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Zeng X, Wang T, Kang Y, Bai G, Ma B. Evaluation of Molecular Simulations and Deep Learning Prediction of Antibodies' Recognition of TRBC1 and TRBC2. Antibodies (Basel) 2023; 12:58. [PMID: 37753972 PMCID: PMC10525649 DOI: 10.3390/antib12030058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/25/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
T cell receptor β-chain constant (TRBC) is a promising class of cancer targets consisting of two highly homologous proteins, TRBC1 and TRBC2. Developing targeted antibody therapeutics against TRBC1 or TRBC2 is expected to eradicate the malignant T cells and preserve half of the normal T cells. Recently, several antibody engineering strategies have been used to modulate the TRBC1 and TRBC2 specificity of antibodies. Here, we used molecular simulation and artificial intelligence methods to quantify the affinity difference in antibodies with various mutations for TRBC1 and TRBC2. The affinity of the existing mutants was verified by FEP calculations aided by the AI. We also performed long-time molecular dynamics simulations to reveal the dynamical antigen recognition mechanisms of the TRBC antibodies.
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Affiliation(s)
- Xincheng Zeng
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (G.B.)
| | - Tianqun Wang
- Shanghai Digiwiser Biological Inc., Shanghai 200240, China; (T.W.); (Y.K.)
| | - Yue Kang
- Shanghai Digiwiser Biological Inc., Shanghai 200240, China; (T.W.); (Y.K.)
| | - Ganggang Bai
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (G.B.)
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (X.Z.); (G.B.)
- Shanghai Digiwiser Biological Inc., Shanghai 200240, China; (T.W.); (Y.K.)
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2
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Destabilization of the Alzheimer's amyloid-β peptide by a proline-rich β-sheet breaker peptide: a molecular dynamics simulation study. J Mol Model 2021; 27:356. [PMID: 34796404 DOI: 10.1007/s00894-021-04968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/25/2021] [Indexed: 11/27/2022]
Abstract
The amyloid-β peptide exists in the form of fibrils in the plaques found in the brains of patients with Alzheimer's disease. One of the therapeutic strategies is the design of molecules which can destabilize these fibrils. We present a designed peptide KLVFFP5 with two segments: the self-recognition sequence KLVFF and a β-sheet breaker proline pentamer. Molecular dynamics simulations and docking results showed that this peptide could bind to the protofibrils and destabilize them by establishing hydrophobic contacts and hydrogen bonds with a higher affinity than the KLVFF peptide. In the presence of the KLVFFP5 peptide, the β-sheet content of the protofibrils was reduced significantly; the hydrogen bonding network and the salt bridges were disrupted to a greater extent than the KLVFF peptide. Our results indicate that the KLVFFP5 peptide is an effective β-sheet disruptor which can be considered in the therapy of Alzheimer's disease.
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3
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Beutgen VM, Schmelter C, Pfeiffer N, Grus FH. Contribution of the Commensal Microflora to the Immunological Homeostasis and the Importance of Immune-Related Drug Development for Clinical Applications. Int J Mol Sci 2021; 22:8896. [PMID: 34445599 PMCID: PMC8396286 DOI: 10.3390/ijms22168896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Not long ago, self-reactive immune activity was considered as pathological trait. A paradigm shift has now led to the recognition of autoimmune processes as part of natural maintenance of molecular homeostasis. The immune system is assigned further roles beneath the defense against pathogenic organisms. Regarding the humoral immune system, the investigation of natural autoantibodies that are frequently found in healthy individuals has led to further hypotheses involving natural autoimmunity in other processes as the clearing of cellular debris or decrease in inflammatory processes. However, their role and origin have not been entirely clarified, but accumulating evidence links their formation to immune reactions against the gut microbiome. Antibodies targeting highly conserved proteins of the commensal microflora are suggested to show self-reactive properties, following the paradigm of the molecular mimicry. Here, we discuss recent findings, which demonstrate potential links of the commensal microflora to the immunological homeostasis and highlight the possible implications for various diseases. Furthermore, specific components of the immune system, especially antibodies, have become a focus of attention for the medical management of various diseases and provide attractive treatment options in the future. Nevertheless, the development and optimization of such macromolecules still represents a very time-consuming task, shifting the need to more medical agents with simple structural properties and low manufacturing costs. Synthesizing only the biologically active sites of antibodies has become of great interest for the pharmaceutical industry and offers a wide range of therapeutic application areas as it will be discussed in the present review article.
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Affiliation(s)
| | | | | | - Franz H. Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center, 55131 Mainz, Germany; (V.M.B.); (C.S.); (N.P.)
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4
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Sun ZT, Ma C, Li GJ, Zheng XY, Hao YT, Yang Y, Wang X. Application of Antibody Fragments Against Aβ With Emphasis on Combined Application With Nanoparticles in Alzheimer's Disease. Front Pharmacol 2021; 12:654611. [PMID: 33967797 PMCID: PMC8100690 DOI: 10.3389/fphar.2021.654611] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases and accumulating evidences suggest a key role of amyloid-β (Aβ) peptide in the pathogenesis of AD. According to the amyloid cascade hypothesis, the imbalance of producing and clearing Aβ is the beginning of neurodegeneration and dementia. Consequently, immunotherapy becomes popular through using antibodies against Aβ. However, many studies of monoclonal antibodies were stopped because adverse effects appeared or there were no evident benefits observed. Some antibody fragments have many advantages over monoclonal antibodies, such as small sizes, lack of the crystallizable fraction (Fc) and so on. There are three main antibody fragments, including single chain variable fragments (scFvs), Fab fragments and single-domain antibody fragments. Nanoparticles can facilitate the entry of drug molecules across the blood-brain barrier, making them become excellent carriers. Various kinds of nanoparticles have been applied in the treatment of AD. The combination of nanoparticles and antibody fragments against amyloid-β can be used in the diagnosis and treatment of Alzheimer’s disease. In this review, we summarize the progress of antibody fragments against amyloid-β in AD, focusing on the combined application with nanoparticles in the diagnosis and treatment of AD.
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Affiliation(s)
- Zhi-Ting Sun
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Chi Ma
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Guang-Jian Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Xiang-Yu Zheng
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Yi-Tong Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Yu Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Xu Wang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
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5
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Frost CV, Zacharias M. From monomer to fibril: Abeta-amyloid binding to Aducanumab antibody studied by molecular dynamics simulation. Proteins 2020; 88:1592-1606. [PMID: 32666627 DOI: 10.1002/prot.25978] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's disease is one of the most common causes of dementia. It is believed that the aggregation of short Aβ-peptides to form oligomeric and protofibrillar amyloid assemblies plays a central role for disease-relevant neurotoxicity. In recent years, passive immunotherapy has been introduced as a potential treatment strategy with anti-amyloid antibodies binding to Aβ-amyloids and inducing their subsequent degradation by the immune system. Although so far mostly unsuccessful in clinical studies, the high-dosed application of the monoclonal antibody Aducanumab has shown therapeutic potential that might be attributed to its much greater affinity to Aβ-aggregates vs monomeric Aβ-peptides. In order to better understand how Aducanumab interacts with aggregated Aβ-forms compared to monomers, we have generated structural model complexes based on the known structure of Aducanumab in complex with an Aβ2 - 7 -eptitope. Structural models of Aducanumab bound to full-sequence Aβ1 - 40 -monomers, oligomers, protofilaments and mature fibrils were generated and investigated using extensive molecular dynamics simulations to characterize the flexibility and possible additional interactions. Indeed, an aggregate-specific N-terminal binding motif was found in case of Aducanumab binding to oligomers, protofilaments and fibrils that is located next to but not overlapping with the epitope binding site found in the crystal structure with Aβ2 - 7 . Analysis of binding energetics indicates that this motif binds weaker than the epitope but likely contributes to Aducanumab's preference for aggregated Aβ-species. The predicted aggregate-specific binding motif could potentially serve as a basis to reengineer Aducanumab for further enhanced preference to bind Aβ-aggregates vs monomers.
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Affiliation(s)
- Christina V Frost
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
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6
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Khorvash M, Blinov N, Ladner-Keay C, Lu J, Silverman JM, Gibbs E, Wang YT, Kovalenko A, Wishart D, Cashman NR. Molecular interactions between monoclonal oligomer-specific antibody 5E3 and its amyloid beta cognates. PLoS One 2020; 15:e0232266. [PMID: 32469918 PMCID: PMC7259632 DOI: 10.1371/journal.pone.0232266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/12/2020] [Indexed: 11/30/2022] Open
Abstract
Oligomeric amyloid β (Aβ) is currently considered the most neurotoxic form of the Aβ peptide implicated in Alzheimer’s disease (AD). The molecular structures of the oligomers have remained mostly unknown due to their transient nature. As a result, the molecular mechanisms of interactions between conformation-specific antibodies and their Aβ oligomer (AβO) cognates are not well understood. A monoclonal conformation-specific antibody, m5E3, was raised against a structural epitope of Aβ oligomers. m5E3 binds to AβOs with high affinity, but not to Aβ monomers or fibrils. In this study, a computational model of the variable fragment (Fv) of the m5E3 antibody (Fv5E3) is introduced. We further employ docking and molecular dynamics simulations to determine the molecular details of the antibody-oligomer interactions, and to classify the AβOs as Fv5E3-positives and negatives, and to provide a rationale for the low affinity of Fv5E3 for fibrils. This information will help us to perform site-directed mutagenesis on the m5E3 antibody to improve its specificity and affinity toward oligomeric Aβ species. We also provide evidence for the possible capability of the m5E3 antibody to disaggregate AβOs and to fragment protofilaments.
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Affiliation(s)
- Massih Khorvash
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Nick Blinov
- Department of Mechanical Engineering, Edmonton, Alberta, Canada
- National Research Council of Canada, Edmonton, Alberta, Canada
| | - Carol Ladner-Keay
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jie Lu
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Judith M. Silverman
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Ebrima Gibbs
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Yu Tian Wang
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering, Edmonton, Alberta, Canada
- National Research Council of Canada, Edmonton, Alberta, Canada
| | - David Wishart
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Neil R. Cashman
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, British Columbia, Canada
- * E-mail:
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7
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Cerofolini L, Ravera E, Bologna S, Wiglenda T, Böddrich A, Purfürst B, Benilova I, Korsak M, Gallo G, Rizzo D, Gonnelli L, Fragai M, De Strooper B, Wanker EE, Luchinat C. Mixing Aβ(1–40) and Aβ(1–42) peptides generates unique amyloid fibrils. Chem Commun (Camb) 2020; 56:8830-8833. [DOI: 10.1039/d0cc02463e] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solid-state NMR experiments reveal that the two isoforms of the beta-amyloid peptide (Aβ(1–40) and Aβ(1–42)) are able to form unique interlaced mixed fibrils.
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8
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Zhang Y, Ren B, Zhang D, Liu Y, Zhang M, Zhao C, Zheng J. Design principles and fundamental understanding of biosensors for amyloid-β detection. J Mater Chem B 2020; 8:6179-6196. [DOI: 10.1039/d0tb00344a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aβ as biomarker in Alzheimer’s disease (AD) drives the significant research efforts for developing different biosensors with different sensing strategies, materials, and mechanisms for Aβ detection.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Baiping Ren
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Dong Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Yonglan Liu
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Mingzhen Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Chao Zhao
- Department of Chemical and Biomolecular Engineering
- The University of Alabama
- USA
| | - Jie Zheng
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
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9
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Zhao J, Nussinov R, Ma B. Antigen binding allosterically promotes Fc receptor recognition. MAbs 2019; 11:58-74. [PMID: 30212263 PMCID: PMC6343797 DOI: 10.1080/19420862.2018.1522178] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/10/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
A key question in immunology is whether antigen recognition and Fc receptor (FcR) binding are allosterically linked. This question is also relevant for therapeutic antibody design. Antibody Fab and Fc domains are connected by flexible unstructured hinge region. Fc chains have conserved glycosylation sites at Asn297, with each conjugated to a core heptasaccharide and forming biantennary Fc glycan. The glycans modulate the Fc conformations and functions. It is well known that the antibody Fab and Fc domains and glycan affect antibody activity, but whether these elements act independently or synergistically is still uncertain. We simulated four antibody complexes: free antibody, antigen-bound antibody, FcR-bound antibody, and an antigen-antibody-FcR complex. We found that, in the antibody's "T/Y" conformation, the glycans, and the Fc domain all respond to antigen binding, with the antibody population shifting to two dominant clusters, both with the Fc-receptor binding site open. The simulations reveal that the Fc-glycan-receptor complexes also segregate into two conformational clusters, one corresponding to the antigen-free antibody-FcR baseline binding, and the other with an antigen-enhanced antibody-FcR interaction. Our study confirmed allosteric communications in antibody-antigen recognition and following FcR activation. Even though we observed allosteric communications through the IgG domains, the most important mechanism that we observed is the communication via population shift, stimulated by antigen binding and propagating to influence FcR recognition.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
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