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For: Farasat A, Rahbarizadeh F, Hosseinzadeh G, Sajjadi S, Kamali M, Keihan AH. Affinity enhancement of nanobody binding to EGFR: in silico site-directed mutagenesis and molecular dynamics simulation approaches. J Biomol Struct Dyn 2016;35:1710-1728. [PMID: 27691399 DOI: 10.1080/07391102.2016.1192065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Number Cited by Other Article(s)
1
Heidari MM, Shirazi EA, Cheraghi SF, Shahshahani R, Rahnama T, Khatami M. CDR grafting and site-directed mutagenesis approach for the generation and affinity maturation of Anti-CD20 nanobody. Mol Biol Rep 2024;51:751. [PMID: 38874667 DOI: 10.1007/s11033-024-09684-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
2
Shojazadeh T, Zolghadr L, Gharaghani S, JafarKhani S, Molaabasi F, Piri H, Gheibi N. New insights into the inhibitory effect of phenol carboxylic acid antioxidants on mushroom tyrosinase by molecular dynamic studies and experimental assessment. J Biomol Struct Dyn 2023;41:13404-13414. [PMID: 36856125 DOI: 10.1080/07391102.2023.2175038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/21/2023] [Indexed: 03/02/2023]
3
Shariatifar H, Farasat A. Affinity enhancement of CR3022 binding to RBD; in silico site directed mutagenesis using molecular dynamics simulation approaches. J Biomol Struct Dyn 2023;41:81-90. [PMID: 34796779 DOI: 10.1080/07391102.2021.2004230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
4
Sepahdar Z, Saghiri R, Miroliaei M, Salimi M. In silico approach to probe the binding affinity between OMVs harboring the ZEGFR affibody and the EGF receptor. J Mol Model 2022;28:113. [PMID: 35381900 DOI: 10.1007/s00894-022-05043-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/25/2022] [Indexed: 11/27/2022]
5
Ahmadi K, Farasat A, Rostamian M, Johari B, Madanchi H. Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study. J Biomol Struct Dyn 2021;40:5566-5576. [PMID: 33438525 PMCID: PMC7814568 DOI: 10.1080/07391102.2021.1871958] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
6
Sharifi J, Khirehgesh MR, Safari F, Akbari B. EGFR and anti-EGFR nanobodies: review and update. J Drug Target 2020;29:387-402. [DOI: 10.1080/1061186x.2020.1853756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
7
Rostamian M, Farasat A, Chegene Lorestani R, Nemati Zargaran F, Ghadiri K, Akya A. Immunoinformatics and molecular dynamics studies to predict T-cell-specific epitopes of four Klebsiella pneumoniae fimbriae antigens. J Biomol Struct Dyn 2020;40:166-176. [PMID: 32820713 DOI: 10.1080/07391102.2020.1810126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
8
Gheibi N, Ghorbani M, Shariatifar H, Farasat A. Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach. PLoS One 2020;15:e0230780. [PMID: 32214349 PMCID: PMC7098580 DOI: 10.1371/journal.pone.0230780] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]  Open
9
Valojerdi FM, Farasat A, Shariatifar H, Gheibi N. Study of HSA interactions with arachidonic acid using spectroscopic methods revealing molecular dynamics of HSA-AA interactions. Biomed Rep 2020;12:125-133. [PMID: 32042421 PMCID: PMC7006104 DOI: 10.3892/br.2019.1270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022]  Open
10
Gheibi N, Ghorbani M, Shariatifar H, Farasat A. In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach. PLoS One 2019;14:e0224095. [PMID: 31622441 PMCID: PMC6797115 DOI: 10.1371/journal.pone.0224095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022]  Open
11
Forouzesh M, Askerovich Mamedov A, Pourabadeh A, Hosseini M, Hosseinzadeh G, Arezumand R. Rational MD simulations for improvement the affinity of nanobody against PlGF (placenta growth factor): mutagenesis based on electrostatic interactions. J Biomol Struct Dyn 2019;38:3750-3756. [PMID: 31524085 DOI: 10.1080/07391102.2019.1664327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
12
Akya A, Farasat A, Ghadiri K, Rostamian M. Identification of HLA-I restricted epitopes in six vaccine candidates of Leishmania tropica using immunoinformatics and molecular dynamics simulation approaches. INFECTION GENETICS AND EVOLUTION 2019;75:103953. [PMID: 31284043 DOI: 10.1016/j.meegid.2019.103953] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/12/2022]
13
Khrustalev VV, Khrustaleva TA, Poboinev VV, Yurchenko KV. Mutational pressure and natural selection in epidermal growth factor receptor gene during germline and somatic mutagenesis in cancer cells. Mutat Res 2019;815:1-9. [PMID: 30974384 DOI: 10.1016/j.mrfmmm.2019.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/15/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
14
Wan S, Yan R, Jiang Y, Li Z, Zhang J, Wu X. Insight into binding mechanisms of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 2019;37:4384-4394. [DOI: 10.1080/07391102.2018.1552197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
15
Ebrahimi Z, Asgari S, Ahangari Cohan R, Hosseinzadeh R, Hosseinzadeh G, Arezumand R. Rational affinity enhancement of fragmented antibody by ligand-based affinity improvement approach. Biochem Biophys Res Commun 2018;506:653-659. [DOI: 10.1016/j.bbrc.2018.10.127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 10/21/2018] [Indexed: 11/28/2022]
16
Rouhani M, Khodabakhsh F, Norouzian D, Cohan RA, Valizadeh V. Molecular dynamics simulation for rational protein engineering: Present and future prospectus. J Mol Graph Model 2018;84:43-53. [DOI: 10.1016/j.jmgm.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 12/19/2022]
17
Farasat A, Rahbarizadeh F, Ahmadvand D, Ranjbar S, Khoshtinat Nikkhoi S. Effective suppression of tumour cells by oligoclonal HER2-targeted delivery of liposomal doxorubicin. J Liposome Res 2018;29:53-65. [DOI: 10.1080/08982104.2018.1430829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
18
Recent advances in the selection and identification of antigen-specific nanobodies. Mol Immunol 2018;96:37-47. [PMID: 29477934 DOI: 10.1016/j.molimm.2018.02.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/12/2018] [Accepted: 02/18/2018] [Indexed: 01/21/2023]
19
Arezumand R, Alibakhshi A, Ranjbari J, Ramazani A, Muyldermans S. Nanobodies As Novel Agents for Targeting Angiogenesis in Solid Cancers. Front Immunol 2017;8:1746. [PMID: 29276515 PMCID: PMC5727022 DOI: 10.3389/fimmu.2017.01746] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022]  Open
20
Farasat A, Rahbarizadeh F, Ahmadvand D, Yazdian F. Optimization of an anti-HER2 nanobody expression using the Taguchi method. Prep Biochem Biotechnol 2017. [DOI: 10.1080/10826068.2017.1342259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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