Molecular docking and molecular dynamics simulation analyses of urea with ammoniated and ammoxidized lignin

Li, Wenzhuo; Zhang, Song; Zhao, Yingying; Huang, Shuaiyu; Zhao, Jianlong

doi:10.1016/j.jmgm.2016.11.005

Cited by 23 publications

(8 citation statements)

References 49 publications

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“…In order to investigate the enhancement mechanism of PDA-AL on the viscosity and mechanical strength of PAM hydrogels, the interactions between PDA, AL, and PAM were simulated by molecular dynamics model using radial distribution function (RDF, see Supporting Information for the specific simulation calculation parameters). − Prior to the calculation, the initial geometry structural models were set. The initial geometry structure models of PDA, AL, AM chain, PDA-AL, pure PAM hydrogel, and PDA-AL-PAM structures were illustrated in Figure S5 and Figure a-c.…”

Section: Resultsmentioning

confidence: 99%

Self-Adhesive and Conductive Dual-Network Polyacrylamide Hydrogels Reinforced by Aminated Lignin, Dopamine, and Biomass Carbon Aerogel for Ultrasensitive Pressure Sensor

Chen

Zheng

et al. 2022

ACS Appl. Mater. Interfaces

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Conductive hydrogels have attracted extensive interest owing to its potential in soft robotics, electronic skin, and human monitoring. However, insufficient mechanical properties, lower adhesivity, and unsatisfactory conductivity seriously hinder potential applications in this emerging field. Herein, a highly elastic conductive hydrogel with a combination of favorable mechanical properties, self-adhesiveness, and excellent electrical performance was achieved by the synergistic effect of aminated lignin (AL), polydopamine (PDA), polyacrylamide (PAM) chains, and biomass carbon aerogel (C-SPF). In detail, AL was applied to induce slow oxidative polymerization of DA for preparing the sticky hydrogel containing PDA. Then, C-SPF carbon aerogel was used as a matrix to construct a dual-network structured composite hydrogel by combining with the hydrogels derived from PDA, AL, and PAM. The as-prepared conductive hydrogel displayed excellent mechanical performance, strong adhesive strength, and repeatable adhesivity. The prepared hydrogel-based pressure sensor possessed fast response (0.6 s loading and 0.8 s unloading stress time), high response (maximum RCR = 1.8 × 104), wide working pressure range (from 0 to 240.0 kPa), and excellent durability (stable 500 compression cycles with 30% deformation). In addition, the prepared sensor also displayed ultrahigh sensitivity (170 kPa–1), which was near 4 orders of magnitude higher than the conventional lignin-modified PAM hydrogels. The multiple interactions between hydrogel components and the mechanical properties of hydrogel were also verified by molecular dynamics investigation. Moreover, the excellent cytocompatibility and antibacterial activity of this composite hydrogel ensured high potential in various applications such as human/machine interaction, artificial intelligence, personal healthcare, and wearable devices.

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Section: Resultsmentioning

confidence: 99%

Self-Adhesive and Conductive Dual-Network Polyacrylamide Hydrogels Reinforced by Aminated Lignin, Dopamine, and Biomass Carbon Aerogel for Ultrasensitive Pressure Sensor

Chen

Zheng

et al. 2022

ACS Appl. Mater. Interfaces

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“…Two potential candidates for the treatment of Tuberculosis were identified by docking and MD simulations (Isa et al., 2018). A series of MD simulations helped to study the difference between the interactions of lignin, ammoniated lignin and ammoxidized lignin with respect to urea (Li et al., 2017). The fluctuations of a ligand and its receptor were measured by RMSDs against an initial structure, revealing the conformational changed upon ligand binding, and the transformation and translocation of the ligand in the binding pocket.…”

Section: Discussionmentioning

confidence: 99%

Discovery of novel SecA inhibitors against “Candidatus Liberibacter asiaticus” through virtual screening and biological evaluation

Zhang¹,

Han²,

Mao³

et al. 2021

Chem Biol Drug Des

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“Candidatus Liberibacter asiaticus” (Ca. L. asiaticus) is the causal agent of Huanglongbing disease of citrus and current study focuses on the discovery of novel small‐molecule inhibitors against SecA protein of Ca. L. asiaticus. In this study, homologous modeling was used to construct the three‐dimensional structure of SecA. Then, molecular docking‐based virtual screening and two rounds of in vitro bacteriostatic experiments were utilized to identify novel small‐molecule inhibitors of SecA. Encouragingly, 93 compounds were obtained and two of them (P684‐2850, P684‐3808) showed strong antimicrobial activities against Liberibacter crescens BT‐1 in bacteriostatic experiments. Finally, molecular dynamics simulations were employed to explore the binding modes of the receptor–ligand complexes. Results in MD simulations showed that compound P684‐3808 was relatively stable during simulation, while compound P684‐2850 left the binding pocket. Compound P684‐3808 might be suitable as a lead compound for further development of antimicrobial compounds against SecA of Ca. L. asiaticus.

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“…Benserazide : Benserazide is one of the PKM2 inhibitors that directly binds to PKM2 and blocks its activity thus inhibiting aerobic glycolysis and upregulating oxidative phosphorylation (Zhou et al, 2020). Benserazide has been shown to induce cell death in melanoma and colon cancer cells without affecting normal cells (Li, Zhang, Zhao, Huang, & Zhao, 2017; Zhou et al, 2020). In vivo studies have shown that benserazide inhibited tumor growth in the colorectal cancer xenotransplantation model (Szabo, Yoshida, Filakovszky, & Juhasz, 2017).…”

Section: Synthetic Pkm2 Inhibitorsmentioning

confidence: 99%

Cancer metabolism control by natural products: Pyruvate kinase M2 targeting therapeutics

El‐Far

Jaouni

et al. 2022

Phytotherapy Research

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Glycolysis is the primary source of energy for cancer growth and metastasis. The shift in metabolism from mitochondrial oxidative phosphorylation to aerobic glycolysis is called the Warburg effect. Cancer progression due to aerobic glycolysis is often associated with the activation of oncogenes or the loss of tumor suppressors. Therefore, inhibition of glycolysis is one of the effective strategies in cancer control. Pyruvate kinase M2 (PKM2) is a key glycolytic enzyme overexpressed in breast, prostate, lung, colorectal, and liver cancers. Here, we discuss published studies regarding PKM2 inhibitors from natural products that are promising drug candidates for cancer therapy. We have highlighted the potential of natural PKM2 inhibitors for various cancer types. Moreover, we encourage researchers to evaluate the combinational effects between natural and synthetic PKM2 inhibitors. Also, further high‐quality studies are needed to firmly establish the clinical efficacy of natural products.

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Molecular docking and molecular dynamics simulation analyses of urea with ammoniated and ammoxidized lignin

Cited by 23 publications

References 49 publications

Self-Adhesive and Conductive Dual-Network Polyacrylamide Hydrogels Reinforced by Aminated Lignin, Dopamine, and Biomass Carbon Aerogel for Ultrasensitive Pressure Sensor

Self-Adhesive and Conductive Dual-Network Polyacrylamide Hydrogels Reinforced by Aminated Lignin, Dopamine, and Biomass Carbon Aerogel for Ultrasensitive Pressure Sensor

Discovery of novel SecA inhibitors against “Candidatus Liberibacter asiaticus” through virtual screening and biological evaluation

Cancer metabolism control by natural products: Pyruvate kinase M2 targeting therapeutics

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