Molecular Docking for Ligand-Protein Screening

Molecular docking, a computational approach to calculate the binding energy between proteins and ligands [23 (link)], were used for screening the target of PHZ-OH. Given that OMV mediates cytosolic delivery of LPS by clathrin-dependent endocytosis [12 (link)], the crystal structures of potential targets, including LPS-related receptors or endocytosis-associated proteins, were retrieved from http://www.rcsb.org/ (Table S2), while the structural formulas of PHZ-OH was constructed using Chim3D (2010). Molecular docking between PHZ-OH and proteins was conducted by using AutoDock 4.0 and AutoDock Tools 1.5.6, in which independent docking calculation was conducted with 250,0000 evaluations using Lamarckian Genetic Algorithm. To validate the binding of PHZ-OH and AAK1 in physics, surface plasmon resonance was subsequently performed by using BIAcore4000 (BIAcore). The equilibrium-binding constant (KD, the lower value the higher affinity) of PHZ-OH and AAK1 was determined as described previously [24 (link)].

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Yuan C., Ai K., Xiang M., Xie C., Zhao M., Wu M., Li H., Wu Y., Cao Y., Li C., Zhong Y., Pei X., Law H.K., Gao L., Xiao Q, & Yang X. (2022). Novel 1-hydroxy phenothiazinium-based derivative protects against bacterial sepsis by inhibiting AAK1-mediated LPS internalization and caspase-11 signaling. Cell Death & Disease, 13(8), 722.

Publication 2022

AutoDock Tools 1.5.6 BIAcore4000

Binding proteins Clathrin Cytosolic Delivery Endocytosis Formulas Genetic Ligands Lps receptors Proteins Surface plasmon resonance

Corresponding Organization : Central South University

Other organizations : Sun Yat-sen University, The Seventh Affiliated Hospital of Sun Yat-sen University, Second Xiangya Hospital of Central South University, Hong Kong Polytechnic University

Top 5 similar protocols

Variable analysis

independent variables

Molecular docking between PHZ-OH and proteins

dependent variables

Binding energy between proteins and ligands
Equilibrium-binding constant (KD) of PHZ-OH and AAK1

control variables

Crystal structures of potential targets, including LPS-related receptors or endocytosis-associated proteins, retrieved from http://www.rcsb.org/
Structural formulas of PHZ-OH constructed using Chim3D (2010)
Molecular docking conducted using AutoDock 4.0 and AutoDock Tools 1.5.6, with 250,0000 evaluations using Lamarckian Genetic Algorithm
Surface plasmon resonance performed using BIAcore4000 (BIAcore) to validate the binding of PHZ-OH and AAK1

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