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Comparative assessment of different anti-CD147/Basigin 2 antibodies as a potential therapeutic anticancer target by molecular modeling and dynamic simulation

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Abstract

Cluster of differentiation 147 (CD147) is an attractive target for anticancer therapy since it is pivotal in developing and progressing several of malignant tumors in the context of its high expression levels. Although anti-CD147 antibodies by different laboratories are designed for the Ig-like domains of CD147, there is a demand to provide priority among these anti-CD147 antibodies for developing of therapeutic anti-CD147 antibody before experimental validations. This study uses molecular docking and dynamic simulation techniques to compare the binding modes and affinities of nine antibody models against the Ig-like domains of CD147. After obtaining the model antibodies by homology modeling via Robetta, we predicted the CDRs of nine antibodies and the epitopes of CD147 to reach more accurate results for antigen affinity in molecular docking. Next, from HADDOCK 2.4., we meticulously handpicked the most superior model clusters (Z-Score: − 2.5 to − 1.2) and identified that meplazumab had higher affinities according to the success rate as the percentage of a scoring scale. We achieved stable simulations of CD147-antibody interaction. Our outcomes hold hypothetical importance for further experimental cancer research on the design and development of the relevant model antibodies.

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Acknowledgements

This research was partially supported by the supercomputing infrastructure of Poznan Supercomputing Center, and by the e-infrastructure program of the Research Council of Norway, and the supercomputer center of UiT—the Arctic University of Norway. The authors also thankfully acknowledge the computer resources and the technical support provided by the Plataforma Andaluza de Bioinforma ́tica of the University of Ma ́laga. Powered@NLHPC: This research was partially supported by the supercomputing infrastructure of the NLHPC (ECM-02).

Funding

This work has been supported to H.P.-S. by the Fundación Séneca del Centro de Coordinación de la Investigación de la Región de Murcia (under Project 20988/PI/18) and by a grant from Ministerio de Economía y Competitividad de Espan ̃a (CTQ2017-87974-R). M. C.-B. is a predoctoral employed to the training of research staff financed by the Plan Propio de Investigación de la UCAM.

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Authors and Affiliations

  1. Department of Medical Biology, Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey

    Nail Besli

  2. Faculty of Medicine, Medical Program, Istanbul University-Cerrahpasa, Istanbul, Turkey

    Halil İbrahim Bulut

  3. Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey

    İlhan Onaran

  4. Computer Engineering Department, Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), UCAM Universidad Católica de Murcia, Guadalupe, Spain

    Miguel Carmena-Bargueño & Horacio Pérez-Sánchez

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  1. Nail Besli
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  4. Miguel Carmena-Bargueño
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  5. Horacio Pérez-Sánchez
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Contributions

All authors hypothesized the subject. Besli, Bulut and Onaran performed the concept design and writing processes. Data collection and edited of the article were conducted by CARMENA-BARGUEÑO and Besli. PÉREZ-SÁNCHEZ, CARMENA-BARGUEÑO and Besli evaluated the results.

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Correspondence to Horacio Pérez-Sánchez.

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Besli, N., Bulut, H.İ., Onaran, İ. et al. Comparative assessment of different anti-CD147/Basigin 2 antibodies as a potential therapeutic anticancer target by molecular modeling and dynamic simulation. Mol Divers (2024). https://doi.org/10.1007/s11030-024-10832-w

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