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Chemdraw ultra 10

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ChemDraw Ultra 10.0 is a chemical structure drawing software. It allows users to create, edit, and analyze chemical structures and reactions. The software provides tools for drawing and manipulating 2D and 3D molecular structures, as well as features for generating chemical formulas, spectra, and other related information.

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Merck molecular force field, by Merck Group (2 mentions)

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ChemDraw Ultra

5 protocols using chemdraw ultra 10

1

Determining Lipophilicity and Polarity

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The Clog P and Mlog values were calculated using the ChemDraw Ultra 10.0 [57 ] or MedChem Designer (TM) 3.0.0.30 [58 ], respectively.
Skrzypek A., Karpińska M., Juszczak M., Grabarska A., Wietrzyk J., Krajewska-Kułak E., Studziński M., Paszko T, & Matysiak J. (2022). Cholinesterases Inhibition, Anticancer and Antioxidant Activity of Novel Benzoxazole and Naphthoxazole Analogs. Molecules, 27(23), 8511.
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2

Conformational Analysis and Molecular Docking

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The 2D structure of 12 derivatives of bisindole-2-carboxilic acids was sketched in ChemDraw Ultra 10.0, converted to conformation in Chem3D 10.0, and then energy minimized in Discovery Studio 3.5 with a Merck molecular force field (Merck & Co.) until the minimum RMS reached 0.001 in Chem3D Ultra 10.0. The energy optimized conformations in whole conformational space of the derivatives were sampled with systematic search and BEST method of Discovery Studio 3.5, which were practiced with a SMART minimizer using CHARMM force field. The energy threshold was set to 20 kcal/mol at 300 K. The maximum minimization steps were 200 and the minimization root mean squared (RMS) gradient was 0.1 Å. The maximum generated conformations were 255 with a RMS deviation (RMSD) cutoff of 0.2 Å. Top 10 energy optimized conformations of DEBIC were used for the docking to d(CGATCG)2 and P-selectin.
Chen H., Wang W., Zhang X., Liu S., Wang Y., Zhu H., Wu J., Wang Y., Zhao M, & Peng S. (2017). Discovery of DEBIC to correlate P-selectin inhibition and DNA intercalation in cancer therapy and complicated thrombosis. Oncotarget, 9(63), 32119-32133.
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3

Conformational Analysis of THPDTPI

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The 2D structure of THPDTPI was sketched in ChemDraw Ultra 10.0, converted to 3D conformation in Chem3D 10.0, and then energy minimized in Discovery Studio 3.5 with a Merck molecular force field (Merck & Co.) until the minimum RMS reached 0.001. The energy optimized conformations in the whole conformational space of THPDTPI were sampled with systematic search and BEST method of Discovery Studio 3.5, which were practiced with a SMART minimizer using CHARMM force field. The energy threshold was set to 20 kcal/mol at 300 K. The maximum minimization steps were 200 and the minimization root mean squared (RMS) gradient was 0.1 Å. The maximum generated conformations were 255 with a RMS deviation (RMSD) cutoff of 0.2 Å. Top 10 energy optimized conformations of THPDTPI were used for the docking to the active site of P-selectin.
Zhu H., Wang Y., Song C., Feng Q., Wu J., Zhao S., Gui L., Zhang X., Zhao M, & Peng S. (2017). Docking of THPDTPI: to explore P-selectin as a common target of anti-tumor, anti-thrombotic and anti-inflammatory agent. Oncotarget, 9(1), 268-281.
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4

Conformational Analysis of IQCA-TAVV

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The 2D structure of IQCA-TAVV was sketched in ChemDraw Ultra 10.0, converted to 3D conformation in Chem3D 10.0, and then energy was minimized until the minimum RMS to reach 0.001 in Chem3D Ultra 10.0. The energy optimized conformations in the whole conformational space of IQCA-TAVV were sampled with systematic search and BEST method of Discovery Studio 3.5, which were practiced with a SMART minimizer using CHARMM force field. The energy threshold at 300 K was 20 kcal/mol. The maximum minimization steps were 200 and the minimization root mean squared (RMS) gradient was 0.1 Å. The maximum generated conformations were 255 with a RMS deviation (RMSD) cutoff of 0.2 Å. The lowest energy conformation of IQCA-TAVV was used for the docking to the active site of P-selectin and GPIIb/IIIa.
Wu J., Zhu H., Yang G., Wang Y., Wang Y., Zhao S., Zhao M, & Peng S. (2017). IQCA-TAVV: To explore the effect of P-selectin, GPIIb/IIIa, IL-2, IL-6 and IL-8 on deep venous thrombosis. Oncotarget, 8(53), 91391-91401.
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5

Conformational Analysis of PZL318 Compound

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The 2D structure of PZL318 was sketched in ChemDraw Ultra 10.0. The 3D structure was created and energy minimized until the minimum RMS reached 0.001 in Chem3D Ultra 10.0. The 3D structure was then energy minimized in Discovery Studio 2.1 with the Merck molecular force field. The energy-minimized conformation was used as the starting point for the conformation generation for PZL318. Energy-minimized conformations were sampled in the whole conformational space via the systematic search method and the BEST method in Discovery Studio 2.1. The systematic search and BEST methods were both performed with the SMART minimizer using the CHARMM force field. The energy threshold was set to 20 kcal/mol at 300 K. The maximum minimization steps were set to 200, and the minimization RMS gradient was set to 0.1 Å. The maximum generated conformations were set to 255 with an RMSD cutoff of 0.2 Å. The association model shown was proposed according to the 3D structure and the intermolecular interactions identified with the rotating-frame Overhauser spectroscopy (ROESY) 2D NMR and ESI-MS spectra of PZL318.
Li S., Wang Y., Wang F., Wang Y., Zhang X., Zhao M., Feng Q., Wu J., Zhao S., Wu W, & Peng S. (2015). Small molecule PZL318: forming fluorescent nanoparticles capable of tracing their interactions with cancer cells and activated platelets, slowing tumor growth and inhibiting thrombosis. International Journal of Nanomedicine, 10, 5273-5292.
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