AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Eberhardt, Jérôme; Santos-Martins, Diogo; Tillack, Andreas F.; Forli, Stefano

doi:10.1021/acs.jcim.1c00203

Cited by 2,361 publications

(1,521 citation statements)

References 54 publications

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“…To assess possible ligand–AChE interaction, molecular docking experiments were performed using the PyRx docking tool [ 49 ] via the Autodock VINA software [ 50 , 51 ]. The three-dimensional (3D) crystal structures of human AChE enzyme was obtained from the RCSB Protein Data Bank.…”

Section: Methodsmentioning

confidence: 99%

In Vitro and In Silico Kinetic Studies of Patented 1,7-diEthyl and 1,7-diMethyl Aminoalkanol Derivatives as New Inhibitors of Acetylcholinesterase

Grodner

Napiórkowska

Pisklak

2021

IJMS

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Two aminoalkanol derivatives of 1,7-diEthyl-8,9-diphenyl-4azatricyclo (5.2.1.02,6) dec-8-ene-3,5,10-trione and two derivatives of 1,7-diMethyl-8,9-diphenyl-4-azatricyclo (5.2.1.02.6) dec-8-ene-3,5,10-trione were evaluated in vitro for their inhibition efficacy of acetylcholinesterase. The Km, Vmax, slope angles of Lineweaver–Burk plots, Ki and IC50 values showed that all four aminoalkanol derivatives are competitive inhibitors of acetylcholinesterase whose inhibitory potency depends, to a varying extent, on the nature of the four different substituents present in the main compound structure. Studies have shown that the most potent acetylcholinesterase inhibitors are derivatives containing isopropylamine and/or methyl substituents in their structure. In contrast, dimethylamine and/or ethyl substituents seem to have a weaker, albeit visible, effect on the inhibitory potency of acetylcholinesterase. Additionally, docking studies suggest that studied compounds binds with the peripheral anionic site and not enter into the catalytic pocket due to the presence of the sterically extended substituent.

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Section: Methodsmentioning

confidence: 99%

In Vitro and In Silico Kinetic Studies of Patented 1,7-diEthyl and 1,7-diMethyl Aminoalkanol Derivatives as New Inhibitors of Acetylcholinesterase

Grodner

Napiórkowska

Pisklak

2021

IJMS

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“…The construction of a p.Asp170Val mutant was performed by using the mutagenesis toolkit in PyMol [ 14 ] ( , 20 October 2021) and a series of molecular docking experiments were performed to evaluate the affinity of the native ligand (galactose) and the PC Migalastat, using the Autodock-Vina suite of programs and their associated force field [ 15 , 16 ]. Clustering of the various conformations found for each ligand was performed via default root mean square deviation (RMSD) parameters and an exhaustiveness value of 20 [ 17 ].…”

Section: Methodsmentioning

confidence: 99%

The New Pharmacological Chaperones PBXs Increase α-Galactosidase A Activity in Fabry Disease Cellular Models

et al. 2021

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Fabry disease is an X-linked multisystemic disorder caused by the impairment of lysosomal α-Galactosidase A, which leads to the progressive accumulation of glycosphingolipids and to defective lysosomal metabolism. Currently, Fabry disease is treated by enzyme replacement therapy or the orally administrated pharmacological chaperone Migalastat. Both therapeutic strategies present limitations, since enzyme replacement therapy has shown low half-life and bioavailability, while Migalastat is only approved for patients with specific mutations. The aim of this work was to assess the efficacy of PBX galactose analogues to stabilize α-Galactosidase A and therefore evaluate their potential use in Fabry patients with mutations that are not amenable to the treatment with Migalastat. We demonstrated that PBX compounds are safe and effective concerning stabilization of α-Galactosidase A in relevant cellular models of the disease, as assessed by enzymatic activity measurements, molecular modelling, and cell viability assays. This experimental evidence suggests that PBX compounds are promising candidates for the treatment of Fabry disease caused by mutations which affect the folding of α-Galactosidase A, even for GLA variants that are not amenable to the treatment with Migalastat.

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“…For the molecular docking, AutoDock Vina 1.1.2 software [25,26] was used. First, RBD and ACE2 proteins were prepared and converted into PDBQT format using AutoDock Tools 1.5.6 [29].…”

Section: Methodsmentioning

confidence: 99%

“…Next, we removed compounds that could not be properly docked by the molecular docking software (AutoDock Vina 1.1.2 [25,26]), i.e. > 32 rotatable bonds as recommended by the software documentation.…”

Section: Database Creationmentioning

confidence: 99%

Entrectinib - a SARS-CoV-2 inhibitor in Human Lung Tissue (HLT) cells

Peralta-García

Torrens‐Fontanals

Stępniewski

et al. 2021

Preprint

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Since the start of the COVID-19 outbreak, pharmaceutical companies and research groups have focused on the development of vaccines and antiviral drugs against SARS-CoV-2. Here, we apply a drug repurposing strategy to identify potential drug candidates that are able to block the entrance of the virus into human cells. By combining virtual screening with in vitro pseudovirus assays and antiviral assays in Human Lung Tissue (HLT) cells, we identify entrectinib as a promising antiviral drug. We found that part of the antiviral action of entrectinib is mediated by a non-specific mechanism, likely occurring at the viral membrane level. Such a profile could provide entrectinib with protection against the development of drug resistance by emerging SARS-CoV-2 variants.

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AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Cited by 2,361 publications

References 54 publications

In Vitro and In Silico Kinetic Studies of Patented 1,7-diEthyl and 1,7-diMethyl Aminoalkanol Derivatives as New Inhibitors of Acetylcholinesterase

In Vitro and In Silico Kinetic Studies of Patented 1,7-diEthyl and 1,7-diMethyl Aminoalkanol Derivatives as New Inhibitors of Acetylcholinesterase

The New Pharmacological Chaperones PBXs Increase α-Galactosidase A Activity in Fabry Disease Cellular Models

Entrectinib - a SARS-CoV-2 inhibitor in Human Lung Tissue (HLT) cells

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