Molecular Binding Interactions: Their Estimation and Rationalization in QSARs in Terms of Theoretically Derived Parameters

Lewis, David F.; Broughton, Howard B.

doi:10.1100/tsw.2002.343

Cited by 10 publications

(4 citation statements)

References 81 publications

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“…There are also several hydrophobic residue contacts that cooperatively assist in the binding and orientation of the camphor substrate. In fact, a simple calculation based on compound lipophilicity and average hydrogen bond energy gives a good estimate of the camphor substrate binding energy of CYP101, which is in satisfactory agreement with the experimentally determined value [1].…”

Section: Introductionsupporting

confidence: 80%

Hydrogen Bonding in Human P450-Substrate Interactions: A Major Contribution to Binding Affinity

Lewis

2004

The Scientific World JOURNAL

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The importance of hydrogen bonding, a relatively strong intermolecular force of attraction between molecules in biological systems, is discussed in the respect of P450 substrate affinity towards one or more of the human P450 enzymes that are generally associated with drug and other xenobiotic metabolism. It is shown that calculation of hydrogen bond distances and energies based on simple empirical relationships provide values that agree closely with experimental findings. It is thus possible to estimate the hydrogen bond contribution to P450 enzyme-substrate binding affinity based on modelled interactions and by use of these relatively simple formulae, particularly when employed in conjunction with substrate-lipophilicity relationships.

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Section: Introductionsupporting

confidence: 80%

Hydrogen Bonding in Human P450-Substrate Interactions: A Major Contribution to Binding Affinity

Lewis

2004

The Scientific World JOURNAL

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“…Furthermore, every single molecule investigated with higher DM value has been reported to have unique properties [37]. The DM of molecular compounds has been determined to range between 3 and 5 kJ/mol [38]. Practically, all of the DM values observed in this investigation are higher than the approved range.…”

Section: Quantum Chemical Calculationsmentioning

confidence: 75%

In-silico investigation of oxoaporphine alkaloids of Xylopia aethiopica against SARS-COV-2 main protease

Ogunyemi¹,

Oderinlo²

2022

AROC Nat. Prod. Res.

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Background: The ongoing coronavirus pandemic poses a significant social, economic, and health threat worldwide. The situation is exacerbated further by vaccine hesitancy and the ongoing development of mutant strains that could lead to drug resistance. It is therefore critical to find new anti-viral chemotherapeutic agents to reduce or end the epidemic. This study aimed to investigate the antiprotease activity of the oxoaporphine alkaloids in Xylopia aethiopica. Methods: Computational techniques such as molecular docking were used to probe the oxoaporphine alkaloids in the plant for their ability to inhibit the main protease of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The docking score calculations which quantifies the predictive binding affinity of both ligand and target was carried out using Auto-Dock Vina software. Results: The results showed that oxoaporphine alkaloids had a better binding affinity than hydroxychloroquine sulfate (standard). Similarly, the values of the chemical descriptors obtained for these alkaloids revealed notable profiles, and these alkaloids also have good oral bioavailability according to rule of five. Conclusion: These findings imply that these plant-based alkaloids could be investigated further as prospective leads against SARS-CoV-2 main protease. Furthermore, structural-activity relationships on these compounds could be an effective way to mitigate the predicted side effects

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“…This is due to the fact that log P comprises a number of components that relate to various aspects of molecular structure. The two most important components of solvation energy are electrostatic and polarization changes, and therefore it is assumed that log P comprises polarization, electrostatic, and electronic terms (22). The van der Waals area (VDW area) (molecular bulk) and HOMO energy (reactivity), but not μ (molecular polarity) of monomers widely used in dental materials have been linearly correlated with log P (11).…”

Section: Discussionmentioning

confidence: 99%

Cytotoxicity and Pro-inflammatory Properties of Aliphatic Alpha, Beta-unsaturated Acid and Ester Monomers in RAW264.7 Cells and Their Chemical Reactivity

Murakami

Kawata

Suzuki

et al. 2019

In Vivo

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Background/Aim: α,β-Unsaturated ester monomers such as methyl methacrylates (MMA), 2-hydroxyethyl methacrylates (2-HEMA), ethyleneglycol dimethacrylate (EGDMA) and triethyleneglycol dimetacrylate (TEGDMA) have been widely used in dentistry as dental materials. The present study was designed to clarify the proinflammatory activity of monomers. Materials and Methods: The cytotoxicity of the monomers and their effects on the expression of cyclooxygenase-2 (Cox2), nitric oxide synthase 2 (Nos2) and heme oxygenase 1 (Ho-1) mRNAs in RAW264.7 cells were determined using a cell counting kit and real-time reverse transcriptase-polymerase chain reaction, respectively. Results: The cytotoxicity declined in the order n-butyl acrylate (nBA) > acrylic acid > TEGDMA > EGDMA > methacrylic acid ≈ 2-HEMA > lauryl methacrylate > nBMA > MMA. nBA and EGDMA at 1 mM up-regulated the expression of Cox2 mRNA. In contrast, 1 mM nBA and 10 mM 2-HEMA up-regulated the expression of Nos2 mRNA. Up-regulation of Ho-1 mRNA expression was found for 0.1 mM nBA, 1 mM EGDMA and 2 mM TEGDMA. The electrophilicity, ω was calculated on the basis of the density function theory BLYP/6-31G*. Conclusion: nBA and EGDMA with high ω values exerted potent proinflammatory activities. nBA, EGDMA and TEGDMA upregulated Ho-1 gene expression. Ho-1 gene activation of monomers may promote resistance of chemical carcinogenesis in biological systems.

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Molecular Binding Interactions: Their Estimation and Rationalization in QSARs in Terms of Theoretically Derived Parameters

Cited by 10 publications

References 81 publications

Hydrogen Bonding in Human P450-Substrate Interactions: A Major Contribution to Binding Affinity

Hydrogen Bonding in Human P450-Substrate Interactions: A Major Contribution to Binding Affinity

In-silico investigation of oxoaporphine alkaloids of Xylopia aethiopica against SARS-COV-2 main protease

Cytotoxicity and Pro-inflammatory Properties of Aliphatic Alpha, Beta-unsaturated Acid and Ester Monomers in RAW264.7 Cells and Their Chemical Reactivity

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