 and 142 microM, respectively. The maximum activity of the enzyme was expressed during the first 10 days of cell growth.

Cells, Cultured↗
PubMed2004

Conformational search of antisense nucleotides. Part 2.

In this study is presented the phosphorotioate nucleotide compound (1) possessing an unusual moiety with a chiral P and a Se atoms double bonded. It required a force field parameterization for carrying out standard molecular mechanics calculations. A new set of MMFF parameters was developed and applied for the complete conformational search of the diastereoisomers, using both Monte Carlo and molecular dynamics, with the purpose to validate them by the comparison between calculated structural properties and NMR measurements.

Magnetic Resonance Spectroscopy↗
PubMed2003

Synthesis and molecular modelling studies of resorcin[4]arene-capped porphyrins.

Three new resorcin[4]arene-capped porphyrins (3, 5 and 7) different in the porphyrin skeleton, in the linking arms and in the cavity dimensions, have been synthesised. Molecular modelling calculations explored the conformations and the cavity size of the three compounds and showed that their hydrophobic pockets can accommodate one molecule of water or methane (3 and 5), or benzene (7) without any distortion. Notably, the capped porphyrin 5 was able to inhibit the oxidation of Co(II) to Co(III), whereas compound 7 did it only partially.

Journal Article↗
PubMed2003

Importance of the thiomorpholine introduction in new pyrrole derivatives as antimycobacterial agents analogues of BM 212.

During the course of our investigations in the field of azole antimicrobial agents, we have identified BM 212, a pyrrole derivative with good in vitro activity against mycobacteria and candidae. These findings prompted us to prepare new pyrrole derivatives 1-10 in the hope of increasing the activity. The microbiological data showed interesting in vitro activity against Mycobacterium tuberculosis and atypical mycobacteria.

Anti-Bacterial Agents↗
PubMed2003

alpha1-Adrenoceptor antagonists. 5. Pyridazinone-arylpiperazines. Probing the influence on affinity and selectivity of both ortho-alkoxy groups at the arylpiperazine moiety and cyclic substituents at the pyridazinone nucleus.

Our previous work on pyridazinone-arylpiperazine derivatives suggested some structural features that a compound should have to show high affinity and good selectivity for alpha(1) adrenoceptors (AR) with respect to alpha(2)-AR. Accordingly, two classes of new alkoxyphenylpiperazinylheptylpyridazinones were designed and synthesized to evaluate the effect of the alkoxy substituent on affinity and selectivity. As expected, affinity increased with larger alkoxy groups. Affinity values are all comparable with that of the reference compound (prazosin), with the exception of compound 1c found 4.5-fold more active than prazosin.

Adrenergic alpha-1 Receptor Antagonists↗
PubMed2002

Inhibition of amine oxidases activity by 1-acetyl-3,5-diphenyl-4,5-dihydro-(1H)-pyrazole derivatives.

A novel series of 1-acetyl-3,5-diphenyl-4,5-dihydro-(1H)-pyrazole derivatives have been synthesised and investigated for the ability to inhibit selectively monoamine oxidases, swine kidney oxidase, and bovine serum amine oxidase. The newly synthesised compounds 1-6 proved to be reversible and non-competitive inhibitors of all types of the assayed amine oxidases. Compounds inhibit monoamine oxidases potently, displaying low I(50) values of particular interest. In particular 1-acetyl-3-(2,4-dihydroxyphenyl)-5-(3-methylphenyl)-4,5-dihydro-(1H)-pyrazole 6 showed to be a potent monoamine oxidase inhibitor with a K(i) of about 10(-8)M. Further insights in the theoretical evaluation of the possible interactions between the compounds and monoamine oxidase B have been developed through a computational approach.

Amine Oxidase (Copper-Containing)↗
PubMed2002

Synthesis, molecular modeling studies, and pharmacological activity of selective A(1) receptor antagonists.

We present a combined computational study aimed at identifying the three-dimensional structural properties required for different classes of compounds to show antagonistic activity toward the A(1) adenosine receptor (AR). Particularly, an approach combining pharmacophore mapping, molecular alignment, and pseudoreceptor generation was applied to derive a hypothesis of the interaction pathway between a set of A(1) AR antagonists taken from the literature and a model of the putative A(1) receptor. The pharmacophore model consists of seven features and represents an improvement of the N(6)-C8 model, generally reported as the most probable pharmacophore model for A(1) AR agonists and antagonists. It was used to build up a pseudoreceptor model able to rationalize the relationships between structural properties and biological data of, and external to, the training set. In fact, to further assess its statistical significance and predictive power, the pseudoreceptor was employed to predict the free energy of binding associated with compounds constituting a test set. While part of these molecules was also taken from the literature, the remaining compounds were designed and synthesized by our research group. All of the new compounds were tested for their affinity toward A(1), A(2a), and A(3) AR, showing interesting antagonistic activity and A(1) selectivity.

Animals↗
PubMed2002

Alpha(1)-adrenoceptor antagonists. 4. Pharmacophore-based design, synthesis, and biological evaluation of new imidazo-, benzimidazo-, and indoloarylpiperazine derivatives.

As a part of a program aimed at discovering compounds endowed with alpha(1)-adrenoceptor (AR) blocking properties, in this paper we describe the synthesis and biological characterization of the compounds designed to fully match a three-dimensional pharmacophore model for alpha(1)-AR antagonists previously developed by our research group. Accordingly, the structure of trazodone (1), identified during a database search performed by using the model as a 3D query, was chosen as the starting point for this study and modified following suggestions derived from a literature survey. In particular, the triazolopyridine moiety of trazodone was replaced with different heteroaromatic rings (such as imidazole, benzimidazole, and indole), and a pyridazin-3(2H)-one moiety was inserted into the scaffold of the new compounds to increase the overall length of the molecules and to allow for a complete fit into all the pharmacophore features. Our aim was also to study the influence of the position of both the chloro and the methoxy groups on the piperazine phenyl ring, as well as the effect of the lengthening or shortening of the polymethylene spacer linking the phenylpiperazine moiety to the terminal heterocyclic portion. Compounds obtained by such structural optimization share a 6-(imidazol-1-yl)-, 6-(benzimidazol-1-yl)-, or 6-(indol-1-yl)pyridazin-3(2H)-one as a common structural feature that represents an element of novelty in the SAR of arylpiperazine compounds acting toward alpha(1)-AR. Biological evaluation by radioligand receptor binding assays toward alpha(1)-AR, alpha(2)-AR, and 5-HT(1A) serotoninergic receptors indicated compounds characterized by very good alpha(1)-AR affinity and selectivity. Very interestingly, chemical features (such as the o-methoxyphenylpiperazinyl moiety and an alkyl spacer of three or four methylene units) that generally do not allow for 5-HT(1A)/alpha(1) selectivity led to compounds 2c and 6c with a 5-HT(1A)/alpha(1) ratio of 286 and 281, respectively. Finally, compounds with the best alpha(1)-AR affinity profile (2c, 5f, and 6c) were demonstrated to be alpha(1)-AR antagonists.

Adrenergic alpha-Antagonists↗
PubMed2002

Enantioselective guest exchange in a chiral resorcin[4]arene cavity.

Gas-phase proton-bound complexes between a chiral resorcin[4]arene and some representative amino acids, that is, L- and D-alanine or L- and D-serine, were generated in the source of a Fourier transform ion cyclotron resonance mass spectrometer. Gas-phase exchange of the amino acid from the diastereomeric complexes with the enantiomers of 2-butylamine exhibits a significant enantioselectivity, which depends not only upon the configuration of the leaving guest but also on that of the incoming amine. These findings, coupled with molecular dynamic calculations, point to the observed gas-phase enantioselectivity as determined by the effects of the resorcin[4]arene chiral cavity upon the diastereomeric exchange transition structures.

Alanine↗