Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS

Loschwitz, Jennifer; Jäckering, Anna; Keutmann, Monika; Olagunju, Maryam; Olubiyi, Olujide O.; Strodel, Birgit

doi:10.1016/j.dib.2021.106948

Cited by 19 publications

(21 citation statements)

References 18 publications

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“…The atomic charges were calculated using cluster Density Functional Theory (DFT) simulations and the electrostatic potential (ESP) method. Regarding the molecule, the general Amber force field (GAFF) [ 54 ] atom types with ESP [ 55 ] charges were used. The electrostatic potential using the B3LYP functional with the 6-31 + G(d) basis set was employed to extract the partial charges for prednisolone using the CHELPG scheme [ 56 ].…”

Section: Methodsmentioning

confidence: 99%

Nanoscale Iron-Based Metal–Organic Frameworks: Incorporation of Functionalized Drugs and Degradation in Biological Media

Christodoulou

Lyu

Soares

et al. 2023

IJMS

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Metal–organic frameworks (MOFs) attract growing interest in biomedical applications. Among thousands of MOF structures, the mesoporous iron(III) carboxylate MIL-100(Fe) (MIL stands for the Materials of Lavoisier Institute) is among the most studied MOF nanocarrier, owing to its high porosity, biodegradability, and lack of toxicity. Nanosized MIL-100(Fe) particles (nanoMOFs) readily coordinate with drugs leading to unprecedented payloads and controlled release. Here, we show how the functional groups of the challenging anticancer drug prednisolone influence their interactions with the nanoMOFs and their release in various media. Molecular modeling enabled predicting the strength of interactions between prednisolone-bearing or not phosphate or sulfate moieties (PP and PS, respectively) and the oxo-trimer of MIL-100(Fe) as well as understanding the pore filling of MIL-100(Fe). Noticeably, PP showed the strongest interactions (drug loading up to 30 wt %, encapsulation efficiency > 98%) and slowed down the nanoMOFs’ degradation in simulated body fluid. This drug was shown to bind to the iron Lewis acid sites and was not displaced by other ions in the suspension media. On the contrary, PS was entrapped with lower efficiencies and was easily displaced by phosphates in the release media. Noticeably, the nanoMOFs maintained their size and faceted structures after drug loading and even after degradation in blood or serum after losing almost the totality of the constitutive trimesate ligands. Scanning electron microscopy with high annular dark field (STEM-HAADF) in conjunction with X-Ray energy-dispersive spectrometry (XEDS) was a powerful tool enabling the unraveling of the main elements to gain insights on the MOF structural evolution after drug loading and/or upon degradation.

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Section: Methodsmentioning

confidence: 99%

Nanoscale Iron-Based Metal–Organic Frameworks: Incorporation of Functionalized Drugs and Degradation in Biological Media

Christodoulou

Lyu

Soares

et al. 2023

IJMS

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“…Classical molecular dynamics simulations were performed using Gromacs 2021.2 ( , accessed on 15 November 2021) [ 31 ] with the AMBER99 force field [ 32 ]. The topologies of the two compounds were generated using Acpype software [ 33 ] with AMBER atom types.…”

Section: Methodsmentioning

confidence: 99%

Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor

Madeddu

Martino

Pieroni

et al. 2022

IJMS

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Human Topoisomerase I (hTop1p) is a ubiquitous enzyme that relaxes supercoiled DNA through a conserved mechanism involving transient breakage, rotation, and binding. Htop1p is the molecular target of the chemotherapeutic drug camptothecin (CPT). It causes the hTop1p-DNA complex to slow down the binding process and clash with the replicative machinery during the S phase of the cell cycle, forcing cells to activate the apoptotic response. This gives hTop1p a central role in cancer therapy. Recently, two artesunic acid derivatives (compounds c6 and c7) have been proposed as promising inhibitors of hTop1p with possible antitumor activity. We used several computational approaches to obtain in silico confirmations of the experimental data and to form a comprehensive dynamic description of the ligand-receptor system. We performed molecular docking analyses to verify the ability of the two new derivatives to access the enzyme-DNA interface, and a classical molecular dynamics simulation was performed to assess the capacity of the two compounds to maintain a stable binding pose over time. Finally, we calculated the noncovalent interactions between the two new derivatives and the hTop1p receptor in order to propose a possible inhibitory mechanism like that adopted by CPT.

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“…Moreover, the parameterization of GAFF 59 included organic molecules with aromatic, aliphatic, carbonyl, and enol groups that are also present in the systems studied in the present work. In addition, this force field has been successfully validated against experimental data for a wide range of organic molecules by different research groups, 60,61 and it has also been applied to build up the topology of curcumin and piperine. [61][62][63][64] Accordingly, the system was prepared for each MD simulation as follows:…”

Section: Solutions Of Curcumin and Piperinementioning

confidence: 99%

Aggregation patterns of curcumin and piperine mixtures in different polar media

Santos

Abreu

Marques

2023

Phys. Chem. Chem. Phys.

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Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS

Cited by 19 publications

References 18 publications

Nanoscale Iron-Based Metal–Organic Frameworks: Incorporation of Functionalized Drugs and Degradation in Biological Media

Nanoscale Iron-Based Metal–Organic Frameworks: Incorporation of Functionalized Drugs and Degradation in Biological Media

Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor

Aggregation patterns of curcumin and piperine mixtures in different polar media

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