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Pamonsupornwichit T, Kodchakorn K, Udomwong P, Sornsuwan K, Weechan A, Juntit OA, Nimmanpipug P, Tayapiwatana C. Engineering affinity of humanized ScFv targeting CD147 antibody: A combined approach of mCSM-AB2 and molecular dynamics simulations. J Mol Graph Model 2024; 133:108884. [PMID: 39405982 DOI: 10.1016/j.jmgm.2024.108884] [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: 07/16/2024] [Revised: 09/24/2024] [Accepted: 10/11/2024] [Indexed: 10/21/2024]
Abstract
This study aims to assess the effectiveness of mCSM-AB2, a graph-based signature machine learning method, for affinity engineering of the humanized single-chain Fv anti-CD147 (HuScFvM6-1B9). In parallel, molecular dynamics (MD) simulations were used to gain valuable insights into the dynamics and affinity of the HuScFvM6-1B9-CD147 complex. The result analysis involved integrating free energy changes calculated from the mCSM-AB2 with binding free energy predictions from MD simulations. The simulated structures of the modified HuScFvM6-1B9-CD147 domain 1 complex from MD simulations were used to highlight critical residues participating in the binding surface. Interestingly, alterations in the pattern of amino acids of HuScFvM6-1B9 at the complementarity determining regions interacting with the 31EDLGS35 epitope were observed, particularly in mutants that lost binding activity. The predicted mutants of HuScFvM6-1B9 were subsequently engineered and expressed in E. coli for subsequent binding property validation. Compared to WT HuScFvM6-1B9, the mutant HuScFvM6-1B9L1:N32Y exhibited a 1.66-fold increase in binding affinity, with a KD of 1.75 × 10-8 M. While mCSM-AB2 demonstrates insignificant improvement in predicting binding affinity enhancements, it excels at predicting negative effects, aligning well with experimental validation. In addition to binding free energies, total entropy was considered to explain the discrepancy between mCSM-AB2 predictions and experimental results. This study provides guidelines and identifies the limitations of mCSM-AB2 and MD simulations in antibody engineering.
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Affiliation(s)
- Thanathat Pamonsupornwichit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanchanok Kodchakorn
- Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand; Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Piyachat Udomwong
- International College of Digital Innovation, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanokporn Sornsuwan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Anuwat Weechan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - On-Anong Juntit
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Piyarat Nimmanpipug
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [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: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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Franco Machado J, Sá M, Pires I, da Silva MT, Marques F, Coelho JAS, Mendes F, Piedade MFM, Machuqueiro M, Jiménez MA, Garcia MH, Correia JDG, Morais TS. Dual FGFR-targeting and pH-activatable ruthenium-peptide conjugates for targeted therapy of breast cancer. Dalton Trans 2024; 53:7682-7693. [PMID: 38573236 DOI: 10.1039/d4dt00497c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Dysregulation of Fibroblast Growth Factor Receptors (FGFRs) signaling has been associated with breast cancer, yet employing FGFR-targeted delivery systems to improve the efficacy of cytotoxic agents is still sparsely exploited. Herein, we report four new bi-functional ruthenium-peptide conjugates (RuPCs) with FGFR-targeting and pH-dependent releasing abilities, envisioning the selective delivery of cytotoxic Ru complexes to FGFR(+)-breast cancer cells, and controlled activation at the acidic tumoral microenvironment. The antiproliferative potential of the RuPCs and free Ru complexes was evaluated in four breast cancer cell lines with different FGFR expression levels (SKBR-3, MDA-MB-134-VI, MCF-7, and MDA-MB-231) and in human dermal fibroblasts (HDF), at pH 6.8 and pH 7.4 aimed at mimicking the tumor microenvironment and normal tissues/bloodstream pHs, respectively. The RuPCs showed higher cytotoxicity in cells with higher level of FGFR expression at acidic pH. Additionally, RuPCs showed up to 6-fold higher activity in the FGFR(+) breast cancer lines compared to the normal cell line. The release profile of Ru complexes from RuPCs corroborates the antiproliferative effects observed. Remarkably, the cytotoxicity and releasing ability of RuPCs were shown to be strongly dependent on the conjugation of the peptide position in the Ru complex. Complementary molecular dynamic simulations and computational calculations were performed to help interpret these findings at the molecular level. In summary, we identified a lead bi-functional RuPC that holds strong potential as a FGFR-targeted chemotherapeutic agent.
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Affiliation(s)
- João Franco Machado
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
| | - Marco Sá
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Inês Pires
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Miguel Tarita da Silva
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
| | - Fernanda Marques
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - Jaime A S Coelho
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Filipa Mendes
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - M Fátima M Piedade
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - María Angeles Jiménez
- Institute of Physical Chemistry Blas Cabreras (IQF-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - Maria Helena Garcia
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal.
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139, 7), 2695-066 Bobadela LRS, Portugal
| | - Tânia S Morais
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Guo Z, Kundu S. Recent research progress in glycosylphosphatidylinositol-anchored protein biosynthesis, chemical/chemoenzymatic synthesis, and interaction with the cell membrane. Curr Opin Chem Biol 2024; 78:102421. [PMID: 38181647 PMCID: PMC10922524 DOI: 10.1016/j.cbpa.2023.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Glycosylphosphatidylinositol (GPI) attachment to the C-terminus of proteins is a prevalent posttranslational modification in eukaryotic species, and GPIs help anchor proteins to the cell surface. GPI-anchored proteins (GPI-APs) play a key role in various biological events. However, GPI-APs are difficult to access and investigate. To tackle the problem, chemical and chemoenzymatic methods have been explored for the preparation of GPI-APs, as well as GPI probes that facilitate the study of GPIs on live cells. Substantial progress has also been made regarding GPI-AP biosynthesis, which is helpful for developing new synthetic methods for GPI-APs. This article reviews the recent advancements in the study of GPI-AP biosynthesis, GPI-AP synthesis, and GPI interaction with the cell membrane utilizing synthetic probes.
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Affiliation(s)
- Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32611, USA.
| | - Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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Ou YY, Ho QT, Chang HT. Recent advances in features generation for membrane protein sequences: From multiple sequence alignment to pre-trained language models. Proteomics 2023; 23:e2200494. [PMID: 37863817 DOI: 10.1002/pmic.202200494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/22/2023]
Abstract
Membrane proteins play a crucial role in various cellular processes and are essential components of cell membranes. Computational methods have emerged as a powerful tool for studying membrane proteins due to their complex structures and properties that make them difficult to analyze experimentally. Traditional features for protein sequence analysis based on amino acid types, composition, and pair composition have limitations in capturing higher-order sequence patterns. Recently, multiple sequence alignment (MSA) and pre-trained language models (PLMs) have been used to generate features from protein sequences. However, the significant computational resources required for MSA-based features generation can be a major bottleneck for many applications. Several methods and tools have been developed to accelerate the generation of MSAs and reduce their computational cost, including heuristics and approximate algorithms. Additionally, the use of PLMs such as BERT has shown great potential in generating informative embeddings for protein sequence analysis. In this review, we provide an overview of traditional and more recent methods for generating features from protein sequences, with a particular focus on MSAs and PLMs. We highlight the advantages and limitations of these approaches and discuss the methods and tools developed to address the computational challenges associated with features generation. Overall, the advancements in computational methods and tools provide a promising avenue for gaining deeper insights into the function and properties of membrane proteins, which can have significant implications in drug discovery and personalized medicine.
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Affiliation(s)
- Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan
- Graduate Program in Biomedical Informatics, Yuan Ze University, Chung-Li, Taiwan
| | - Quang-Thai Ho
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan
| | - Heng-Ta Chang
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan
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