A ?quasi-flexible? automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation

Alcaro, Stefano; Gasparrini, Francesco; Incani, Ottaviano; Mecucci, S.; Misiti, D.; Pierini, Marco; Villani, Claudio

doi:10.1002/(sici)1096-987x(200005)21:7<515::aid-jcc2>3.0.co;2-5

Cited by 68 publications

(8 citation statements)

References 40 publications

(7 reference statements)

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“…1 After the conformational search of the isolated guest molecules the docking with three "open" conformations of β-cyclodextrin was performed following the "quasiflexible" approach of the methodology. The ensemble obtained after the full minimization of the complex configurations was thermodynamically evaluated with computational estimation of state functions related to the recognition process.…”

Section: Discussionmentioning

confidence: 99%

“…In this study we report an application of the computational method MOLINE (Molecular Interaction Evaluation) created for studying complexes with an unbiased fashion. 1 With respect to recently reported techniques, 2,3 MOLINE is based on a systematic, automatic and quasi-flexible docking approach that prevents the influence of the chemist's intuition in the configuration generation. The inclusion molecular system focused in this work is based on β-cyclodextrin as host ( Figure 1) and a set of pharmaceutical organic molecules as guests.…”

Section: Introductionmentioning

confidence: 99%

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Molecular modeling of β-cyclodextrin inclusion complexes with pharmaceutical compounds

Alcaro

Battaglia

Ortuso³

2004

Arkivoc

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Ten molecularly diverse compounds, selected on the basis of the standard free energy of complexation with β-cyclodextrin, have been used as training set of molecular docking experiments. After the conformational search of each compound the Molecular Interaction Evaluation (MOLINE) program has been adopted to generate the inclusion geometries. The recognition process has been thermodynamically evaluated by the computational method, theoretical and experimental free energies of complexation have been compared obtaining an high correlation (r 2 > 0.9). A statistical and graphical analysis of the binding inclusion geometries completed the work.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular modeling of β-cyclodextrin inclusion complexes with pharmaceutical compounds

Alcaro

Battaglia

Ortuso³

2004

Arkivoc

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“…In both cases, docking is a combination of two components: a search strategy and a scoring function [Taylor et al, 2002]. The computational method MOLINE (Molecular Interaction Evaluation) was created to study complexes in an unbiased fashion [Alcaro et al, 2000]. It is based on a systematic, automatic and quasi-flexible docking approach that prevents the influence of the chemist`s intuition on generating the configuration.…”

Section: Selective Formation Of Complexesmentioning

confidence: 99%

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

Yunta¹

2012

Bioinformatics

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“…The reduced number of selected structures was used to investigate the molecular basis of the difference in the calculated binding energies of both ligands for the bI to bIII-tubulin isoform. Finally, in all simulations, the average drug-protein binding energies (DG-, DH-and DS-values) were computed according to the MOLINE methodology reported by some of us [28]. The results are reported in Table 1.…”

Section: Molecular Dynamics and Thermodynamics Calculationsmentioning

confidence: 99%

“…In details, conformations with an internal energy difference lower than 1 kcalAEmol )1 were duplicated if their RMS deviation, after superposition of the whole coordinate set, was lower than 0.25 Å . Binding energies and Boltzmann analysis were carried out using the thermodynamic module of the moline program [28].…”

Section: Molecular Dynamicsmentioning

confidence: 99%

The βI/βIII‐tubulin isoforms and their complexes with antimitotic agents

et al. 2006

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Both microtubule destabilizer and stabilizer agents are important molecules in anticancer therapy. In particular, paclitaxel has been demonstrated to be effective for the treatment of ovarian, breast, and nonsmall cell lung carcinomas. It has been shown that emergence of resistance against this agent correlates with an increase in the relative abundance of tubulin isoform βIII and that the more recently discovered IDN5390 can be effectively used once resistance has emerged. In this paper, we analyze the binding modes of these antimitotic agents to type I and III isoforms of β‐tubulin by computational methods. Our results are able to provide a molecular explanation of the experimental data. Using the same protocol, we could also show that no preference for any of the two isoforms can be detected for epothilone A, a potentially very interesting drug for which no data about the emergence of resistance is currently available. Our analysis provides structural insights about the recognition mode and the stabilization mechanism of these antimitotic agents and provides useful suggestions for the design of more potent and selective antimitotic agents.

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A ?quasi-flexible? automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation

Cited by 68 publications

References 40 publications

Molecular modeling of β-cyclodextrin inclusion complexes with pharmaceutical compounds

Molecular modeling of β-cyclodextrin inclusion complexes with pharmaceutical compounds

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

The βI/βIII‐tubulin isoforms and their complexes with antimitotic agents

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