Innovative CDR grafting and computational methods for PD-1 specific nanobody design
IntroductionThe development of nanobodies targeting Programmed Cell Death Protein-1 (PD-1) offers a promising approach in cancer immunotherapy. This study aims to design and characterize a PD-1-specific nanobody using an integrated computational and experimental approach.MethodsAn in silico design s...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2024.1488331/full |
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| author | Jagadeeswara Reddy Devasani Girijasankar Guntuku Nalini Panatula Murali Krishna Kumar Muthyala Mary Sulakshana Palla Teruna J. Siahaan |
| author_facet | Jagadeeswara Reddy Devasani Girijasankar Guntuku Nalini Panatula Murali Krishna Kumar Muthyala Mary Sulakshana Palla Teruna J. Siahaan |
| author_sort | Jagadeeswara Reddy Devasani |
| collection | DOAJ |
| description | IntroductionThe development of nanobodies targeting Programmed Cell Death Protein-1 (PD-1) offers a promising approach in cancer immunotherapy. This study aims to design and characterize a PD-1-specific nanobody using an integrated computational and experimental approach.MethodsAn in silico design strategy was employed, involving Complementarity-Determining Region (CDR) grafting to construct the nanobody sequence. The three-dimensional structure of the nanobody was predicted using AlphaFold2, and molecular docking simulations via ClusPro were conducted to evaluate binding interactions with PD-1. Physicochemical properties, including stability and solubility, were analyzed using web-based tools, while molecular dynamics (MD) simulations assessed stability under physiological conditions. The nanobody was produced and purified using Ni-NTA chromatography, and experimental validation was performed through Western blotting, ELISA, and dot blot analysis.ResultsComputational findings demonstrated favorable binding interactions, stability, and physicochemical properties of the nanobody. Experimental results confirmed the nanobody’s specific binding affinity to PD-1, with ELISA and dot blot analyses providing evidence of robust interaction.DiscussionThis study highlights the potential of combining computational and experimental approaches for engineering nanobodies. The engineered PD-1 nanobody exhibits promising characteristics, making it a strong candidate for further testing in cancer immunotherapy applications. |
| format | Article |
| id | doaj-art-fa834efd4d2a491b9340252ab1d82d55 |
| institution | Kabale University |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Bioinformatics |
| spelling | doaj-art-fa834efd4d2a491b9340252ab1d82d552025-01-17T06:51:17ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-01-01410.3389/fbinf.2024.14883311488331Innovative CDR grafting and computational methods for PD-1 specific nanobody designJagadeeswara Reddy Devasani0Girijasankar Guntuku1Nalini Panatula2Murali Krishna Kumar Muthyala3Mary Sulakshana Palla4Teruna J. Siahaan5Pharmaceutical Biotechnology Division, A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, IndiaPharmaceutical Biotechnology Division, A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, IndiaPharmaceutical Biotechnology Division, A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, IndiaPharmaceutical Chemistry Division, A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, IndiaGITAM School of Pharmacy, GITAM Deemed to be University, Visakhapatnam, Andhra Pradesh, IndiaDepartment of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS, United StatesIntroductionThe development of nanobodies targeting Programmed Cell Death Protein-1 (PD-1) offers a promising approach in cancer immunotherapy. This study aims to design and characterize a PD-1-specific nanobody using an integrated computational and experimental approach.MethodsAn in silico design strategy was employed, involving Complementarity-Determining Region (CDR) grafting to construct the nanobody sequence. The three-dimensional structure of the nanobody was predicted using AlphaFold2, and molecular docking simulations via ClusPro were conducted to evaluate binding interactions with PD-1. Physicochemical properties, including stability and solubility, were analyzed using web-based tools, while molecular dynamics (MD) simulations assessed stability under physiological conditions. The nanobody was produced and purified using Ni-NTA chromatography, and experimental validation was performed through Western blotting, ELISA, and dot blot analysis.ResultsComputational findings demonstrated favorable binding interactions, stability, and physicochemical properties of the nanobody. Experimental results confirmed the nanobody’s specific binding affinity to PD-1, with ELISA and dot blot analyses providing evidence of robust interaction.DiscussionThis study highlights the potential of combining computational and experimental approaches for engineering nanobodies. The engineered PD-1 nanobody exhibits promising characteristics, making it a strong candidate for further testing in cancer immunotherapy applications.https://www.frontiersin.org/articles/10.3389/fbinf.2024.1488331/fullcancer immunotherapynanobodyprogrammed cell death protein-1complementarity-determining regionWestern blotELISA |
| spellingShingle | Jagadeeswara Reddy Devasani Girijasankar Guntuku Nalini Panatula Murali Krishna Kumar Muthyala Mary Sulakshana Palla Teruna J. Siahaan Innovative CDR grafting and computational methods for PD-1 specific nanobody design Frontiers in Bioinformatics cancer immunotherapy nanobody programmed cell death protein-1 complementarity-determining region Western blot ELISA |
| title | Innovative CDR grafting and computational methods for PD-1 specific nanobody design |
| title_full | Innovative CDR grafting and computational methods for PD-1 specific nanobody design |
| title_fullStr | Innovative CDR grafting and computational methods for PD-1 specific nanobody design |
| title_full_unstemmed | Innovative CDR grafting and computational methods for PD-1 specific nanobody design |
| title_short | Innovative CDR grafting and computational methods for PD-1 specific nanobody design |
| title_sort | innovative cdr grafting and computational methods for pd 1 specific nanobody design |
| topic | cancer immunotherapy nanobody programmed cell death protein-1 complementarity-determining region Western blot ELISA |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2024.1488331/full |
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