Initial coordinates of BCD were extracted from a published X-ray structure of a CD–protein complex (Kondo, Ohtaki, Tonozuka, Sakano, & Kamitori, 2001 (link)). Initial 3D coordinates of SBECD were built using Chemaxon tools based on BCD crystal structure. In the course of molecular docking calculations, the number of random substitutions on beta-cyclodextrin was kept at 6 as the average substitution degree of SBECD is 6.5 sulfobutyl-groups per beta-cyclodextrin ring. Initial coordinates of REM were built and optimized using Marvin software (Chemaxon Inc, Budapest, Hungary). Semiempirical energy minimization and calculation of partial charges were performed for further minimization purposes using the PM6 method by MOPAC2009 package. Molecular docking calculations were carried out using the Autodock Vina software integrated in the Molecular Docking Server (http://www.dockingserver.com ) (Bikadi & Hazai, 2009 (link); Trott & Olson, 2010 (link)). Water molecules and heteroatoms were removed from the structures, since water is implicitly included in Autodock. Simulation boxes were centered on cyclodextrin. A simulation box of 22 × 22 × 22 Å was used in each docking calculation with an exhaustiveness option of 8 (average accuracy).
Marvin software
Manufactured by ChemAxon
Sourced in Hungary
Marvin is a chemical structure editor and viewer software developed by ChemAxon. It allows users to draw, edit, and visualize chemical structures and molecules. The software provides basic functionalities for manipulating and exploring chemical compounds.
Automatically generated - may contain errors
Lab products found in correlation
6 protocols using marvin software
1
Molecular Docking of Cyclodextrin Derivatives
2
Quantum Chemical Modeling of Pg-3-glc
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The initial 3D structure of Ppg-3-glc is retrieved from PubChem. It was first optimized using the PM7 semiempirical quantum chemical method [30 (link)] implemented in MOPAC2016 [31 (link)]. The solvation effects were simulated using the COSMO model of water. The PRECISE keyword was used to increase the convergence criteria. VegaZZ 3.2.0 was used as a GUI [32 (link)]. The pKa values of Pg-3-glc were predicted using ChemAxon’s Marvin software.
DFT calculations were performed using M062X, since it proved to be highly accurate for predicting thermodynamic aspects of the antioxidant activity for many compounds [33 (link)]. The 6-31+g(d,p) basis set was used, and solvation effects were simulated using the SMD models of water and pentyl ethanoate. The enthalpies for solvated e– and H+ ion were taken from the literature [34 (link)]. Frequency calculations confirmed the absence of imaginary vibrational frequencies in optimized geometries and provided zero-point energy and thermal enthalpy corrections that are necessary for studying the thermodynamics of the antioxidant activity of Pg-3-glc. All calculations were done in Gaussian 16, version B.01 [35 ].
DFT calculations were performed using M062X, since it proved to be highly accurate for predicting thermodynamic aspects of the antioxidant activity for many compounds [33 (link)]. The 6-31+g(d,p) basis set was used, and solvation effects were simulated using the SMD models of water and pentyl ethanoate. The enthalpies for solvated e– and H+ ion were taken from the literature [34 (link)]. Frequency calculations confirmed the absence of imaginary vibrational frequencies in optimized geometries and provided zero-point energy and thermal enthalpy corrections that are necessary for studying the thermodynamics of the antioxidant activity of Pg-3-glc. All calculations were done in Gaussian 16, version B.01 [35 ].
3
Determination of Oxime Group pKa by Oximolysis
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Acid dissociation constant (Ka) of the oxime group was determined by measuring the degradation of ATCh (1 mM) by 100 µM oxime (oximolysis) at 412 nm and in pH range 4.4–11.3 (0.1 M phosphate buffer; pH < 9.25 was prepared with 0.2 M NaOH) as described previously (20). pKa values were calculated using the modified equation described previously [34 (link)]:
where v is the rate of oximolysis, k is oximolysis constant and n is Hill coefficient. Oximolysis was measured in triplicates and corrected for spontaneous degradation of ATCh and DTNB at different pH.
Since the acid-base equilibrium of other functional groups may interfere with the pKa determination from oximolysis (as seen from the Hill coefficients if n < 1), pKa values were also predicted in silico using Marvin software (version 16.11.7.0, ChemAxon, Budapest, Hungary). In such a way in silico determined pKa values of the oxime group will serve as a confirmation of the pKa values of the oxime group determined in vitro.
where v is the rate of oximolysis, k is oximolysis constant and n is Hill coefficient. Oximolysis was measured in triplicates and corrected for spontaneous degradation of ATCh and DTNB at different pH.
Since the acid-base equilibrium of other functional groups may interfere with the pKa determination from oximolysis (as seen from the Hill coefficients if n < 1), pKa values were also predicted in silico using Marvin software (version 16.11.7.0, ChemAxon, Budapest, Hungary). In such a way in silico determined pKa values of the oxime group will serve as a confirmation of the pKa values of the oxime group determined in vitro.
4
Peptide Structure Generation Protocol
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Peptide
sequences were converted to two-
and three-dimensional structures. All structures of amphiphilic peptides
were built using Marvin software 19.17.0, 2019, ChemAxon (www.chemaxon.com ). Briefly, the
FASTA formats of peptide sequences were prepared and converted to
images of one-dimensional (1D) structures by the Molconvert command.
Terminal acetyl and amine groups were added manually where needed
for the whole-peptide structures and also for all Ala-AAi-Ala tri-peptide
structures. Charges were then applied to the structures at pH 7.00.
The generated 1D structures were converted to two-dimensional (2D)
and three-dimensional (3D) structures by Marvin software’s
command-line options, where the MMFF94 force field was used to optimize
the 3D structures. This step is presented as the “Structure
Drawing” node inFigure 1 . The commands used for the generation of peptide structures
are summarized inTables S1–S3 .
The generated structures are provided as a separate zip file.
sequences were converted to two-
and three-dimensional structures. All structures of amphiphilic peptides
were built using Marvin software 19.17.0, 2019, ChemAxon (
FASTA formats of peptide sequences were prepared and converted to
images of one-dimensional (1D) structures by the Molconvert command.
Terminal acetyl and amine groups were added manually where needed
for the whole-peptide structures and also for all Ala-AAi-Ala tri-peptide
structures. Charges were then applied to the structures at pH 7.00.
The generated 1D structures were converted to two-dimensional (2D)
and three-dimensional (3D) structures by Marvin software’s
command-line options, where the MMFF94 force field was used to optimize
the 3D structures. This step is presented as the “Structure
Drawing” node in
are summarized in
The generated structures are provided as a separate zip file.
5
Estimating PUFA pKa for IKs Channels
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pKa, the negative log of the acid dissociation constant, values of PUFA analogues in solution were calculated using Marvin Software (ChemAxon). However, studies of PUFAs in lipid bilayers and our previous studies on PUFA–IKs channel interactions showed that there is a large difference in the pKa values in solution (calculated according to the structure) compared with the measured pKa of PUFAs in the lipid bilayer (Börjesson and Elinder, 2011 (link); Elinder and Liin, 2017 (link)) and in close contact with the IKs channel (Elinder and Liin, 2017 (link); Liin et al., 2015 (link)). The average difference between the calculated solution pKa values and experimental found pKa values for PUFAs associated with IKs channels is ∼3.5 (Liin et al., 2015 (link)). We therefore added this correction factor to the calculated solution pKa values to generate our estimated pKa value for PUFAs associated with the IKs channel.
6
Lipinski's Rule of 5 for Drug-likeness
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Lipinski's rule of 5 or Pfizer's rule of 5 is an essential parameter to determine the drug-likeness properties of small molecules. Any proposed ligand follows this rule means it could be absorbed orally, while violating the rule leads to absorption and permeation problems. Designing small lead molecules in most current drug discovery projects should follow this rule to proceed as a drug candidate molecule (42, 43) . The calculations were achieved using Chemaxon's Marvin Software (38).
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