From GROMACS to LAMMPS: GRO2LAM

Thielemann, Hernan Nicolas Chavez; Cardellini, Annalisa; Fasano, Matteo; Bergamasco, Luca; Alberghini, Matteo; Ciorra, Gianmarco; Chiavazzo, Eliodoro; Asinari, Pietro

doi:10.1007/s00894-019-4011-x

Cited by 33 publications

(21 citation statements)

References 52 publications

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“…Bulk zeolite simulations, instead, are carried out for 2 ns in the canonical ensemble (300 K; velocity rescaling thermostat with 0.1 ps time constant 68 ) under equilibrium conditions. Atomistic simulations are performed by GROMACS software (2 fs time step; leap-frog algorithm) 71,72 . Further details on the simulation protocol can be found elsewhere 38,39 .…”

Section: Methodsmentioning

confidence: 99%

Mechanistic correlation between water infiltration and framework hydrophilicity in MFI zeolites

Fasano

Bevilacqua

Chiavazzo

et al. 2019

Sci Rep

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Hydrophobic zeolites are nanoporous materials that are attracting an increasing interest, especially for catalysis, desalination, energy storage and biomedical applications. Nevertheless, a more profound understanding and control of water infiltration in their nanopores is still desirable to rationally design zeolite-based materials with tailored properties. In this work, both atomistic simulations and previous experimental data are employed to investigate water infiltration in hydrophobic MFI zeolites with different concentration of hydrophilic defects. Results show that limited concentrations of defects (e.g. 1%) induce a change in the shape of infiltration isotherms (from type-V to type-I), which denotes a sharp passage from typical hydrophobic to hydrophilic behavior. A correlation parametrized on both energy and geometric characteristics of the zeolite (infiltration model) is then adopted to interpolate the infiltration isotherms data by means of a limited number of physically-meaningful parameters. Finally, the infiltration model is combined with the water-zeolite interaction energy computed by simulations to correlate the water intrusion mechanism with the atomistic details of the zeolite crystal, such as defects concentration, distribution and hydrophilicity. The suggested methodology may allow a faster (more than one order of magnitude) and more systematic preliminary computational screening of innovative zeolite-based materials for energy storage, desalination and biomedical purposes.

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Section: Methodsmentioning

confidence: 99%

Mechanistic correlation between water infiltration and framework hydrophilicity in MFI zeolites

Fasano

Bevilacqua

Chiavazzo

et al. 2019

Sci Rep

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“…MD studies were conducted using high-performance computing (HPC) from Centro de Computação de Alto Desempenho at the University of São Paulo (USP). For MD simulations, we used GROMACS 2019.3 software [ 68 , 69 ] with the Charmm36 force field [ 70 ], and ligands were parameterized by CGenFF [ 69 , 71 ]. We obtained the initial coordinates to conduct the MD simulations from the docking poses of the ligands obtained by Glide and GOLD (as described in Section 4.2 and Section 4.5 ).…”

Section: Methodsmentioning

confidence: 99%

Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases

Silva

Borges

Santos

et al. 2021

IJMS

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Glycogen synthase kinase-3 beta (GSK-3β) is an enzyme pertinently linked to neurodegenerative diseases since it is associated with the regulation of key neuropathological features in the central nervous system. Among the different kinds of inhibitors of this kinase, the allosteric ones stand out due to their selective and subtle modulation, lowering the chance of producing side effects. The mechanism of GSK-3β allosteric modulators may be considered still vague in terms of elucidating a well-defined binding pocket and a bioactive pose for them. In this context, we propose to reinvestigate and reinforce such knowledge by the application of an extensive set of in silico methodologies, such as cavity detection, ligand 3D shape analysis and docking (with robust validation of corresponding protocols), and molecular dynamics. The results here obtained were consensually consistent in furnishing new structural data, in particular by providing a solid bioactive pose of one of the most representative GSK-3β allosteric modulators. We further applied this to the prospect for new compounds by ligand-based virtual screening and analyzed the potential of the two obtained virtual hits by quantum chemical calculations. All potential hits achieved will be subsequently tested by in vitro assays in order to validate our approaches as well as to unveil novel chemical entities as GSK-3β allosteric modulators.

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“…Moreover, the evaluation of possible interactions was performed using PMV [ 61 ] and LigPlot ® [ 64 ]. The molecular dynamic was performed with the molecular complex formed by two domains of ZIKV viral protein E and the compound with a virucidal activity for 50 ns using the GROningen MAchine for Chemical Simulations (GROMACS 5.1.4, (accessed on 8 September 2020)) [ 65 , 66 ], as previously described [ 60 ].…”

Section: Methodsmentioning

confidence: 99%

In Vitro and In Silico Anti-Arboviral Activities of Dihalogenated Phenolic Derivates of L-Tyrosine

et al. 2021

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Despite the serious public health problem represented by the diseases caused by dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) viruses, there are still no specific licensed antivirals available for their treatment. Here, we examined the potential anti-arbovirus activity of ten di-halogenated compounds derived from L-tyrosine with modifications in amine and carboxyl groups. The activity of compounds on VERO cell line infection and the possible mechanism of action of the most promising compounds were evaluated. Finally, molecular docking between the compounds and viral and cellular proteins was evaluated in silico with Autodock Vina®, and the molecular dynamic with Gromacs®. Only two compounds (TDC-2M-ME and TDB-2M-ME) inhibited both ZIKV and CHIKV. Within the possible mechanism, in CHIKV, the two compounds decreased the number of genome copies and in the pre-treatment strategy the infectious viral particles. In the ZIKV model, only TDB-2M-ME inhibited the viral protein and demonstrate a virucidal effect. Moreover, in the U937 cell line infected with CHIKV, both compounds inhibited the viral protein and TDB-2M-ME inhibited the viral genome too. Finally, the in silico results showed a favorable binding energy between the compounds and the helicases of both viral models, the NSP3 of CHIKV and cellular proteins DDC and β2 adrenoreceptor.

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From GROMACS to LAMMPS: GRO2LAM

Cited by 33 publications

References 52 publications

Mechanistic correlation between water infiltration and framework hydrophilicity in MFI zeolites

Mechanistic correlation between water infiltration and framework hydrophilicity in MFI zeolites

Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases

In Vitro and In Silico Anti-Arboviral Activities of Dihalogenated Phenolic Derivates of L-Tyrosine

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