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Chem3d pro 14

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Chem3D Pro 14.0 is a molecular modeling and visualization software. It enables users to build, edit, and manipulate 3D molecular structures. The software provides tools for drawing, measuring, and optimizing molecular models.

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Lab products found in correlation

Discovery studio, by Dassault Systèmes (2 mentions) Chembiodraw ultra 14, by PerkinElmer (2 mentions) Chemdraw 18, by PerkinElmer (1 mentions) Discovery studio 2016, by Dassault Systèmes (1 mentions) Pymol v1, by Schrödinger (1 mentions) Protein preparation wizard, by Schrödinger (1 mentions) Uv 2550 spectrometer, by Beckman Coulter (1 mentions) Nicolet 380 ft ir instrument, by Thermo Fisher Scientific (1 mentions) Aviii spectrometer, by Bruker (1 mentions) Silica gel, by Qingdao Marine Chemical (1 mentions) Sephadex lh 20, by Merck Group (1 mentions) Silica gel g plates, by Qingdao Marine Chemical (1 mentions) Maestro 12, by Schrödinger (1 mentions)

11 protocols using chem3d pro 14

1

Molecular Docking of Photosynthesis Inhibitors

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The crystal structure information of the D1 protein of C. reinhardtii was obtained from the Protein Data Bank (https://rcsb.org, accessed on 17 January 2023, PDB code: 6KAC; the resolution: 2.70 Å). Its dimeric structure was optimized by CHARMm force field using Discovery Studio (version 2016, BIOVIA, San Diego, CA, USA). The structures of DCMU and the four mycotoxins as ligands were constructed using ChemDraw 18.0 (Cambridge Soft, MA, USA). The ligand structures were energetically minimized using the MM2 energy minimizations tool in Chem3D Pro 14.0 (Cambridge Soft, MA, USA). The possible binding site of ligands docking was set to the QB binding site in the D1 crystal structure of C. reinhardtii (PDB: 6KAC). The molecular docking was performed with CDocker in Discovery Studio. For the setting of the docking parameters, the Top Hits was set to 10, and the Pose Cluster Radius was set to 0.5 Å. We used the default values for the other parameters.
Shi J., Jiang M., Wang H., Luo Z., Guo Y., Chen Y., Zhao X., Qiang S., Strasser R.J., Kalaji H.M, & Chen S. (2023). Effects of Mycotoxin Fumagillin, Mevastatin, Radicicol, and Wortmannin on Photosynthesis of Chlamydomonas reinhardtii. Plants, 12(3), 665.
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2

Inhibitor Docking of HDAC8 Complexes

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Inhibitor docking studies were performed using AutoDock Vina (Trott and Olson, 2010 (link)). The 6 hydroxamic acid HDACi were first energy-minimized and converted to .pdb files using ChemBioDraw Ultra 14.0 and Chem3D Pro 14.0 (CambridgeSoft). Chain A of the HDAC8-Compound 6 complex (less the potassium ions, solvent, and the inhibitor) was used as the model; the catalytic zinc was included in the model. Residues F152, F208, and M274 were defined as flexible residues. The search space was defined as following: center_x = 37.141, center_y = 11.218, and center_z = 120.589, with size_x = 54, size_y = 38, size_z = 48, with the spacing set to 0.375 Å and the exhaustiveness set to 25 iterations. The .pdbqt output files were analyzed in Pymol, which was compiled from an open source.
Tabackman A.A., Frankson R., Marsan E.S., Perry K, & Cole K.E. (2016). Structure of ‘Linkerless’ Hydroxamic Acid Inhibitor-HDAC8 Complex Confirms the Formation of an Isoform-Specific Subpocket. Journal of structural biology, 195(3), 373-378.
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3

Molecular Docking of Bioactive Compounds with iNOS

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The crystal structure of iNOS (PDB ID: 3E6T) was obtained from the Protein Data Bank of RCSB (Research Collaboratory for Structural Bioinformatics). Docking simulations between bioactive compounds and iNOS were performed using the Maestro software suite 2015 (Schrodinger, New York, NY, USA). The ligand molecules were drawn with Chem3D Pro 14.0 (CambridgeSoft, Waltham, MA, USA) and optimized by the Ligprep module of Maestro. The protein receptor was prepared by deleting the ligand and water molecules and then was adopted for molecular docking with ligands. The reported inhibitor binding sites of iNOS was chosen as the binding pocket [73 (link)].
Zhu S.S., Zhang Y.F., Ding M., Zeng K.W., Tu P.F, & Jiang Y. (2022). Anti-Neuroinflammatory Components from Clausena lenis Drake. Molecules, 27(6), 1971.
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4

Homology Modeling and Docking of D1 Protein

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The target D1 protein of A. adenophora can be provided on the basis of the amino acid sequence (reference sequence no. YP 004564352.1). The sequence of amino acid was obtained from NCBI, in FASTA format. Evolutionary related protein structures were searched for by the BLAST databases through the SWISS-MODEL Template Library (SMTL) [53 (link)]. Searched templates of D1 protein were estimated using Global Model Quality Estimate (GMQE) and Quaternary Structure Quality Estimate (QSQE) and ranked by the expected quality of the resulting models. The protein structures of top-ranked templates were selected from the Protein Data Bank (PDB) and built the homology model of A. adenophora D1 protein by the Protein Module of Discovery Studio. The chemical structure of CA was constructed with the software of ChemBioDraw Ultra 14.0 (CambridgeSoft, Cambridge, MA, USA), and the Chem3D Pro 14.0 (CambridgeSoft, Cambridge, MA, USA) was used to minimize energy. The docking was performed by DS-CDocker in Discovery Studio 2016 (BIOVIA, San Diego, CA, USA). The polar was added to the protein during energy minimization and molecular refinement.
Jiang M., Yang Q., Wang H., Luo Z., Guo Y., Shi J., Wang X., Qiang S., Strasser R.J, & Chen S. (2022). Effect of Mycotoxin Cytochalasin A on Photosystem II in Ageratina adenophora. Plants, 11(20), 2797.
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5

Molecular Modeling and Ligand Optimization

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Molecular modeling experiments were performed using Discovery Studio (version 2016, BIOVIA, USA). The structures of different ligands were constructed using ChemDraw 18.0 software (Cambridge Soft, USA). The ligand structures were energetically minimized using MM2 energy minimizations in Chem3D Pro 14.0 (Cambridge Soft, USA).
Wang H., Yao Q., Guo Y., Zhang Q., Wang Z., Strasser R.J., Valverde B.E., Chen S., Qiang S, & Kalaji H.M. (2021). Structure-based ligand design and discovery of novel tenuazonic acid derivatives with high herbicidal activity. Journal of Advanced Research, 40, 29-44.
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6

Computational Docking of AKR1C3 Inhibitors

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Ligand binding poses generated using a LigAlign v1.0 plugin (University of Toronto) installed onto Pymol v1.7.6 (Schrödinger). The crystal structure of AKR1C3 in complex with NADP+ and 3’-[(4-nitronaphthalen-1-yl)amino]benzoic acid (PBD codes: 4DBS) was used as a template to determine interactions of compounds in the AKR1C3 binding pockets. The crystal structures of the AR-LBD in complex with S-1 (PDB code: 2AXA) and AR-LBD W741L mutant complex with R-bicalutamide (PBD code: 1Z95) were used as templates to superimpose AKR1C3 inhibitors in AR-LBD and compare these poses to those observed with known AR antagonists. Water molecules and original ligands were removed from the structures and hydrogens were manually added using AutoDockTools-1.5.6 (Scripps Research Institute). Ligands (Compounds 2, 3, 4) were generated as PDB files using Chem 3D Pro 14.0 (Cambridgesoft). All ligand bonds were identified as flexible. Parameters for the gridbox were determined from the original ligand binding sites with the size of 40 for all the coordinates (see Table 1 in Supporting Information). Docking experiments were performed using AutoDock Vina (Scripps Research Institute) [30 (link)].
Wangtrakuldee P., Adeniji A.O., Zang T., Duan L., Khatri B., Twenter B.M., Estrada M.A., Higgins T.F., Winkler J.D, & Penning T.M. (2019). A 3-(4-Nitronaphthen-1-yl) amino-benzoate analog as a Bifunctional AKR1C3 Inhibitor with AR Antagonist Activity: Head to Head Comparison with Other Advanced AKR1C3 Targeted Therapeutics. The Journal of steroid biochemistry and molecular biology, 192, 105283.
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7

Computational Analysis of Quercetin Conformations

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The preferential conformation was analyzed based on force fields by computational chemistry. In brief, the energy minimization of quercetin and QDAD was respectively calculated through molecular mechanics II (MM2) using the Chem3D Pro14.0 program (PerkinElmer, Waltham, MA, USA) [53 (link),54 (link),55 (link),56 (link)]. The preferential conformation has been expressed using the molecular models in Figure 1C,D.
Q-TOF-MS analysis is characterized by highly accurate m/z values, particularly molecular weights. The molecular weight calculation based on the formula is vital for a comparison with the m/z values from the Q-TOF-MS analysis. In the present study, the molecular weight calculations were conducted based on the accurate relative atomic masses. The relative atomic masses of C, H, O, and N were 12.0000, 1.007825, 15.994915, and 14.003074, respectively [57 ].
Li X., Zeng J., Liu Y., Liang M., Liu Q., Li Z., Zhao X, & Chen D. (2020). Inhibitory Effect and Mechanism of Action of Quercetin and Quercetin Diels-Alder anti-Dimer on Erastin-Induced Ferroptosis in Bone Marrow-Derived Mesenchymal Stem Cells. Antioxidants, 9(3), 205.
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8

Protein-Ligand Interaction Modeling

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The three-dimensional structure of the protein was downloaded from RCSB Protein Data Bank (www.rcsb.org) Protein Receptor with Ligand Molecule (PDB ID: 3ETR) [29 (link)], and the structure of compound 6k was constructed in the MOE module. The protein was processed using Schrödinger’s Protein Preparation Wizard [30 ], including removed crystal water, added missing hydrogen atoms and repaired missing bond information and peptide fragments. The Ligprep 3.3 module was used to generate stereoisomers of test compound, and the protonation states of ligands at pH 7.0 ± 2.0 were generated with Epik 3.1. Protonation and energy optimization were performed to obtain the 3D configuration using Chem3D Pro 14.0 (PerkinElmer, America). After the grid file was generated, the compound was docked using the Standard Precision mode of Ligand docking in the Glide module, and the optimal configuration was selected for force analysis and plotted with Pymol.
Wang M.X., Qin H.W., Liu C., Lv S.M., Chen J.S., Wang C.G., Chen Y.Y., Wang J.W., Sun J.Y, & Liao Z.X. (2022). Synthesis and biological evaluation of thiazolidine-2-thione derivatives as novel xanthine oxidase inhibitors. PLoS ONE, 17(5), e0268531.
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9

Chromatographic Separation and Structural Analysis

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Silica gel (60–80, 200–300 mesh, Qingdao Marine Chemical Co., Ltd., Qingdao, China), ODS gel (20–45 µm, Fuji Silysia Chemical Co., Ltd., Greenville, NC, USA), and Sephadex LH-20 (Merck, Kenilworth, NJ, USA) were used for column chromatography. TLC was conducted on precoated Silica gel G plates (Qingdao Marine Chemical Co., Ltd.), and spots were detected by spraying with 5% H2SO4 in EtOH followed by heating. Optical rotation was measured on a Rudolph Autopol III polarimeter. UV spectra were performed on a Shimadzu UV-2550 spectrometer (Beckman, Brea, CA, USA). IR absorptions were obtained on a Nicolet 380 FT-IR instrument (Thermo, Waltham, MA, USA) using KBr pellets. 1D and 2D-NMR spectra were recorded on Bruker AV III spectrometer (Bruker, Billerica, MA, USA) (1H-NMR at 500 MHz and 13C NMR at 125 MHz) using TMS as the internal standard. Chem3D Pro 14.0 (PerkinElmer, Waltham, MA, USA) was used for building these 3D models and calculating energy minimizations.
Qiu L., Wang P., Liao G., Zeng Y., Cai C., Kong F., Guo Z., Proksch P., Dai H, & Mei W. (2018). New Eudesmane-Type Sesquiterpenoids from the Mangrove-Derived Endophytic Fungus Penicillium sp. J-54. Marine Drugs, 16(4), 108.
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10

Conformational Analysis of Butein and (S)-Butin

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The preferential conformation was analyzed based on force fields by computational chemistry. In brief, the energy minimization of butein and (S)-butin were respectively calculated through molecular mechanics II (MM2) using the Chem3D Pro14.0 program (PerkinElmer, Waltham, MA, USA) [102 (link),103 (link)].
The Q-TOF-MS analysis is characterized by highly accurate m/z values, particularly molecular weights. The molecular weight calculation based on the formula is vital for comparison with the m/z values from the Q-TOF-MS analysis. In the present study, the molecular weight calculations were conducted based on the accurate relative atomic masses. The relative atomic masses of C, H, O, and N were 12.0000, 1.007825, 15.994915, and 14.003074, respectively [70 ].
Liu J., Li X., Cai R., Ren Z., Zhang A., Deng F, & Chen D. (2020). Simultaneous Study of Anti-Ferroptosis and Antioxidant Mechanisms of Butein and (S)-Butin. Molecules, 25(3), 674.
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