In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation
Hirudin is an anticoagulant agent of the salivary glands of the medicinal leech. Recombinant hirudin (r-Hir) displays certain drawbacks including bleeding and immunogenicity. To solve these problems, cysteine-specific PEGylation has been proposed as a successful technique. However, proper selection...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wolters Kluwer Medknow Publications
2017-01-01
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| Series: | Research in Pharmaceutical Sciences |
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| Online Access: | http://www.rpsjournal.net/article.asp?issn=1735-5362;year=2017;volume=12;issue=1;spage=60;epage=66;aulast=Sajjadi |
| _version_ | 1818656468631552000 |
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| author | Seyed Mehdi Sajjadi Hamzeh Rahimi Saeed Mohammadi Mohammad Faranoush Hasan Mirzahoseini Gholamreza Toogeh |
| author_facet | Seyed Mehdi Sajjadi Hamzeh Rahimi Saeed Mohammadi Mohammad Faranoush Hasan Mirzahoseini Gholamreza Toogeh |
| author_sort | Seyed Mehdi Sajjadi |
| collection | DOAJ |
| description | Hirudin is an anticoagulant agent of the salivary glands of the medicinal leech. Recombinant hirudin (r-Hir) displays certain drawbacks including bleeding and immunogenicity. To solve these problems, cysteine-specific PEGylation has been proposed as a successful technique. However, proper selection of the appropriate cysteine residue for substitution is a critical step. This study has, for the first time, used a computational approach aimed at identifying a single potential PEGylation site for replacement by cysteine residue in the hirudin variant 3 (HV3). Homology modeling (HM) was performed using MODELLER. All non-cysteine residues of the HV3 were replaced with the cysteine. The best model was selected based on the results of discrete optimized protein energy score, PROCHECK software, and Verify3D. The receptor binding was investigated using protein-protein docking by ClusPro web tool which was then visualized using LigPlot+ software and PyMOL. Finally, multiple sequence alignment (MSA) using ClustalW software and disulfide bond prediction were performed. According to the results of HM and docking, Q33C, which was located on the surface of the protein, was the best site for PEGylation. Furthermore, MSA showed that Q33 was not a conserved residue and LigPlot+ software showed that it is not involved in the hirudin-thrombin binding pocket. Moreover, prediction softwares established that it is not involved in disulfide bond formation. In this study, for the first time, the utility of the in silico approach for creating a cysteine analogue of HV3 was introduced. Our study demonstrated that the substitution of Q33 by cysteine probably has no effect on the biological activity of the HV3. However, experimental analyses are required to confirm the results. |
| first_indexed | 2024-12-17T03:26:04Z |
| format | Article |
| id | doaj.art-379210573aed4d51ae7887c679971840 |
| institution | Directory Open Access Journal |
| issn | 1735-5362 1735-9414 |
| language | English |
| last_indexed | 2024-12-17T03:26:04Z |
| publishDate | 2017-01-01 |
| publisher | Wolters Kluwer Medknow Publications |
| record_format | Article |
| series | Research in Pharmaceutical Sciences |
| spelling | doaj.art-379210573aed4d51ae7887c6799718402022-12-21T22:05:24ZengWolters Kluwer Medknow PublicationsResearch in Pharmaceutical Sciences1735-53621735-94142017-01-01121606610.4103/1735-5362.199048In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylationSeyed Mehdi SajjadiHamzeh RahimiSaeed MohammadiMohammad FaranoushHasan MirzahoseiniGholamreza ToogehHirudin is an anticoagulant agent of the salivary glands of the medicinal leech. Recombinant hirudin (r-Hir) displays certain drawbacks including bleeding and immunogenicity. To solve these problems, cysteine-specific PEGylation has been proposed as a successful technique. However, proper selection of the appropriate cysteine residue for substitution is a critical step. This study has, for the first time, used a computational approach aimed at identifying a single potential PEGylation site for replacement by cysteine residue in the hirudin variant 3 (HV3). Homology modeling (HM) was performed using MODELLER. All non-cysteine residues of the HV3 were replaced with the cysteine. The best model was selected based on the results of discrete optimized protein energy score, PROCHECK software, and Verify3D. The receptor binding was investigated using protein-protein docking by ClusPro web tool which was then visualized using LigPlot+ software and PyMOL. Finally, multiple sequence alignment (MSA) using ClustalW software and disulfide bond prediction were performed. According to the results of HM and docking, Q33C, which was located on the surface of the protein, was the best site for PEGylation. Furthermore, MSA showed that Q33 was not a conserved residue and LigPlot+ software showed that it is not involved in the hirudin-thrombin binding pocket. Moreover, prediction softwares established that it is not involved in disulfide bond formation. In this study, for the first time, the utility of the in silico approach for creating a cysteine analogue of HV3 was introduced. Our study demonstrated that the substitution of Q33 by cysteine probably has no effect on the biological activity of the HV3. However, experimental analyses are required to confirm the results.http://www.rpsjournal.net/article.asp?issn=1735-5362;year=2017;volume=12;issue=1;spage=60;epage=66;aulast=Sajjadiin silico ; hirudin variant 3; pegylation |
| spellingShingle | Seyed Mehdi Sajjadi Hamzeh Rahimi Saeed Mohammadi Mohammad Faranoush Hasan Mirzahoseini Gholamreza Toogeh In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation Research in Pharmaceutical Sciences in silico ; hirudin variant 3; pegylation |
| title | In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation |
| title_full | In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation |
| title_fullStr | In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation |
| title_full_unstemmed | In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation |
| title_short | In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation |
| title_sort | in silico designing of a new cysteine analogue of hirudin variant 3 for site specific pegylation |
| topic | in silico ; hirudin variant 3; pegylation |
| url | http://www.rpsjournal.net/article.asp?issn=1735-5362;year=2017;volume=12;issue=1;spage=60;epage=66;aulast=Sajjadi |
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