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Hifumi E, Ito Y, Tsujita M, Taguchi H, Uda T. Enzymatization of mouse monoclonal antibodies to the corresponding catalytic antibodies. Sci Rep 2024; 14:12184. [PMID: 38806597 PMCID: PMC11133420 DOI: 10.1038/s41598-024-63116-6] [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: 03/21/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
Catalytic antibodies possess a dual function that enables both antigen recognition and degradation. However, their time-consuming preparation is a significant drawback. This study developed a new method for quickly converting mice monoclonal antibodies into catalytic antibodies using site-directed mutagenesis. Three mice type monoclonal antibodies targeting hemagglutinin molecule of influenza A virus could be transformed into the catalytic antibodies by deleting Pro95 in CDR-3 of the light chain. No catalytic activity was observed for monoclonal antibodies and light chains. In contrast, the Pro95-deleted light chains exhibited a catalytic activity to cleave the antigenic peptide including the portion of conserved region of hemagglutinin molecule. The affinity of the Pro95-deleted light chains to the antigen increased approximately 100-fold compared to the wild-type light chains. In the mutants, three residues (Asp1, Ser92, and His93) come closer to the appropriate position to create the catalytic site and contributing to the enhancement of both catalytic function and immunoreactivity. Notably, the Pro95-deleted catalytic light chains could suppress influenza virus infection in vitro assay, whereas the parent antibody and the light chain did not. This strategy offers a rapid and efficient way to create catalytic antibodies from existing antibodies, accelerating the development for various applications in diagnostic and therapeutic applications.
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Affiliation(s)
- Emi Hifumi
- Institute for Research Management, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan.
- Research Center for GLOBAL/LOCAL Infectious Diseases, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan.
| | - Yuina Ito
- Institute for Research Management, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan
- Graduate School of Engineering, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan
| | - Moe Tsujita
- Institute for Research Management, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan
- Graduate School of Engineering, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan
| | - Hiroaki Taguchi
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka, 510-0293, Japan
| | - Taizo Uda
- Institute for Research Management, Oita University, 700 Dannoharu, Oita-shi, Oita, 870-1192, Japan
- Materials Open Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), Fukuoka, 819-0388, Japan
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Obtaining Highly Active Catalytic Antibodies Capable of Enzymatically Cleaving Antigens. Int J Mol Sci 2022; 23:ijms232214351. [PMID: 36430828 PMCID: PMC9697424 DOI: 10.3390/ijms232214351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
A catalytic antibody has multiple functions compared with a monoclonal antibody because it possesses unique features to digest antigens enzymatically. Therefore, many catalytic antibodies, including their subunits, have been produced since 1989. The catalytic activities often depend on the preparation methods and conditions. In order to elicit the high catalytic activity of the antibodies, the most preferable methods and conditions, which can be generally applicable, must be explored. Based on this view, systematic experiments using two catalytic antibody light chains, #7TR and H34, were performed by varying the purification methods, pH, and chemical reagents. The experimental results obtained by peptidase activity tests and kinetic analysis, revealed that the light chain's high catalytic activity was observed when it was prepared under a basic condition. These data imply that a small structural modulation of the catalytic antibody occurs during the purification process to increase the catalytic activity while the antigen recognition ability is kept constant. The presence of NaCl enhanced the catalytic activity. When the catalytic light chain was prepared with these preferable conditions, #7TR and H34 hugely enhanced the degradation ability of Amyloid-beta and PD-1 peptide, respectively.
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A new catalytic site functioning in antigen cleavage by H34 catalytic antibody light chain. Sci Rep 2022; 12:19185. [PMID: 36357546 PMCID: PMC9649737 DOI: 10.1038/s41598-022-23689-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
The cleavage reactions of catalytic antibodies are mediated by a serine protease mechanism involving a catalytic triad composed of His, Ser, and Asp residues, which reside in the variable region. Recently, we discovered a catalytic antibody, H34 wild type (H34wt), that is capable of enzymatically cleaving an immune-check point PD-1 peptide and recombinant PD-1; however, H34wt does not contain His residues in the variable region. To clarify the reason behind the catalytic features of H34wt and the amino acid residues involved in the catalytic reaction, we performed site-directed mutagenesis focusing on the amino acid residues involved in the cleavage reaction, followed by catalytic activity tests, immunological reactivity evaluation, and molecular modeling. The results revealed that the cleavage reaction by H34wt proceeds through the action of a new catalytic site composed of Arg, Thr, and Gln. This new scheme differs from that of the serine protease mechanism of catalytic antibodies.
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Hifumi E, Taguchi H, Nonaka T, Harada T, Uda T. Finding and characterizing a catalytic antibody light chain, H34, capable of degrading the PD-1 molecule. RSC Chem Biol 2021; 2:220-229. [PMID: 34458785 PMCID: PMC8341958 DOI: 10.1039/d0cb00155d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
Programmed cell death 1 (PD-1) is an immune checkpoint molecule regulating T-cell function. Preventing PD-1 binding to its ligand PD-L1 has emerged as an important tool in immunotherapy. Here, we describe a unique human catalytic antibody light chain, H34, which mediates enzymatic degradation of human PD-1 peptides and recombinant human PD-1 protein and thus functions to prevent the binding of PD-1 with PD-L1. H34 degraded one half of the PD-1 molecules within about 6 h under the experimental conditions. Investigating the acquisition of the catalytic function by H34, which belongs to subgroup I and lacks a Pro95 residue in CDR-3, revealed the importance of this sequence, as a Pro95-reconstituted mutant (H34-Pro95(+)) exhibited very little catalytic activity to cleave PD-1. Interestingly, EDTA inhibited the catalytic activity of H34, which could work as a metallo-protease. Zn2+ or Co2+ ions may work as a cofactor. It is meaningfull that H34 was obtained from the human antibody gene taken from a healthy volunteer, suggesting that we potentially have such unique molecules in our body.
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Affiliation(s)
- Emi Hifumi
- Oita University, Research Promotion Institute 700 Dannoharu Oita-shi Oita 870-1192 Japan
| | - Hiroaki Taguchi
- Suzuka University of Medical Science, Faculty of Pharmaceutical Sciences 3500-3 Minamitamagaki-cho Suzuka 510-0293 Japan
| | - Tamami Nonaka
- Oita University, Research Promotion Institute 700 Dannoharu Oita-shi Oita 870-1192 Japan
| | - Takunori Harada
- Oita University, Faculty of Science & Technology, Division of Applied Chemistry 700 Dannoharu Oita-shi Oita 870-1192 Japan
| | - Taizo Uda
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT) 4-1 Kyudai-shinmachi Fukuoka 879-5593 Japan
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Hifumi E, Taguchi H, Tsuda H, Minagawa T, Nonaka T, Uda T. A new algorithm to convert a normal antibody into the corresponding catalytic antibody. SCIENCE ADVANCES 2020; 6:eaay6441. [PMID: 32232151 PMCID: PMC7096177 DOI: 10.1126/sciadv.aay6441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Over thousands of monoclonal antibodies (mAbs) have been produced so far, and it would be valuable if these mAbs could be directly converted into catalytic antibodies. We have designed a system to realize the above concept by deleting Pro95, a highly conserved residue in CDR-3 of the antibody light chain. The deletion of Pro95 is a key contributor to catalytic function of the light chain. The S35 and S38 light chains have identical amino acid sequences except for Pro95. The former, with Pro95 did not show any catalytic activity, whereas the latter, without Pro95, exhibited peptidase activity. To verify the generality of this finding, we tested another light chain, T99wt, which had Pro95 and showed little catalytic activity. In contrast, a Pro95-deleted mutant enzymatically degraded the peptide substrate and amyloid-beta molecule. These two cases demonstrate the potential for a new method of creating catalytic antibodies from the corresponding mAbs.
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Affiliation(s)
- Emi Hifumi
- Oita University, Research Promotion Institute, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
| | - Hiroaki Taguchi
- Suzuka University of Medical Science, Faculty of Pharmaceutical Sciences, 3500-3 Minamitamagaki-cho, Suzuka 510-0293, Japan
| | - Haruna Tsuda
- Oita University, Research Promotion Institute, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
- Oita University, Department of Applied Chemistry, Faculty of Engineering, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
| | - Tetsuro Minagawa
- Oita University, Research Promotion Institute, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
- Oita University, Department of Applied Chemistry, Faculty of Engineering, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
| | - Tamami Nonaka
- Oita University, Research Promotion Institute, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
| | - Taizo Uda
- Oita University, Research Promotion Institute, 700 Dannoharu, Oita-shi, Oita 870-1192, Japan
- Nanotechnology Laboratory, Institute of Systems, Information Technologies and Nanotechnologies (ISIT), 4-1 Kyudai-shinmachi, Fukuoka 879-5593, Japan
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Hifumi E, Taguchi H, Toorisaka E, Uda T. New technologies to introduce a catalytic function into antibodies: A unique human catalytic antibody light chain showing degradation of β-amyloid molecule along with the peptidase activity. FASEB Bioadv 2019; 1:93-104. [PMID: 32123823 PMCID: PMC6996398 DOI: 10.1096/fba.1025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/04/2018] [Accepted: 10/12/2018] [Indexed: 12/20/2022] Open
Abstract
Since the discovery of a natural catalytic antibody in 1989, many catalytic antibodies targeting peptides, nucleotides, virus and bacterial proteins, and many molecules have been prepared. Although catalytic antibodies should have features superior to non-catalytic monoclonal antibodies, the reports on catalytic antibodies are far fewer than those on normal (non-catalytic) antibodies. Nowadays, we can obtain any monoclonal antibody we want, which is not the case for catalytic antibodies. To overcome this drawback of catalytic antibodies, much basic research must be done. As one way to attain this purpose, we have been making a protein bank of human antibody light chains, in which the light chains were expressed, purified, and stored for use in screening against many kinds of antigen, to then get clues to introducing a catalytic function in normal antibodies. As the number of stored light chains in the above protein bank has reached the hundreds, in this study, we screened them against amyloid-beta (Aβ), which is well-known as one of the molecules causing Alzheimer's disease. We found two interesting light chains, #7TR and #7GY. The former could degrade both a fluorescence resonance energy transfer-Aβ substrate and Aβ1-40 full peptide. In contrast, #7GY, whose sequence is identical to that of #7TR except for the amino acids at the 29th and 30th positions, did not degrade the FRET-Aβ substrate at all. By using a synthetic substrate, Arg-pNA, the difference between the chemical features of the two light chains was investigated in detail. In addition, we found that the presence of Zn(II) ion hugely influenced the catalytic activity of the #7TR light chain but not #7GY. Through these facts and the discussion, we propose one of the clues to how to put a catalytic function in a normal (non-catalytic) antibody.
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Affiliation(s)
- Emi Hifumi
- Research Promotion Institute, Oita UniversityOitaJapan
| | - Hiroaki Taguchi
- Faculty of Pharmaceutical SciencesSuzuka University of Medical ScienceSuzukaJapan
| | - Eiichi Toorisaka
- Faculty of Engineering, Department of Sustainable EngineeringYamaguchi UniversityYamaguchiJapan
| | - Taizo Uda
- Faculty of Engineering, Department of Applied ChemistryOita UniversityOitaJapan
- Nanotechnology LaboratoryInstitute of Systems, Information Technologies and Nanotechnologies (ISIT)FukuokaJapan
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Hifumi E, Arakawa M, Matsumoto S, Yamamoto T, Katayama Y, Uda T. Biochemical features and antiviral activity of a monomeric catalytic antibody light-chain 23D4 against influenza A virus. FASEB J 2015; 29:2347-58. [PMID: 25713031 DOI: 10.1096/fj.14-264275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/26/2015] [Indexed: 02/02/2023]
Abstract
Catalytic antibodies have exhibited interesting functions against some infectious viruses such as HIV, rabies virus, and influenza virus in vitro as well as in vivo. In some cases, a catalytic antibody light chain takes on several structures from the standpoint of molecular size (monomer, dimer, etc.) and/or isoelectronic point. In this study, we prepared a monomeric 23D4 light chain by mutating the C-terminal Cys to Ala of the wild-type. The mutated 23D4 molecule took a simple monomeric form, which could hydrolyze synthetic 4-methyl-coumaryl-7-amide substrates and a plasmid DNA. Because the monomeric 23D4 light chain suppressed the infection of influenza virus A/Hiroshima/37/2001 in an in vitro assay, the corresponding experiments were conducted in vivo, after the virus strain (which was taken from a human patient) was successfully adapted into BALB/cN Sea mice. In the experiments, a mixture of the monomeric 23D4 and the virus was nasally administered 1) with preincubation and 2) without preincubation. As a result, the monomeric 23D4 clearly exhibited the ability to suppress the influenza virus infection in both cases, indicating a potential drug for preventing infection of the influenza A virus.
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Affiliation(s)
- Emi Hifumi
- *Research Promotion Institute, Oita University, Oita-shi, Oita, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, Kawaguchi, Saitama, Japan; Faculty of Medicine, Oita University, Yufu-city, Oita, Japan; Department of Applied Chemistry; Oita University, Oita-shi, Oita, Japan; Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan; and Institute of Systems, Information Technologies and Nanotechnologies, Nanotechnology Laboratory, Fukuoka, Japan
| | - Mitsue Arakawa
- *Research Promotion Institute, Oita University, Oita-shi, Oita, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, Kawaguchi, Saitama, Japan; Faculty of Medicine, Oita University, Yufu-city, Oita, Japan; Department of Applied Chemistry; Oita University, Oita-shi, Oita, Japan; Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan; and Institute of Systems, Information Technologies and Nanotechnologies, Nanotechnology Laboratory, Fukuoka, Japan
| | - Shingo Matsumoto
- *Research Promotion Institute, Oita University, Oita-shi, Oita, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, Kawaguchi, Saitama, Japan; Faculty of Medicine, Oita University, Yufu-city, Oita, Japan; Department of Applied Chemistry; Oita University, Oita-shi, Oita, Japan; Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan; and Institute of Systems, Information Technologies and Nanotechnologies, Nanotechnology Laboratory, Fukuoka, Japan
| | - Tatsuhiro Yamamoto
- *Research Promotion Institute, Oita University, Oita-shi, Oita, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, Kawaguchi, Saitama, Japan; Faculty of Medicine, Oita University, Yufu-city, Oita, Japan; Department of Applied Chemistry; Oita University, Oita-shi, Oita, Japan; Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan; and Institute of Systems, Information Technologies and Nanotechnologies, Nanotechnology Laboratory, Fukuoka, Japan
| | - Yoshiki Katayama
- *Research Promotion Institute, Oita University, Oita-shi, Oita, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, Kawaguchi, Saitama, Japan; Faculty of Medicine, Oita University, Yufu-city, Oita, Japan; Department of Applied Chemistry; Oita University, Oita-shi, Oita, Japan; Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan; and Institute of Systems, Information Technologies and Nanotechnologies, Nanotechnology Laboratory, Fukuoka, Japan
| | - Taizo Uda
- *Research Promotion Institute, Oita University, Oita-shi, Oita, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, Kawaguchi, Saitama, Japan; Faculty of Medicine, Oita University, Yufu-city, Oita, Japan; Department of Applied Chemistry; Oita University, Oita-shi, Oita, Japan; Graduate School of Systems Life Sciences, Kyushu University, Nishi-ku, Fukuoka, Japan; and Institute of Systems, Information Technologies and Nanotechnologies, Nanotechnology Laboratory, Fukuoka, Japan
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Hifumi E, Fujimoto N, Arakawa M, Saito E, Matsumoto S, Kobayashi N, Uda T. Biochemical features of a catalytic antibody light chain, 22F6, prepared from human lymphocytes. J Biol Chem 2013; 288:19558-68. [PMID: 23677996 PMCID: PMC3707657 DOI: 10.1074/jbc.m113.454579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human antibody light chains belonging to subgroup II of germ line genes were amplified by a seminested PCR technique using B-lymphocytes taken from a human adult infected with influenza virus. Each gene of the human light chains was transferred into the Escherichia coli system. The recovered light chain was highly purified using a two-step purification system. Light chain 22F6 showed interesting catalytic features. The light chain cleaved a peptide bond of synthetic peptidyl-4-methyl-coumaryl-7-amide (MCA) substrates, such as QAR-MCA and EAR-MCA, indicating amidase activity. It also hydrolyzed a phosphodiester bond of both DNA and RNA. From the analysis of amino acid sequences and molecular modeling, the 22F6 light chain possesses two kinds of active sites as amidase and nuclease in close distances. The 22F6 catalytic light chain could suppress the infection of influenza virus type A (H1N1) of Madin-Darby canine kidney cells in an in vitro assay. In addition, the catalytic light chain clearly inhibited the infection of the influenza virus of BALB/c mice via nasal administration in an in vivo assay. In the experiment, the titer in the serum of the mice coinfected with the 22F6 light chain and H1N1 virus became considerably lowered compared with that of 22F6-non-coinfected mice. Note that the catalytic light chain was prepared from human peripheral lymphocyte and plays an important role in preventing infection by influenza virus. Considering the fact that the human light chain did not show any acute toxicity for mice, our procedure developed in this study must be unique and noteworthy for developing new drugs.
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Affiliation(s)
- Emi Hifumi
- Research Center for Applied Medical Engineering, Oita University, Dan-noharu 700, Oita-shi, Oita 870-1192, Japan.
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