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Li Y.,Nankai University | Sun J.,Nankai University | Li D.,Nankai University | Lin J.,Nankai University | Lin J.,Tianjin Joint Academy of Biomedicine and Technology
Physical Chemistry Chemical Physics | Year: 2016

The human glucagon receptor (GCGR) is a class B G-protein-coupled receptor (GPCR). The GCGR can be activated by glucagon and regulates the release of glucose. The GCGR has been proposed to be an important drug target for type 2 diabetes. Based on the structural model of a full-length glucagon-bound GCGR (glu-GCGR), we performed accelerated molecular dynamics (aMD) simulations, potential of mean force (PMF) calculations, cross-correlation analysis and community network analysis to study the activation mechanism and the conformational dynamics during the activation process. The PMF map depicts three different conformational states of the GCGR: the inactive, intermediate and active states. The activation of the GCGR is characterized by the outward movement of the intracellular side of helix VI. In the active state of the GCGR, the Arg1732.46-Ser3506.41 and Glu2453.50-Thr3516.42 hydrogen bonds break, and the χ1 rotamer of Phe3225.54 changes from perpendicular to parallel to helix VI. The binding of the agonist glucagon decreases the correlated motions of the extracellular loops (ELCs) and the helices around the glucagon-binding site. During the activation of the GCGR, the connections between the intracellular sides of helices become weaker, and the connections between glucagon and ECLs and the extracellular sides of helices become stronger. These facilitate G-protein coupling on the intracellular side and glucagon binding on the extracellular side, and stabilize the GCGR in the active state. We expect that this study can provide useful information on the activation mechanism of the GCGR and facilitate the future design of GCGR inhibitors. © 2016 the Owner Societies. Source

Fu W.,Chinese PLA General Hospital | Fu W.,International Medical University | Fu W.,Tianjin Joint Academy of Biomedicine and Technology | Wang X.,Nagoya University | And 14 more authors.
Amino Acids | Year: 2015

Abstract Previously, we reported on the crystal structures of the Fab fragments of two food and drug administration approved therapeutic antibodies, Infliximab and Adalimumab, in complex with TNFα. The structurally identified epitopes on TNFα reveal the mechanism of TNFα inhibition by partially overlapping with the TNFα-receptor interface. In this study, we launched a screen of a phage display library to isolate novel anti-TNFα antibodies based on the adalimumab epitope. Structural analysis, the phage display antibody isolation technology, step-by-step antibody optimization, complementarity-determining region residues random mutagenesis, phage ELISA, binding affinity characterization, and cell signaling assays were used for the development and optimization of the novel anti-TNFα antibodies. Moreover, one of the novel antibodies, hAta09, has a superior inhibitory effect on TNFα function and signaling. Taken together, our report established that the novel anti-TNFα antibody hAta09 may achieve clinical efficacy in a TNFα-associated disease. © 2015 Springer-Verlag Wien. Source

Xu J.,Nankai University | Xu J.,Tianjin Joint Academy of Biomedicine and Technology | Wang Z.,Nankai University | Liu P.,Nankai University | And 3 more authors.
Molecular BioSystems | Year: 2015

The human corticotropin-releasing factor receptor type 1 (CRF1R) is a class B G-protein-coupled receptor (GPCR), which mediates the response to stress and has been considered as a drug target for depression and anxiety. Based on the CRF1R-antagonist crystal structure, we study the binding mechanism of two distinct antagonists, CP-376395 and MTIP, and the dynamics behaviors of CRF1R induced by an antagonist binding. Key residues interacting with both antagonists and residues specifically binding to one of them are identified. Both antagonists interact with Asn283, Phe203, Met206, Leu280, Tyr316, Leu323, Leu287, Phe284, Val279, Leu319, Phe207, Gly210 and Phe362. CP-376395 specifically binds to Glu209 and Phe160, while MTIP specifically binds to Leu320, Leu213, Ile290, Phe162 and Val313. The total binding free energy of MTIP is lower than that of CP-376395; this is consistent with the experimental observation that MTIP shows higher binding affinity than CP-376395. The conformational dynamic behaviors of antagonist bound holo-CRF1R were found to be different from those of apo-CRF1R in three aspects: (i) the "ionic lock" between side chains of Arg151 in TM2 and Glu209 in TM3 was broken in apo-CRF1R, but was formed in holo-CRF1Rs; (ii) Phe203 in TM3 and Tyr327 in TM6 were in close proximity to each other in apo-CRF1R, while they were far apart resulting from the shift of TM6 in holo-CRF1Rs; and (iii) the "rotamer toggle switch", Tyr327/Leu323/Phe284, adopted different rotameric conformations in apo-CRF1R and holo-CRF1Rs. We hope that our results could be helpful in further development of the drug design of CRF1R. © The Royal Society of Chemistry. Source

Hu S.,International Medical University | Hu S.,Cancer Center | Hu S.,Tianjin Joint Academy of Biomedicine and Technology | Dai H.,Nanjing University | And 11 more authors.
Cancer Letters | Year: 2015

Dysfunction of the epidermal growth factor receptor (EGFR) family, is the key process in tumorigenesis, and anti-EGFR therapeutic strategies such as cetuximab therapy now are used in the treatment of cancer. However, resistance to cetuximab is commonly reported. Comprehensive blockade of EGFR signaling using different antibodies might be critical to treat cancer effectively and limit drug resistance with potent novel mechanisms. Here, we launch a screen of a phage display library to isolate a novel anti-EGFR antibody, YAH627. YAH627 exhibits superior efficacy in inhibiting EGFR activation, particularly by blocking EGF/HRG-induced EGFR/HER3 heterodimerization and signaling, verifying it as an impressive candidate for clinical translation as a therapeutic antibody. Moreover, we use epitope analysis validates that the epitope of this antibody is within domains II and IV of EGFR and traps EGFR in a silent conformation. Moreover, combining YAH627 with cetuximab produces synergistic antitumor activity in vitro and in vivo. Taken together, our report establishes that YAH627 possesses a novel mechanism of action that, in combination with cetuximab, may achieve clinical efficacy in EGFR-driven cancers. © 2014 Elsevier Ireland Ltd. Source

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