1
|
Nasrin SR, Yamashita T, Ikeguchi M, Torisawa T, Oiwa K, Sada K, Kakugo A. Tensile Stress on Microtubules Facilitates Dynein-Driven Cargo Transport. NANO LETTERS 2024. [PMID: 38916205 DOI: 10.1021/acs.nanolett.4c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Mechanical stress significantly affects the physiological functions of cells, including tissue homeostasis, cytoskeletal alterations, and intracellular transport. As a major cytoskeletal component, microtubules respond to mechanical stimulation by altering their alignment and polymerization dynamics. Previously, we reported that microtubules may modulate cargo transport by one of the microtubule-associated motor proteins, dynein, under compressive mechanical stress. Despite the critical role of tensile stress in many biological functions, how tensile stress on microtubules regulates cargo transport is yet to be unveiled. The present study demonstrates that the low-level tensile stress-induced microtubule deformation facilitates dynein-driven transport. We validate our experimental findings using all-atom molecular dynamics simulation. Our study may provide important implications for developing new therapies for diseases that involve impaired intracellular transport.
Collapse
Affiliation(s)
- Syeda Rubaiya Nasrin
- Graduate School of Science, Department of Physics and Astronomy, Kyoto University, Kyoto, 606-8152, Japan
| | - Takefumi Yamashita
- Department of Physical University, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa-ku, Tokyo, 142-8501, Japan
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takayuki Torisawa
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Sokendai, Mishima, 411-8540, Japan
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Science, Department of Physics and Astronomy, Kyoto University, Kyoto, 606-8152, Japan
| |
Collapse
|
2
|
Hu S, Liu Y, Yang Y, Xu L. Structural insights into instability of the nucleosome driven by histone variant H3T. Biochem Biophys Res Commun 2024; 727:150307. [PMID: 38917618 DOI: 10.1016/j.bbrc.2024.150307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
The testis-specific histone variant H3T plays a crucial role in chromatin reorganization during spermatogenesis by destabilizing nucleosomes. However, the structure basis for the nucleosome instability driven by H3T is not fully understand. In this study, we determinate the crystal structure of H3T-H4 in complex with histone chaperone ASF1a at 2.8 Å resolution. Our findings reveal that H3T-H4 binds ASF1a similarly to the conventional H3.1-H4 complex. However, significant structural differences are observed in the H3 α1 helix, the N- and C-terminal region of α2, and N-terminal region of L2. These differences are driven by H3T-specific residues, particularly Val111. Unlike the smaller Ala111 in H3.1, we find that bulkier residue Val111 fits well within the ASF1-H3T-H4 complex, but is difficult to arrange in nucleosome structure. Given that H3.1-Ala111/H3T-Val111 is located at the DNA binding and tetramerization interface of H3-H4, it is likely that Ala111Val substitution will lead to the instability of the corresponding area in nucleosome, contributing to instability of H3T-containing nucleosome. These structural findings may elucidate the role of H3T in chromatin reorganization during spermatogenesis.
Collapse
Affiliation(s)
- Shenglin Hu
- College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Hefei, Anhui, 230027, China
| | - Yongrui Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yang Yang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Li Xu
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, 100089, China.
| |
Collapse
|
3
|
Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [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] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
Collapse
Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
| |
Collapse
|
4
|
Miyanabe K, Yamashita T, Tsumoto K. Thermodynamic and molecular dynamic insights into how fusion influences peptide-tag recognition of an antibody. Sci Rep 2024; 14:8685. [PMID: 38622354 PMCID: PMC11018781 DOI: 10.1038/s41598-024-59355-2] [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: 12/27/2023] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
To understand the effect of protein fusion on the recognition of a peptide-tag by an antibody, we fused a CCR5-derived peptide-tag (pep1) to GFP and investigated its recognition by an anti-pep1 antibody, 4B08. First, to characterize the thermodynamic properties associated with the pep1-4B08 binding, isothermal titration calorimetry experiments were conducted. It was found that pep1 fused to the C-terminus of GFP (GFP-CT) enhanced the enthalpic gain by 2.1 kcal mol-1 and the entropic loss only by 0.9 kcal mol-1, resulting in an 8-fold increase in the binding affinity compared to the unfused pep1. On the other hand, pep1 fused to the N-terminus of GFP (GFP-NT) enhanced the enthalpic gain by 3.0 kcal mol-1 and the entropic loss by 3.2 kcal mol-1, leading to no significant enhancement of the binding affinity. To gain deeper insights, molecular dynamics simulations of GFP-NT, GFP-CT, and pep1 were performed. The results showed that the location of the fusion point sensitively affects the interaction energy, the solvent accessible surface area, and the fluctuation of pep1 in the unbound state, which explains the difference in the experimental thermodynamic properties.
Collapse
Affiliation(s)
- Kazuhiro Miyanabe
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| |
Collapse
|
5
|
Ozawa T, Ikeda Y, Chen L, Suzuki R, Hoshino A, Noguchi A, Kita S, Anraku Y, Igarashi E, Saga Y, Inasaki N, Taminishi S, Sasaki J, Kirita Y, Fukuhara H, Maenaka K, Hashiguchi T, Fukuhara T, Hirabayashi K, Tani H, Kishi H, Niimi H. Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1. Structure 2024; 32:263-272.e7. [PMID: 38228146 DOI: 10.1016/j.str.2023.12.013] [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: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
SARS-CoV-2 rapidly mutates and acquires resistance to neutralizing antibodies. We report an in-silico-designed antibody that restores the neutralizing activity of a neutralizing antibody. Our previously generated antibody, UT28K, exhibited broad neutralizing activity against mutant variants; however, its efficacy against Omicron BA.1 was compromised by the mutation. Using previously determined structural information, we designed a modified-UT28K (VH T28R/N57D), UT28K-RD targeting the mutation site. In vitro and in vivo experiments demonstrated the efficacy of UT28K-RD in neutralizing Omicron BA.1. Although the experimentally determined structure partially differed from the predicted model, our study serves as a successful case of antibody design, wherein the predicted amino acid substitution enhanced the recognition of the previously elusive Omicron BA.1. We anticipate that numerous similar cases will be reported, showcasing the potential of this approach for improving protein-protein interactions. Our findings will contribute to the development of novel therapeutic strategies for highly mutable viruses, such as SARS-CoV-2.
Collapse
Affiliation(s)
- Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan; Center for Advanced Antibody Drug Development, University of Toyama, Toyama, Japan.
| | - Yoshiki Ikeda
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshidahonnmachi, Sakyo-ku, Kyoto, Japan.
| | - Liuan Chen
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Noguchi
- Department of Diagnostic Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Emiko Igarashi
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Yumiko Saga
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Noriko Inasaki
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Shunta Taminishi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hideo Fukuhara
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Kenichi Hirabayashi
- Department of Diagnostic Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan; Center for Advanced Antibody Drug Development, University of Toyama, Toyama, Japan
| | - Hideki Niimi
- Center for Advanced Antibody Drug Development, University of Toyama, Toyama, Japan; Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| |
Collapse
|
6
|
Yamaguchi K, Anzai I, Maeda R, Moriguchi M, Watanabe T, Imura A, Takaori-Kondo A, Inoue T. Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant. J Biochem 2023; 173:115-127. [PMID: 36413757 DOI: 10.1093/jb/mvac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants associated with the adaptive evolution of the virus is prolonging the global coronavirus disease 2019 (COVID-19) pandemic. The modification of neutralizing antibodies based on structural information is expected to be a useful approach to rapidly combat emerging variants. A dimerized variable domain of heavy chain of heavy chain antibody (VHH) P17 that has highly potent neutralizing activity against SARS-CoV-2 has been reported but the mode of interaction with the epitope remains unclear. Here, we report the X-ray crystal structure of the complex of monomerized P17 bound to the SARS-CoV-2 receptor binding domain (RBD) and investigated the binding activity of P17 toward various variants of concern (VOCs) using kinetics measurements. The structure revealed details of the binding interface and showed that P17 had an appropriate linker length to have an avidity effect and recognize a wide range of RBD orientations. Furthermore, we identified mutations in known VOCs that decrease the binding affinity of P17 and proposed methods for the acquisition of affinity toward the Omicron RBD because Omicron is currently the most predominant VOC. This study provides information for the rational design of effective VHHs for emerging VOCs.
Collapse
Key Words
- Crystal structure
Abbreviations: ACE2, angiotensin converting enzyme 2; BLI, biolayer interferometry; CDR, complementarity-determining region; COVID-19, coronavirus disease 2019; cryo-EM, cryo-electron microscopy; EDTA, ethylenediaminetetraacetic acid; IPTG, Isopropyl β-d-1-thiogalactopyranoside; mAb, monoclonal antibody; PBS, phosphate-buffered saline; RBD, receptor binding domain;
SARS-CoV-2, severe acute respiratory syndrome coronavirus-2; VdW, Van der Waals; VHH, variable domain of heavy chain of heavy chain antibody; VOC, variants of concern
- SARS-CoV-2
- VHH
- recognition mechanism
Collapse
Affiliation(s)
- Keishi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Ryota Maeda
- COGNANO Inc., 64-101 Kamitakano Higashiyama, Sakyo-ku, Kyoto, 601-1255, Japan
| | - Maiko Moriguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Akihiro Imura
- COGNANO Inc., 64-101 Kamitakano Higashiyama, Sakyo-ku, Kyoto, 601-1255, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
7
|
Truong PL, Yin Y, Lee D, Ko SH. Advancement in COVID-19 detection using nanomaterial-based biosensors. EXPLORATION (BEIJING, CHINA) 2023; 3:20210232. [PMID: 37323622 PMCID: PMC10191025 DOI: 10.1002/exp.20210232] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/11/2022] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has exemplified how viral growth and transmission are a significant threat to global biosecurity. The early detection and treatment of viral infections is the top priority to prevent fresh waves and control the pandemic. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified through several conventional molecular methodologies that are time-consuming and require high-skill labor, apparatus, and biochemical reagents but have a low detection accuracy. These bottlenecks hamper conventional methods from resolving the COVID-19 emergency. However, interdisciplinary advances in nanomaterials and biotechnology, such as nanomaterials-based biosensors, have opened new avenues for rapid and ultrasensitive detection of pathogens in the field of healthcare. Many updated nanomaterials-based biosensors, namely electrochemical, field-effect transistor, plasmonic, and colorimetric biosensors, employ nucleic acid and antigen-antibody interactions for SARS-CoV-2 detection in a highly efficient, reliable, sensitive, and rapid manner. This systematic review summarizes the mechanisms and characteristics of nanomaterials-based biosensors for SARS-CoV-2 detection. Moreover, continuing challenges and emerging trends in biosensor development are also discussed.
Collapse
Affiliation(s)
- Phuoc Loc Truong
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Yiming Yin
- New Materials InstituteDepartment of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingboChina
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
| | - Daeho Lee
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Seung Hwan Ko
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
- Institute of Advanced Machinery and Design (SNU‐IAMD)/Institute of Engineering ResearchSeoul National UniversityGwanak‐guSeoulKorea
| |
Collapse
|
8
|
Yamashita T. Molecular Dynamics Simulation for Investigating Antigen-Antibody Interaction. Methods Mol Biol 2023; 2552:101-107. [PMID: 36346587 DOI: 10.1007/978-1-0716-2609-2_4] [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] [Indexed: 06/16/2023]
Abstract
Molecular dynamics (MD) simulation is a computational method which elucidates the protein dynamics. Following analyses characterize the dynamics and structural change as well as interaction energy. To characterize the protein structure effectively, the internal angular coordinates are often useful. Directional analysis provides the averages and variances of those coordinates in a mathematically rigorous way. Here, we describe not only a standard MD simulation procedure for the antigen-antibody system but also an umbrella sampling method following a multistep targeted MD simulation (US/mTMD), which is useful for evaluating the free energy profile along the antigen-antibody dissociation coordinate.
Collapse
Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
9
|
Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
Collapse
Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
10
|
Zhang Q, Miyamoto A, Watanabe S, Arimori T, Sakai M, Tomisaki M, Kiuchi T, Takagi J, Watanabe N. Engineered fast-dissociating antibody fragments for multiplexed super-resolution microscopy. CELL REPORTS METHODS 2022; 2:100301. [PMID: 36313806 PMCID: PMC9606137 DOI: 10.1016/j.crmeth.2022.100301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 08/31/2022] [Indexed: 05/22/2023]
Abstract
Image reconstruction by integrating exchangeable single-molecule localization (IRIS) achieves multiplexed super-resolution imaging by high-density labeling with fast exchangeable fluorescent probes. However, previous methods to develop probes for individual targets required a great amount of time and effort. Here, we introduce a method for generating recombinant IRIS probes with a new mutagenesis strategy that can be widely applied to existing antibody sequences. Several conserved tyrosine residues at the base of complementarity-determining regions were identified as candidate sites for site-directed mutagenesis. With a high probability, mutations at candidate sites accelerated the off rate of recombinant antibody-based probes without compromising specific binding. We were able to develop IRIS probes from five monoclonal antibodies and three single-domain antibodies. We demonstrate multiplexed localization of endogenous proteins in primary neurons that visualizes small synaptic connections with high binding density. It is now practically feasible to generate fast-dissociating fluorescent probes for multitarget super-resolution imaging.
Collapse
Affiliation(s)
- Qianli Zhang
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Akitoshi Miyamoto
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Shin Watanabe
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Takao Arimori
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masanori Sakai
- Kyoto University Faculty of Engineering, Kyoto 606-8317, Japan
| | - Madoka Tomisaki
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Tai Kiuchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Naoki Watanabe
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| |
Collapse
|
11
|
Li Y, Li P, Ke Y, Yu X, Yu W, Wen K, Shen J, Wang Z. A rare monoclonal antibody discovery based on indirect competitive screening of a single hapten-specific rabbit antibody secreting cell. Analyst 2022; 147:2942-2952. [PMID: 35674177 DOI: 10.1039/d2an00678b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A rare antibody that is able to tolerate physio-chemical factors is preferred and highly demanded in diagnosis and therapy. Rabbit monoclonal antibodies (RmAbs) are distinguished owing to their high affinity and stability. However, the efficiency and availability of traditional methods for RmAb discovery are limited, particularly for small molecules. Here, we present an indirect competitive screening method in nanowells, named CSMN, for single rabbit antibody-secreting cells (ASCs) selection with 20.6 h and propose an efficient platform for RmAb production against small molecules within 5.8 days for the first time. Chloramphenicol (CAP) as an antibacterial agent poses a great threat to public health. We applied CSMN to select CAP-specific ASCs and produced one high-affinity RmAb, surprisingly showed extremely halophilic properties with an IC50 of 0.08 ng mL-1 in the saturated salt solution, which has not yet been seen for other antibodies. The molecular dynamic simulation showed that the negatively charged surface improved the stability of the RmAb structure with additional disulfide bonds compared with mouse antibodies. Moreover, the reduced solvent accessible surface area of the binding pocket increased the interactions of RmAb with CAP in a saturated salt solution. Furthermore, RmAb was used to develop an immunoassay for the detection of CAP in real biological samples with simple pretreatment, shorter assay time, and higher sensitivity. The results demonstrated that the practical and efficient CSMN is suitable for rare RmAb discovery against small molecules.
Collapse
Affiliation(s)
- Yuan Li
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Peipei Li
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Yuebin Ke
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, 518000 Shenzhen, China
| | - Xuezhi Yu
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Wenbo Yu
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Kai Wen
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Jianzhong Shen
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Zhanhui Wang
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| |
Collapse
|
12
|
Debnath U, Verma S, Patra J, Mandal SK. A review on recent synthetic routes and computational approaches for antibody drug conjugation developments used in anti-cancer therapy. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
13
|
Vander Mause ER, Atanackovic D, Lim CS, Luetkens T. Roadmap to affinity-tuned antibodies for enhanced chimeric antigen receptor T cell function and selectivity. Trends Biotechnol 2022; 40:875-890. [DOI: 10.1016/j.tibtech.2021.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022]
|
14
|
Yamada K, Mizukoshi N, Kawata A, Ono M, Hizono T, Hashimoto K, Azuma N. Isolation of a novel variant of secretory component with low affinity to dimeric immunoglobulin a by immobilised metal ion affinity chromatography. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins. MEMBRANES 2021; 11:membranes11110823. [PMID: 34832053 PMCID: PMC8625833 DOI: 10.3390/membranes11110823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 02/03/2023]
Abstract
Membrane proteins reside in the lipid bilayer of biomembranes and the structure and function of these proteins are closely related to their interactions with lipid molecules. Structural analyses of interactions between membrane proteins and lipids or detergents that constitute biological or artificial model membranes are important for understanding the functions and physicochemical properties of membrane proteins and biomembranes. Determination of membrane protein structures is much more difficult when compared with that of soluble proteins, but the development of various new technologies has accelerated the elucidation of the structure-function relationship of membrane proteins. This review summarizes the development of heavy atom derivative detergents and lipids that can be used for structural analysis of membrane proteins and their interactions with detergents/lipids, including their application with X-ray free-electron laser crystallography.
Collapse
|
16
|
Qiao X, Qu L, Guo Y, Hoshino T. Secondary Structure and Conformational Stability of the Antigen Residues Making Contact with Antibodies. J Phys Chem B 2021; 125:11374-11385. [PMID: 34615354 DOI: 10.1021/acs.jpcb.1c05997] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibodies are crucial biomolecules that bring high therapeutic efficacy in medicine and accurate molecular detection in diagnosis. Many studies have been devoted to analyzing the antigen-antibody interaction from the importance of understanding the antibody recognition mechanism. However, most of the previous studies examined the characteristic of the antibody for interaction. It is also informative to clarify the significant antigen residues contributing to the binding. To characterize the molecular interaction of antigens, we computationally analyzed 350 antigen-antibody complex structures by molecular mechanics (MM) calculations and molecular dynamics (MD) simulations. Based on the MM calculations, the antigen residues contributing to the binding were extracted from all the 350 complexes. The extracted residues are located at the antigen-antibody interface and are responsible for making contact with the antibody. The appearances of the charged polar residues, Asp, Glu, Arg, and Lys, were noticeably large. In contrast, the populations of the hydrophobic residues, Leu, Val, and Ala, were relatively low. The appearance frequencies of the other amino acid residues were almost close to the abundance of general proteins of eukaryotes. The binding score indicated that the hydrophilic interaction was dominant at the antigen-antibody contact instead of the hydrophobic one. The positively charged residues, Arg and Lys, remarkably contributed to the binding compared to the negatively charged ones, Asp and Glu. Considerable contributions were also observed for the noncharged polar residues, Asn and Gln. The analysis of the secondary structures of the extracted antigen residues suggested that there was no marked difference in recognition by antibodies among helix, sheet, turn, and coil. A long helix of the antigen sometimes made contact with antibody complementarity-determining regions, and a large sheet also frequently covered the antibody heavy and light chains. The turn structure was the most popularly observed at the contact with antibody among 350 complexes. Three typical complexes were picked up for each of the four secondary structures. MD simulations were performed to examine the stability of the interfacial structures of the antigens for these 12 complex models. The alterations of secondary structures were monitored through the simulations. The structural fluctuations of the contact residues were low compared with the other domains of antigen molecules. No drastic conversion was observed for every model during the 100 ns simulation. The motions of the interfacial antigen residues were small compared to the other residues on the protein surface. Therefore, diverse molecular conformations are possible for antibody recognition as long as the target areas are polar, nonflexible, and protruding on the protein surface.
Collapse
Affiliation(s)
- Xinyue Qiao
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Liang Qu
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| |
Collapse
|
17
|
Mahmood MI, Yamashita T. Influence of Lipid Bilayer on the GPCR Structure: Comparison of All-Atom Lipid Force Fields. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Md. Iqbal Mahmood
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| |
Collapse
|
18
|
Nasrin SR, Ganser C, Nishikawa S, Kabir AMR, Sada K, Yamashita T, Ikeguchi M, Uchihashi T, Hess H, Kakugo A. Deformation of microtubules regulates translocation dynamics of kinesin. SCIENCE ADVANCES 2021; 7:eabf2211. [PMID: 34644102 PMCID: PMC10763888 DOI: 10.1126/sciadv.abf2211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Microtubules, the most rigid components of the cytoskeleton, can be key transduction elements between external forces and the cellular environment. Mechanical forces induce microtubule deformation, which is presumed to be critical for the mechanoregulation of cellular events. However, concrete evidence is lacking. In this work, with high-speed atomic force microscopy, we unravel how microtubule deformation regulates the translocation of the microtubule-associated motor protein kinesin-1, responsible for intracellular transport. Our results show that the microtubule deformation by bending impedes the translocation dynamics of kinesins along them. Molecular dynamics simulation shows that the hindered translocation of kinesins can be attributed to an enhanced affinity of kinesins to the microtubule structural units in microtubules deformed by bending. This study advances our understanding of the role of cytoskeletal components in mechanotransduction.
Collapse
Affiliation(s)
| | - Christian Ganser
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Seiji Nishikawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | | | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayuki Uchihashi
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|
19
|
Watanabe Y, Tanabe A, Hamakubo T, Nagatoishi S, Tsumoto K. Development of biparatopic bispecific antibody possessing tetravalent scFv-Fc capable of binding to ROBO1 expressed in hepatocellular carcinoma cells. J Biochem 2021; 170:307-315. [PMID: 33844018 DOI: 10.1093/jb/mvab049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022] Open
Abstract
There is no standard structural format of the biparatopic bispecific antibody (bbsAb) which is used against the target molecule because of the diversity of biophysical features of bispecific antibodies (bsAbs). It is therefore essential that the interaction between the antibody and antigen is quantitatively analyzed to design antibodies that possess the desired properties. Here, we generated bsAbs, namely, a tandem scFv-Fc, a diabody-Fc, and an immunofusion-scFv-Fc-scFv, that possessed four scFv arms at different positions and were capable of recognizing the extracellular domains of ROBO1. We examined the interactions between these bsAbs and ROBO1 at the biophysical and cellular levels. Of these, immunofusion-B2212A scFv-Fc-B5209B scFv was stably expressed with the highest relative yield. The kinetic and thermodynamic features of the interactions of each bsAb with soluble ROBO1 (sROBO1) were validated using surface plasmon resonance and isothermal titration calorimetry. In all bsAbs, the immunofusion-scFv-Fc-scFv format showed homogeneous interaction with the antigen with higher affinity compared with that of monospecific antibodies. In conclusion, our study presents constructive information to design druggable bbsAbs in drug applications.
Collapse
Affiliation(s)
- Yuji Watanabe
- Departmant of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Aki Tanabe
- Departmant of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugimachi, Nakahara-ku, Kawasaki 211-8533, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Departmant of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| |
Collapse
|
20
|
Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies. Int J Mol Sci 2021; 22:ijms22115989. [PMID: 34206009 PMCID: PMC8198660 DOI: 10.3390/ijms22115989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/29/2021] [Indexed: 01/16/2023] Open
Abstract
Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the mechanism of action into the progression of immune responses. Multiple strategies, including phage display and hybridoma technologies, have been used to enhance the affinity of antibodies for their respective epitopes. Here, we investigate the TLR4 antibody-binding epitope by computational-driven approach. We demonstrate that three important residues, i.e., Y328, N329, and K349 of TLR4 antibody binding epitope identified upon in silico mutagenesis, affect not only the interaction and binding affinity of antibody but also influence the structural integrity of TLR4. Furthermore, we predict a novel epitope at the TLR4-MD2 interface which can be targeted and explored for therapeutic antibodies and small molecules. This technique provides an in-depth insight into antibody-antigen interactions at the resolution and will be beneficial for the development of new monoclonal antibodies. Computational techniques, if coupled with experimental methods, will shorten the duration of rational design and development of antibody therapeutics.
Collapse
|
21
|
Qu L, Qiao X, Qi F, Nishida N, Hoshino T. Analysis of Binding Modes of Antigen-Antibody Complexes by Molecular Mechanics Calculation. J Chem Inf Model 2021; 61:2396-2406. [PMID: 33934602 DOI: 10.1021/acs.jcim.1c00167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Antibodies are one of the most important protein molecules in biopharmaceutics. Due to the recent advance in technology for producing monoclonal antibodies, many structural data are available on the antigen-antibody complexes. To characterize the molecular interaction in antigen-antibody recognition, we computationally analyzed 500 complex structures by molecular mechanics calculations. The presence of Ser and Tyr is markedly large in the complementarity-determining regions (CDRs). Although Ser is abundant in CDRs, its contribution to the binding score is not large. Instead, Tyr, Asp, Glu, and Arg significantly contribute to the molecular interaction from the viewpoint of the binding score. The decomposition of the binding score suggests that the hydrophilic interaction is predominant in all CDRs compared with the hydrophobic one. The contribution of the heavy chain is larger than that of the light chain. In particular, H2 and H3 largely contribute to the binding interaction. Tyr is a main contributing residue both in H2 and H3. The positively charged residue Arg also significantly contributes to the binding score in H3, while the contribution of Lys is small. The appearance of Ser is remarkable in H2, and Asp is abundant in H3. The non-charged polar residues, Thr, Asn, and Gln, appear much in H2, compared to appearing in H3. The negatively charged residues Asp and Glu significantly contribute to the binding score in H3. The contributions of Phe and Trp are not large in spite that the aromatic residues are capable of making the π-π or CH-π interaction. Gly is commonly abundant both in H2 and H3. The average distance of the shortest direct hydrogen bond between the antigen and antibody is longer than that of the hydrogen bonds observed in the complexes between compounds and their target proteins. Therefore, the antigen-antibody interface is not so tight as the compound-target protein interface. The calculation of shape complementarity is consistent with the result of the hydrogen bonds in that the fitness of the antigen-antibody contact is not so high as that of the compound-target protein contact. There exist many water molecules at the antigen-antibody interface. These findings suggest that Tyr, Asp, Glu, and Arg are rich in H3 and work as major contributors for the interaction with the antigen. Ser, Thr, Asn, and Gln are rich in H2 and support the interaction with enhancing molecular fitness. Gly is helpful in increasing flexibility and geometrical diversity. Because the antigen-antibody binding is fundamentally hydrophilic-driven, the non-polar residues are unfavorable for mediating the contact even for the aromatic residues such as Phe and Trp.
Collapse
Affiliation(s)
- Liang Qu
- Graduate School of Pharmaceutical Sciences, Chiba UniversityRINGGOLD, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Xinyue Qiao
- Graduate School of Pharmaceutical Sciences, Chiba UniversityRINGGOLD, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Fei Qi
- Graduate School of Pharmaceutical Sciences, Chiba UniversityRINGGOLD, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba UniversityRINGGOLD, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba UniversityRINGGOLD, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| |
Collapse
|
22
|
Ito M, Takino N, Nomura T, Kan A, Muramatsu SI. Engineered adeno-associated virus 3 vector with reduced reactivity to serum antibodies. Sci Rep 2021; 11:9322. [PMID: 33927271 PMCID: PMC8084969 DOI: 10.1038/s41598-021-88614-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
The natural serotypes of adeno-associated virus (AAV) or their variants, such as AAV8 and AAV5, are commonly used as vectors in the clinical programs for liver-targeted gene therapy. While AAV8 vectors are not highly efficient at targeting primary human hepatocytes, AAV3 vectors have recently demonstrated remarkable efficiency at targeting both human and non-human primate hepatocytes. However, the presence of high levels of neutralizing antibodies (NAbs) impedes transduction into hepatocytes, representing a major obstacle to the clinical application of AAV3 vectors. Herein, we engineered the viral capsid to reduce its reactivity with pre-existing NAbs, thereby enhancing the transduction efficiency. By introducing three substitutions (S472A, S587A, and N706A) on the surface loop of AAV3B capsid protein, we generated a triple mutant AAV3 (AAV.GT5) vector with less reactivity to anti-AAV capsid NAbs. While the transduction efficiency of AAV.GT5 into human hepatocellular cell lines was similar to those of parental AAV3B, it was 50-fold higher for hepatocytes derived from humanized mice compared to AAV8 vectors. Moreover, the AAV.GT5 vector yield was similar to those of the AAV2 and AAV3B vectors. Thus, high resistance to pre-existing NAbs makes AAV.GT5 a promising candidate for future liver-targeted gene therapy clinical trials.
Collapse
Affiliation(s)
- Mika Ito
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, Japan
| | - Naomi Takino
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, Japan
| | | | | | - Shin-Ichi Muramatsu
- Division of Neurological Gene Therapy, Center for Open Innovation, Jichi Medical University, Tochigi, Japan. .,Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
23
|
Okajima R, Hiraoka S, Yamashita T. Environmental Effects on Salt Bridge Stability in the Protein-Protein Interface: The Case of Hen Egg-White Lysozyme and Its Antibody, HyHEL-10. J Phys Chem B 2021; 125:1542-1549. [PMID: 33544613 DOI: 10.1021/acs.jpcb.0c09248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We studied the stability of two salt bridges between hen egg-white lysozyme (HEL) and its antibody, HyHEL-10, by using molecular dynamics simulations. It was observed that one salt bridge, D32H-K97Y, was stable, whereas the other, D99H-K97Y, was not. To understand this difference, we compared several reduced salt bridge models that incorporated the salt bridges and nearby residues. The results showed the importance of nearby residues, especially Y33H and W98H. Furthermore, to understand the effects of nearby salt bridges, we investigated two mutants, D32HA and D99HA. We found that the D32HA mutation considerably stabilized the D99H-K97Y salt bridge. The reduced model analysis indicated that this can be largely attributed to a conformational change of the main chain.
Collapse
Affiliation(s)
- Ryo Okajima
- Department of Basic Science, Graduate School of Arts and Sciences, the University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.,Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, the University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| |
Collapse
|
24
|
Nagano K, Tsutsumi Y. Phage Display Technology as a Powerful Platform for Antibody Drug Discovery. Viruses 2021; 13:178. [PMID: 33504115 PMCID: PMC7912188 DOI: 10.3390/v13020178] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/06/2021] [Accepted: 01/21/2021] [Indexed: 12/18/2022] Open
Abstract
Antibody drugs with a high affinity and specificity are effective and safe for intractable diseases, such as cancers and autoimmune diseases. Furthermore, they have played a central role in drug discovery, currently accounting for eight of the top 20 pharmaceutical products worldwide by sales. Forty years ago, clinical trials on antibody drugs that were thought to be a magic bullet failed, partly due to the immunogenicity of monoclonal antibodies produced in mice. The recent breakthrough in antibody drugs is largely because of the contribution of phage display technology. Here, we reviewed the importance of phage display technology as a powerful platform for antibody drug discovery from various perspectives, such as the development of human monoclonal antibodies, affinity enhancement of monoclonal antibodies, and the identification of therapeutic targets for antibody drugs.
Collapse
MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/metabolism
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibody Affinity
- Autoantibodies/immunology
- Cell Surface Display Techniques
- Drug Discovery
- High-Throughput Screening Assays
- Humans
- Mice
- Peptide Library
Collapse
Affiliation(s)
- Kazuya Nagano
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 1-6, Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
25
|
Occupation of a thermoresistant-scaffold (αRep) at SP1-NC cleavage site disturbs the function of HIV-1 protease. Biosci Rep 2020; 40:225239. [PMID: 32519747 PMCID: PMC7313444 DOI: 10.1042/bsr20201131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 11/25/2022] Open
Abstract
HIV-1 nucleocapsid (NC) becomes an attractive target for the development of novel anti-HIV-1 agents. Discovering of non-antibody scaffolds that disrupt the function of NC will be a potential aspect for disturbing viral maturation process. Correspondingly, we explored the specific binding site of the thermoresistant-scaffold protein, αRep9A8 which formerly demonstrated the inhibitory effect on HIV-1 replication. The portion of Gag, CA21-SP1-NC has been used as a template for designing nine overlapping peptides (P4–P12). The P9 peptide showed the strongest binding activity followed by P8 and P12 respectively. The amino acid sequences on those peptides resemble the N-terminal domain of the NC proximity to the SP1-NC initial cleavage site and across the conserved CCHC zinc finger 1 (ZF1) of NC. The interaction KD between αRep9A8 with its target was 224.9 ± 57.4 nM. Consequently, αRep9A8 demonstrated the interference of the HIV-1 protease function by hindering a protease cleavage site. The released NC product from CA21-SP1-NC was diminished. The present study provided an additional information of αRep9A8 function in interfering of viral maturation processes resulting in the decremental efficiency of viral infectivity.
Collapse
|
26
|
Kuroda D, Tsumoto K. Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design. J Pharm Sci 2020; 109:1631-1651. [DOI: 10.1016/j.xphs.2020.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/25/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022]
|
27
|
Saponin Facilitates Anti-Robo1 Immunotoxin Cytotoxic Effects on Maxillary Sinus Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2020; 2020:9593516. [PMID: 32256588 PMCID: PMC7086449 DOI: 10.1155/2020/9593516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/08/2019] [Accepted: 01/18/2020] [Indexed: 01/06/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide. The standard treatment of surgery, chemotherapy, and radiotherapy can result in long-term complications which lower the patient's quality of life, such as eating disorders, speech problems, and disfiguring or otherwise untoward cosmetic issues. Antibody therapy against cancer-specific antigens is advantageous in terms of its lesser side effects achieved by its greater specificity, though the antitumor activity is still usually not enough to obtain a complete cure. Robo1, an axon guidance receptor, has received considerable attention as a possible drug target in various cancers. We have shown previously the enhanced cytotoxic effects of saporin-conjugated anti-Robo1 immunotoxin (IT-Robo1) on the HNSCC cell line HSQ-89 in combination with a photochemical internalization technique. Considering the light source, which has only limited tissue penetrance, we examined the drug internalization effect of saponin. Treatment with saponin facilitated significant cytotoxic effects of IT-Robo1 on HSQ-89 cells. Saponin exerts its own nonspecific cytotoxicity, which may cover the actual extent of the internalization effect. We thus examined whether a flashed treatment with saponin exerted a significant specific cytotoxic effect on cancer cells. The combination of an immunotoxin with saponin also exhibited a significant tumor-suppressive effect on mice HSQ-19 xenografts. These results suggest the utility of saponin treatment as an enhancer of immunotoxin treatment in cancer.
Collapse
|
28
|
Akiba H, Takayanagi K, Kusano-Arai O, Iwanari H, Hamakubo T, Tsumoto K. Generation of biparatopic antibody through two-step targeting of fragment antibodies on antigen using SpyTag and SpyCatcher. ACTA ACUST UNITED AC 2020; 25:e00418. [PMID: 31993343 PMCID: PMC6976922 DOI: 10.1016/j.btre.2020.e00418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 12/25/2022]
Abstract
Biparatopic fragment antibodies can overcome deficiencies in avidity of conventional antibody fragments. Here, we describe a technology for generating biparatopic antibodies through two-step targeting using a pair of polypeptides, SpyTag and SpyCatcher, that spontaneously react to form a covalent bond between antibody fragments. In this method, two antibody fragments, each targeting different epitopes of the antigen, are fused to SpyTag and to SpyCatcher. When the two polypeptides are serially added to the antigen, their proximity on the antigen results in covalent bond formation and generation of a biparatopic antibody. We validated the system with purified recombinant antigen. Results in antigen-overexpressing cells were promising although further optimization will be required. Because this strategy results in high-affinity targeting with a bipartite molecule that has considerably lower molecular weight than an antibody, this technology is potentially useful for diverse applications.
Collapse
Affiliation(s)
- Hiroki Akiba
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kensuke Takayanagi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Osamu Kusano-Arai
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Hiroko Iwanari
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Takao Hamakubo
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.,Department of Protein-protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugimachi, Nakahara-ku, Kawasaki, 211-8533, Japan
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| |
Collapse
|