AN IN SILICO APPROACH TO DESIGN PEPTIDE MIMETICS BASED ON DOCKING AND MOLECULAR DYNAMICS SIMULATION OF EGFR–MATUZUMAB COMPLEX

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EBRAHIMI MALIHE; MANI VARNOSFADERANI AHMAD; KHAYAMIAN TAGHI; GHARAGHANI SAJJAD

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Journal: JOURNAL OF THE IRANIAN CHEMICAL SOCIETY(JICS) Year:2016 | Volume:13 | Issue:10 Page(s): 0-0

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Title

AN IN SILICO APPROACH TO DESIGN PEPTIDE MIMETICS BASED ON DOCKING AND MOLECULAR DYNAMICS SIMULATION OF EGFR–MATUZUMAB COMPLEX

Author(s)

EBRAHIMI MALIHE | MANI VARNOSFADERANI AHMAD | KHAYAMIAN TAGHI | GHARAGHANI SAJJAD | Issue Writer Certificate

Keywords

EPITOPE PARATOPE ALANINE

SCANNING HOT

SPOT DOCKING MOLECULAR

DYNAMICS

Abstract

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular DYNAMICS simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.

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APA: Copy

EBRAHIMI, MALIHE, MANI VARNOSFADERANI, AHMAD, KHAYAMIAN, TAGHI, & GHARAGHANI, SAJJAD. (2016). AN IN SILICO APPROACH TO DESIGN PEPTIDE MIMETICS BASED ON DOCKING AND MOLECULAR DYNAMICS SIMULATION OF EGFR–MATUZUMAB COMPLEX. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY(JICS), 13(10), 0-0. SID. https://sid.ir/paper/283235/en

Vancouver: Copy

EBRAHIMI MALIHE, MANI VARNOSFADERANI AHMAD, KHAYAMIAN TAGHI, GHARAGHANI SAJJAD. AN IN SILICO APPROACH TO DESIGN PEPTIDE MIMETICS BASED ON DOCKING AND MOLECULAR DYNAMICS SIMULATION OF EGFR–MATUZUMAB COMPLEX. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY(JICS)[Internet]. 2016;13(10):0-0. Available from: https://sid.ir/paper/283235/en

IEEE: Copy

MALIHE EBRAHIMI, AHMAD MANI VARNOSFADERANI, TAGHI KHAYAMIAN, and SAJJAD GHARAGHANI, “AN IN SILICO APPROACH TO DESIGN PEPTIDE MIMETICS BASED ON DOCKING AND MOLECULAR DYNAMICS SIMULATION OF EGFR–MATUZUMAB COMPLEX,” JOURNAL OF THE IRANIAN CHEMICAL SOCIETY(JICS), vol. 13, no. 10, pp. 0–0, 2016, [Online]. Available: https://sid.ir/paper/283235/en

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