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Tu W. Mapping the epitope of PD-L1 to the paratope of the antibody durvalumab using molecular dynamics simulation. Am J Transl Res 2024; 16:85-97. [PMID: 38322578 PMCID: PMC10839400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/12/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVES Durvalumab, a human monoclonal antibody that stops PD-L1 from attaching itself to CD80 and PD-1, was approved by the Food and Drug Administration for use in cancer therapy. An essential stage in antibody optimization is mapping paratope residues to epitope residues. In this study, our earlier computer-aided method based on molecular dynamics (MD) simulations was used to observe the paratope residues on durvalumab and their companions on PD-L1. METHODS The durvalumab/PD-L1 complex model was obtained from the Protein Data Bank and used in a rectangular box for solvation. On durvalumab, the paratope residues and their companions on PD-L1 were identified using MD simulations. The interface residues were ranked on the basis of their contributions to the binding of durvalumab and PD-L1 by assessing the stability of hydrogen bonds and salt bridges. This assessment was conducted using free and guided MD simulations. RESULTS Seventeen residues, including ASP26, GLU58, GLU60, ASP61, ARG113, ARG125, and THR127 on PD-L1 and H31ARG, H52LYS, H53GLN, H57GLU, H99GLU, H103PHE, H113ARG, L28ARG, L31SER, and L92TYR on durvalumab, were expected to be necessary for the binding of durvalumab to PD-L1. ASP26, ARG113, and ARG125 on PD-L1 were essential for its binding to PD-1. Eight residues (GLU60, ASP61, and THR127 on PD-L1 and L31SER, H99GLU, H53GLU, H31ARG, and H113ARG on durvalumab) were newly found, and two residues (LYS124 on PD-L1 and L94SER on durvalumab) proven nonessential for complexation, compared to the findings from the examined crystal structure. CONCLUSIONS The antithrombotic antibody of durvalumab's paratope may be effectively mapped to the PD-L1 epitope using the existing computer method. This information will help optimize durvalumab.
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Affiliation(s)
- Wenjian Tu
- School of Biology and Biological Engineering, South China University of Technology, Higher Education MegaCenterNo. 382 East Outer Loop Road, Guangzhou 510006, Guangdong, China
- Guangdong Vocational Institute of SportGuangzhou 510663, Guangdong, China
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Schreiner W, Karch R, Cibena M, Tomasiak L, Kenn M, Pfeiler G. Clustering molecular dynamics conformations of the CC'-loop of the PD-1 immuno-checkpoint receptor. Comput Struct Biotechnol J 2023; 21:3920-3932. [PMID: 37602229 PMCID: PMC10432919 DOI: 10.1016/j.csbj.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/16/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Molecular mechanisms within the checkpoint receptor PD-1 are essential for its activation by PD-L1 as well as for blocking such an activation via checkpoint inhibitors. We use molecular dynamics to scrutinize patterns of atomic motion in PD-1 without a ligand. Molecular dynamics is performed for the whole extracellular domain of PD-1, and the analysis focuses on its CC'-loop and some adjacent Cα-atoms. We extend previous work by applying common nearest neighbor clustering (Cnn) and compare the performance of this method with Daura clustering as well as UMAP dimension reduction and subsequent agglomerative linkage clustering. As compared to Daura clustering, we found Cnn less sensitive to cutoff selection and better able to return representative clusters for sets of different 3D atomic conformations. Interestingly, Cnn yields results quite similar to UMAP plus linkage clustering.
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Affiliation(s)
- Wolfgang Schreiner
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, A-1090, Vienna, Austria
| | - Rudolf Karch
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, A-1090, Vienna, Austria
| | - Michael Cibena
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, A-1090, Vienna, Austria
| | - Lisa Tomasiak
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, A-1090, Vienna, Austria
| | - Michael Kenn
- Medical University of Vienna, Center for Medical Data Science, Spitalgasse 23, A-1090, Vienna, Austria
| | - Georg Pfeiler
- Medical University of Vienna, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Währinger Gürtel 18-20, A-1090, Vienna, Austria
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Zhang S, Liu Q, Wei Y, Xiong Y, Gu Y, Huang Y, Tang F, Ouyang Y. Anterior gradient-2 regulates cell communication by coordinating cytokine-chemokine signaling and immune infiltration in breast cancer. Cancer Sci 2023. [PMID: 36853166 DOI: 10.1111/cas.15775] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023] Open
Abstract
Anterior gradient-2 (AGR2) is crucial to breast cancer progression. However, its role in the tumor immune microenvironment remains unclear. RNA sequencing expression profiles and associated clinical information were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases, respectively. The AGR2 expression patterns were verified using clinical samples of breast cancer. Based on single-cell transcriptomic data, AGR2 expression patterns were identified and cell communication analysis was carried out. Furthermore, the roles of AGR2 in breast tumor progression were explored by a series of functional experiments. We found that DNA methylation was an important mechanism for regulating the expression patterns of AGR2. Patients with AGR2 low expression displayed an immune "hot" and immunosuppressive phenotype characterized by high abundance of tumor immune cell infiltration and increased enrichment scores for transforming growth factor-β (TGF-β) and epithelial-mesenchymal transition pathways, whereas patients with AGR2 high expression showed an opposite immunologic feature with a lack of immune cell infiltration, suggestive of an immune "cold" and desert phenotype. Moreover, single-cell analysis further revealed that AGR2 in malignant cells alters cell-cell interactions by coordinating cytokine-chemokine signaling and immune infiltration. Notably, two immunotherapy cohorts revealed that AGR2-coexpressed genes could serve as prognostic indicators of patient survival. In conclusion, AGR2 could promote breast cancer progression by affecting the tumor immune microenvironment. Patients with AGR2 low expression could be suitable for combination treatment with immune checkpoint inhibitor agents and TGF-β blockers. Therefore, this study provides a theoretical foundation for developing a strategy for personalized immunotherapy to patients with breast cancer.
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Affiliation(s)
- Shichao Zhang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Qin Liu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yimei Wei
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yu Xiong
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yan Gu
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Ya Huang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Fuzhou Tang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yan Ouyang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
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Kenn M, Karch R, Tomasiak L, Cibena M, Pfeiler G, Koelbl H, Schreiner W. Molecular dynamics identifies semi-rigid domains in the PD-1 checkpoint receptor bound to its natural ligand PD-L1. Front Bioeng Biotechnol 2022; 10:838129. [PMID: 36277392 PMCID: PMC9582661 DOI: 10.3389/fbioe.2022.838129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Cells in danger of being erroneously attacked by leucocytes express PD-L1 on their surface. These cells activate PD-1 on attacking leucocytes and send them to death, thus curbing erroneous, autoimmune attack. Unfortunately, cancer cells exploit this mechanism: By expressing PD-L1, they guard themselves against leucocyte attack and thereby evade immune clearance. Checkpoint inhibitors are drugs which re-enable immune clearance of cancer cells by blocking the binding of PD-L1 to PD-1 receptors. It is therefore of utmost interest to investigate these binding mechanisms. We use three 600 ns all-atom molecular dynamics simulations to scrutinize molecular motions of PD-1 with its binding partner, the natural ligand PD-L1. Usually, atomic motion patterns are evaluated against whole molecules as a reference, disregarding that such a reference is a dynamic entity by itself, thus degrading stability of the reference. As a remedy, we identify semi-rigid domains, lending themselves as more stable and reliable reference frames against which even minute differences in molecular motion can be quantified precisely. We propose an unsupervised three-step procedure. In previous work of our group and others, minute differences in motion patterns proved decisive for differences in function. Here, several highly reliable frames of reference are established for future investigations based on molecular motion.
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Affiliation(s)
- Michael Kenn
- Institute for Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Rudolf Karch
- Institute for Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Lisa Tomasiak
- Institute for Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Michael Cibena
- Institute for Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Georg Pfeiler
- Division of General Gynecology and Gynecologic Oncology, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Heinz Koelbl
- Division of General Gynecology and Gynecologic Oncology, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Schreiner
- Institute for Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
- *Correspondence: Wolfgang Schreiner,
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Ponce LF, Leon K, Valiente PA. Unraveling a Conserved Conformation of the FG Loop upon the Binding of Natural Ligands to the Human and Murine PD1. J Phys Chem B 2022; 126:1441-1446. [PMID: 35167293 DOI: 10.1021/acs.jpcb.1c09463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The activation of T cells is normally accompanied by inhibitory mechanisms within which the PD1 receptor stands out. PD1 drives T cells to an unresponsive state called exhaustion, characterized by a markedly decreased capacity to exert effector functions upon binding the ligands PDL1 and PDL2. For this reason, PD1 has become one of the most important targets in cancer immunotherapy. Despite the numerous studies about PD1 signaling modulation, how the PD1 signaling pathway is activated upon the ligands' binding remains an open question. In this work, we used molecular dynamics simulations to assess the differences of the PD1 motion in the free state and in complex with the ligands. We found that, in both human and murine systems, the binding of PDL1 and PDL2 stabilizes the conformation of the FG loop similarly. This result, combined with the conservation of the FG loop residues across species, suggests that the conformation of the FG loop is somehow related to the signaling process. We also found a high similarity between the PD1-PDL1 structures with the variable region of an antibody structure, where the FG loop occupies a similar position to the CDR3 light chain.
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Affiliation(s)
- Luis F Ponce
- Molecular System Biology Department, Center of Molecular Immunology, Havana, Havana 11600, Cuba.,Center for Molecular Simulations, Biological Science Department, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Kalet Leon
- Molecular System Biology Department, Center of Molecular Immunology, Havana, Havana 11600, Cuba
| | - Pedro A Valiente
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Havana 10400, Cuba.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Tavares ABMLA, Lima Neto JX, Fulco UL, Albuquerque EL. Blockade of the checkpoint PD-1 by its ligand PD-L1 and the immuno-oncological drugs pembrolizumab and nivolumab. Phys Chem Chem Phys 2021; 23:21207-21217. [PMID: 34533552 DOI: 10.1039/d1cp03064g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We investigate the interaction between the programmed cell death protein 1 (PD-1) and the programmed cell death ligand 1 (PD-L1), as well as the immuno-oncological drugs pembrolizumab (PEM), and nivolumab (NIV), through quantum chemistry methods based on the Density Functional Theory (DFT) and the molecular fractionation with conjugate caps (MFCC) scheme, in order to map their hot-spot regions. Our results showed that the total interaction energy order of the three complexes is in good agreement with the experimental binding affinity order: PD-1/PEM > PD-1/NIV > PD-1/PD-L1. Besides, a detailed investigation revealed the energetically most relevant residue-residue pairs-interaction for each complex. Our computational results give a better understanding of the interaction mechanism between the protein PD-1 and its ligands (natural and inhibitors), unleashing the immune surveillance to destroy the cancer cells by decreasing their immune evasion. They are also an efficient alternative towards the development of new small-molecules and antibody-based drugs, pointing out to new treatments for cancer therapy.
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Affiliation(s)
- Ana Beatriz M L A Tavares
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil. .,Hospital das Clínicas, Universidade Federal de Pernambuco, 50.670-901, Recife-PE, Brazil
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - E L Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
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