Personal Experience with Four Kinds of Chemical Structure Drawing Software: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch

Li, Zhenjiang; Hong-gui, Wan; Shi, Yuhu; Ouyang, Pingkai

doi:10.1021/ci049794h

Cited by 249 publications

(131 citation statements)

References 3 publications

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“…To determine the distance between the exocyclic 6-nitrogen and the first branched carbon (carbon atom forming covalent bonds with at least three other carbons and/or heteroatoms), molecules were drawn in the ACD/ ChemSketch software (Li et al, 2004). The sketched molecules were optimized using the 3D viewer module.…”

Section: Methodsmentioning

confidence: 99%

Dissecting interactions between nucleosides and germination receptors in Bacillus cereus 569 spores

et al. 2010

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Bacillus cereus 569 spores germinate either with inosine as a sole germinant or with a combination of nucleosides and L-alanine. Whereas the inosine-only germination pathway requires the presence of two different germination receptors (GerI and GerQ) to be activated, the nucleoside/alanine germination pathway only needs one of the two receptors. To differentiate how nucleoside recognition varies between the inosine-only germination pathway and the nucleoside/ alanine germination pathway, we tested 61 purine analogues as agonists and antagonists of the two pathways in wild-type, DgerI and DgerQ spores. The structure-activity relationships of germination agonists and antagonists suggest that the inosine-only germination pathway is restricted to recognize a single germinant (inosine), but can be inhibited in predictable patterns by structurally distinct purine nucleosides. B. cereus spores encoding GerI as the only nucleoside receptor (DgerQ mutant) showed a germination inhibition profile similar to wild-type spores treated with inosine only. Thus, GerI seems to have a well-organized binding site that recognizes inosine and inhibitors through specific substrate-protein interactions. Structure-activity analysis also showed that the nucleoside/alanine germination pathway is more promiscuous toward purine nucleoside agonists, and is only inhibited by hydrophobic analogues. B. cereus spores encoding GerQ as the only nucleoside receptor (DgerI mutant) behaved like wild-type spores treated with inosine and L-alanine. Thus, the GerQ receptor seems to recognize substrates in a more flexible binding site through non-specific interactions. We propose that the GerI receptor is responsible for germinant detection in the inosine-only germination pathway. On the other hand, supplementing inosine with L-alanine allows bypassing of the GerI receptor to activate the more flexible GerQ receptor.

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Section: Methodsmentioning

confidence: 99%

Dissecting interactions between nucleosides and germination receptors in Bacillus cereus 569 spores

et al. 2010

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“…The molecular structures of the compounds were drawn using the ChemDraw(Li. Pet al 13 , Balachandran et al 14 )software and the Small Incision Lenticule Extraction(SMILES) (David et al 15 )format of the structure was pasted on the data warrior software. The teratogenicity was calculated using the insilico first software.…”

Section: Methodsmentioning

confidence: 99%

Screening and Toxicity Risk Assessment of Selected Compounds to Target Cancer using QSAR and Pharmacophore Modelling

Kumar¹,

Kabilan²,

Parthasarathy³

2017

IJPTR

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:To target TGFβ type I receptor, around 63 compounds have been identified from the binding database and3D-QSAR study was carried out using PHASE of Schrodinger software. Through thorough validation, a best pharmacophore model screened 4000 compounds from National Cancer Institute(NCI) and Zinc database. Further docking studies around 4000 molecules were docked by targeting the protein TGFβ type I (PDBID: 1VJY). Based on docking or Glide score 25best compounds were identified. In addition to these, QikProp module 7 lead compounds were screened and their toxicity parameters evaluated using OSIRIS property explorer and Molinspiration and ToxTree software. The molecular parameters like clogS, clogP and Molecular weight were calculated using Molinspiration software as well as the drug-likeness and drug score using the OSIRIS property explorer. Their toxicity parameters like mutagenic, tumorigenic, irritant and reproductive effective were calculated using data warrior. The teratogenicity of the compounds was calculated using insilico first software and its toxicity to S.typhimurium TA100 mutagen, eye irritation as well as corrosion, skin sensitation alerts, negative for genotoxic carcinogenicity and non genotoxic carcinogenicity. From the results the compound 7 (Zinc-69489055) was found to be safe to use as a drug. Hence, the compound could be further redesigned, synthesized to target cancer.

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“…Ramachandran plot [20][21][22][23] and ERRAT [24] were used to analyze the allowed dihedral phi and psi rotation of amino acids in the protein backbones and the quality of refined 3D structure, respectively. [25,26] for the molecular docking experiments and their conformational energy was minimized by using a MMFF94 force field. 30 molecules of Cinchona alkaloids were designed by substituting the -R group positions of Cinchona ( Table 1).…”

Section: Protein Structure Preparationmentioning

confidence: 99%

In Silico Screening and Designing Synthesis of Cinchona Alkaloids Derivatives as Potential Anticancer

Hanafi

Rosmalena

Prasasty

et al. 2017

JTLS

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P-glycoprotein (P-gp) resistance in cancer cells decreases the intracellular accumulation of various anticancer drugs. This multidrug resistance (MDR) protein can be modulated by number of non-cytotoxic drugs. We have screened 30 cinchona alkaloids derivatives as a potent P-gp inhibitor agent in silico. Hereby, we report the highest potential inhibitions of P-gp is Cinchonidine isobutanoate through molecular docking approach with affinity energy -8.6 kcal/mol and inhibition constant, Ki is 4.89 × 10 -7 M. Cinchonidine isobutanoate is also known has molecular weight below 500, Log P value 3.5, which is indicated violation free of Lipinski`s rule of five. Thus, Cinchonidine isobutanoate is the most potent compound as anticancer compare to other Cinchona alkaloids. Ultimately, we design Cinchonidine isobutanoate for further lead synthesis by using DBSA, act as a combined Brønsted acid-surfactantcatalyst (BASC) to obtain a high concentration of organic product by forming micellar aggregates which are very powerful catalytic application in a water environment.

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Personal Experience with Four Kinds of Chemical Structure Drawing Software: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch

Cited by 249 publications

References 3 publications

Dissecting interactions between nucleosides and germination receptors in Bacillus cereus 569 spores

Dissecting interactions between nucleosides and germination receptors in Bacillus cereus 569 spores

Screening and Toxicity Risk Assessment of Selected Compounds to Target Cancer using QSAR and Pharmacophore Modelling

In Silico Screening and Designing Synthesis of Cinchona Alkaloids Derivatives as Potential Anticancer

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