151
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Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 2020; 21:1549-1567. [PMID: 31626279 PMCID: PMC7947987 DOI: 10.1093/bib/bbz095] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
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152
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T-cell repertoire analysis and metrics of diversity and clonality. Curr Opin Biotechnol 2020; 65:284-295. [PMID: 32889231 DOI: 10.1016/j.copbio.2020.07.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
Abstract
The recent developments of high-throughput bulk and single-cell sequencing technologies accelerated the understanding of the complexity of immune repertoire dynamics combined to transcriptomics. Also, profiling of cellular repertoires in health or disease requires statistical metrics to capture clonal diversity characterized by clones frequency, repertoire richness and convergence. Here we present the common technologies of bulk and single-cell sequencing of T-cell receptors (TCRs), discuss current knowledge regarding computational tools clustering and predicting specificity of TCR repertoires based on shared structural motifs and review main indices for repertoire diversity and convergence analyses. These tools represent potential biomarkers to decipher the fitness of immune repertoires in diseased or treated patients but also the presages and promises of computational approaches to revolutionize personalized immunotherapy.
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153
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020; 11:1986. [PMID: 32983137 PMCID: PMC7485114 DOI: 10.3389/fimmu.2020.01986] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage–derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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154
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Hobson BD, Kong L, Hartwick EW, Gonzalez RL, Sims PA. Elongation inhibitors do not prevent the release of puromycylated nascent polypeptide chains from ribosomes. eLife 2020; 9:60048. [PMID: 32844746 PMCID: PMC7490010 DOI: 10.7554/elife.60048] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Puromycin is an amino-acyl transfer RNA analog widely employed in studies of protein synthesis. Since puromycin is covalently incorporated into nascent polypeptide chains, anti-puromycin immunofluorescence enables visualization of nascent protein synthesis. A common assumption in studies of local messenger RNA translation is that the anti-puromycin staining of puromycylated nascent polypeptides in fixed cells accurately reports on their original site of translation, particularly when ribosomes are stalled with elongation inhibitors prior to puromycin treatment. However, when we attempted to implement a proximity ligation assay to detect ribosome-puromycin complexes, we found no evidence to support this assumption. We further demonstrated, using biochemical assays and live cell imaging of nascent polypeptides in mammalian cells, that puromycylated nascent polypeptides rapidly dissociate from ribosomes even in the presence of elongation inhibitors. Our results suggest that attempts to define precise subcellular translation sites using anti-puromycin immunostaining may be confounded by release of puromycylated nascent polypeptide chains prior to fixation.
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Affiliation(s)
- Benjamin D Hobson
- Department of Systems Biology, Columbia University Irving Medical Center, New York, United States.,Medical Scientist Training Program, Columbia University Irving Medical Center, New York, United States
| | - Linghao Kong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, United States
| | - Erik W Hartwick
- Department of Chemistry, Columbia University, New York, United States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, United States
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, United States.,Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, United States.,Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, United States
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155
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Kamata-Sakurai M, Narita Y, Hori Y, Nemoto T, Uchikawa R, Honda M, Hironiwa N, Taniguchi K, Shida-Kawazoe M, Metsugi S, Miyazaki T, Wada NA, Ohte Y, Shimizu S, Mikami H, Tachibana T, Ono N, Adachi K, Sakiyama T, Matsushita T, Kadono S, Komatsu SI, Sakamoto A, Horikawa S, Hirako A, Hamada K, Naoi S, Savory N, Satoh Y, Sato M, Noguchi Y, Shinozuka J, Kuroi H, Ito A, Wakabayashi T, Kamimura M, Isomura F, Tomii Y, Sawada N, Kato A, Ueda O, Nakanishi Y, Endo M, Jishage KI, Kawabe Y, Kitazawa T, Igawa T. Antibody to CD137 Activated by Extracellular Adenosine Triphosphate Is Tumor Selective and Broadly Effective In Vivo without Systemic Immune Activation. Cancer Discov 2020; 11:158-175. [PMID: 32847940 DOI: 10.1158/2159-8290.cd-20-0328] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/09/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022]
Abstract
Agonistic antibodies targeting CD137 have been clinically unsuccessful due to systemic toxicity. Because conferring tumor selectivity through tumor-associated antigen limits its clinical use to cancers that highly express such antigens, we exploited extracellular adenosine triphosphate (exATP), which is a hallmark of the tumor microenvironment and highly elevated in solid tumors, as a broadly tumor-selective switch. We generated a novel anti-CD137 switch antibody, STA551, which exerts agonistic activity only in the presence of exATP. STA551 demonstrated potent and broad antitumor efficacy against all mouse and human tumors tested and a wide therapeutic window without systemic immune activation in mice. STA551 was well tolerated even at 150 mg/kg/week in cynomolgus monkeys. These results provide a strong rationale for the clinical testing of STA551 against a broad variety of cancers regardless of antigen expression, and for the further application of this novel platform to other targets in cancer therapy. SIGNIFICANCE: Reported CD137 agonists suffer from either systemic toxicity or limited efficacy against antigen-specific cancers. STA551, an antibody designed to agonize CD137 only in the presence of extracellular ATP, inhibited tumor growth in a broad variety of cancer models without any systemic toxicity or dependence on antigen expression.See related commentary by Keenan and Fong, p. 20.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Mika Kamata-Sakurai
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan.
| | - Yoshinori Narita
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Yuji Hori
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Takayuki Nemoto
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Ryo Uchikawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Masaki Honda
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Naoka Hironiwa
- Chugai Pharmabody Research Pte. Ltd., Synapse, Singapore
| | - Kenji Taniguchi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Meiri Shida-Kawazoe
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Shoichi Metsugi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Taro Miyazaki
- Clinical Development Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Naoko A Wada
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yuki Ohte
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Shun Shimizu
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Hirofumi Mikami
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Tatsuhiko Tachibana
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Natsuki Ono
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Kenji Adachi
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Tetsushi Sakiyama
- Pharmaceutical Technology Division, Chugai Pharmaceutical Co., Ltd., Kita-ku, Tokyo, Japan
| | - Tomochika Matsushita
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Shojiro Kadono
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Shun-Ichiro Komatsu
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Akihisa Sakamoto
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Sayuri Horikawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Ayano Hirako
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Koki Hamada
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Sotaro Naoi
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Nasa Savory
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yasuko Satoh
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Motohiko Sato
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yuki Noguchi
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Junko Shinozuka
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Haruka Kuroi
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Ami Ito
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Tetsuya Wakabayashi
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Masaki Kamimura
- Chugai Research Institute for Medical Science, Inc., Kamakura, Kanagawa, Japan
| | - Fumihisa Isomura
- Chugai Research Institute for Medical Science, Inc., Gotemba, Shizuoka, Japan
| | - Yasushi Tomii
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Noriaki Sawada
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Atsuhiko Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Otoya Ueda
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yoshito Nakanishi
- Project & Lifecycle Management Unit, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Mika Endo
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Kou-Ichi Jishage
- Chugai Research Institute for Medical Science, Inc., Kamakura, Kanagawa, Japan.,Chugai Research Institute for Medical Science, Inc., Gotemba, Shizuoka, Japan
| | - Yoshiki Kawabe
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Takehisa Kitazawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Tomoyuki Igawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan.,Chugai Pharmabody Research Pte. Ltd., Synapse, Singapore
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156
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Niamsuphap S, Fercher C, Kumble S, Huda P, Mahler SM, Howard CB. Targeting the undruggable: emerging technologies in antibody delivery against intracellular targets. Expert Opin Drug Deliv 2020; 17:1189-1211. [DOI: 10.1080/17425247.2020.1781088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Suchada Niamsuphap
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
| | - Christian Fercher
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
- ARC Centre of Excellence in Convergent BioNano Science and Technology, AIBN, University of Queensland, Brisbane, Australia
| | - Sumukh Kumble
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
| | - Pie Huda
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
- Centre for Advanced Imaging (CAI), University of Queensland, Brisbane, Australia
| | - Stephen M Mahler
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
| | - Christopher B Howard
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
- Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia
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157
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Barrientos RC, Bow EW, Whalen C, Torres OB, Sulima A, Beck Z, Jacobson AE, Rice KC, Matyas GR. Novel Vaccine That Blunts Fentanyl Effects and Sequesters Ultrapotent Fentanyl Analogues. Mol Pharm 2020; 17:3447-3460. [PMID: 32787282 PMCID: PMC7482402 DOI: 10.1021/acs.molpharmaceut.0c00497] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Active
immunization is an emerging potential modality to combat
fatal overdose amid the opioid epidemic. In this study, we described
the design, synthesis, formulation, and animal testing of an efficacious
vaccine against fentanyl. The vaccine formulation is composed of a
novel fentanyl hapten conjugated to tetanus toxoid (TT) and adjuvanted
with liposomes containing monophosphoryl lipid A adsorbed on aluminum
hydroxide. The linker and hapten N-phenyl-N-(1-(4-(3-(tritylthio)propanamido)phenethyl)piperidin-4-yl)propionamide
were conjugated sequentially to TT using amine-N-hydroxysuccinimide-ester
and thiol–maleimide reaction chemistries, respectively. Conjugation
was facile, efficient, and reproducible with a protein recovery of
>98% and a hapten density of 30–35 per carrier protein molecule.
In mice, immunization induced high and robust antibody endpoint titers
in the order of >106 against the hapten. The antisera
bound
fentanyl, carfentanil, cyclopropyl fentanyl, para-fluorofentanyl, and furanyl fentanyl in vitro with
antibody-drug dissociation constants in the range of 0.36–4.66
nM. No cross-reactivity to naloxone, naltrexone, methadone, or buprenorphine
was observed. In vivo, immunization shifted the antinociceptive
dose–response curve of fentanyl to higher doses. Collectively,
these preclinical results showcased the desired traits of a potential
vaccine against fentanyl and demonstrated the feasibility of immunization
to combat fentanyl-induced effects.
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Affiliation(s)
- Rodell C Barrientos
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States.,U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Eric W Bow
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse and the National Institute on Alcohol Abuse and Alcoholism, Department of Health and Human Services, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892-3373, United States
| | - Connor Whalen
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
| | - Oscar B Torres
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States.,U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Agnieszka Sulima
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse and the National Institute on Alcohol Abuse and Alcoholism, Department of Health and Human Services, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892-3373, United States
| | - Zoltan Beck
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States.,U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Arthur E Jacobson
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse and the National Institute on Alcohol Abuse and Alcoholism, Department of Health and Human Services, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892-3373, United States
| | - Kenner C Rice
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse and the National Institute on Alcohol Abuse and Alcoholism, Department of Health and Human Services, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892-3373, United States
| | - Gary R Matyas
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, Maryland 20910, United States
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158
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Brooks BD, Closmore A, Yang J, Holland M, Cairns T, Cohen GH, Bailey-Kellogg C. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules 2020; 25:molecules25163659. [PMID: 32796656 PMCID: PMC7464469 DOI: 10.3390/molecules25163659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58102, USA
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
- Correspondence: ; Tel.: +1-435-222-1403
| | - Adam Closmore
- Department of Pharmacy, North Dakota State University, Fargo, ND 58102, USA;
| | - Juechen Yang
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Michael Holland
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Tina Cairns
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
| | - Gary H. Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
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159
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Designing a new bispecific tandem single-chain variable fragment antibody against tumor necrosis factor-α and interleukin-23 using in silico studies for the treatment of rheumatoid arthritis. J Mol Model 2020; 26:225. [PMID: 32778954 DOI: 10.1007/s00894-020-04510-5] [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: 03/05/2020] [Accepted: 08/05/2020] [Indexed: 10/23/2022]
Abstract
Rheumatoid arthritis disease is a chronic auto-immune inflammatory disease that mainly causes synovial joint inflammation and cartilage destruction. The tumor necrosis factor-α (TNF-α) is a pivotal cytokine that plays an important role in rheumatoid arthritis. The treatments focusing on a single cytokine inhibition are clinically able to produce meaningful responses in only about half of the treated patients due to multiple cytokines involved in this disease. In the present study, a bispecific tandem single-chain variable fragment was designed in order to suppress both human tumor necrosis factor-α and interleukin-23 (IL23) as a potential therapeutic drug candidate for this disease. To do so, at first, eight bispecific tandem single-chain variable fragment models were built against tumor necrosis factor-α and interleukin-23 cytokines with different domain orders by the homology modeling, and then 50 ns molecular dynamics simulation was performed for each one and then structural properties were exploited. The MD simulation results indicate the fact that the domains' order strongly affects tandem single-chain variable fragment properties, and in overall, the fragment VLAIL23+Linker+VHAIL23+linker+VLATNF+Linker +VHATNF +His6 (VL and VH are light and heavy chain variable fragments and AIL23 and ATNF are anti-interleukin 23 and anti-tumor necrosis factor-α, respectively, and His6 is the six histidine) not only separated antibody domains accurately but also had better stability and solvation free energy. Therefore, this structure can be considered as an effective potential drug for rheumatoid arthritis. It is expected that the findings of this research could shed a light on the treatment approaches of the rheumatoid arthritis disease.
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160
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Field Study on the Immunological Response and Protective Effect of a Licensed Autogenous Vaccine to Control Streptococcus suis Infections in Post-Weaned Piglets. Vaccines (Basel) 2020; 8:vaccines8030384. [PMID: 32674276 PMCID: PMC7565864 DOI: 10.3390/vaccines8030384] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/17/2020] [Accepted: 07/03/2020] [Indexed: 01/02/2023] Open
Abstract
Streptococcus suis is one of the most important bacterial pathogens in weaned piglets and responsible for serious economic losses to the swine industry. Currently, mostly autogenous vaccines composed of killed bacteria (bacterins) are available. However, immunological and protective data from field studies are missing. We report for the first time a comparative field study on the immunological response induced by an autogenous vaccine applied to either piglets or sows in a farm with recurrent S. suis problems. (I) Piglets from non-vaccinated sows received an autogenous bacterin during the first week and at three weeks of age. (II) Sows received the vaccine at five and three weeks pre-farrowing and piglets were non-vaccinated. Levels, isotype profile and opsonophagocytosis capacity of the serum antibodies induced by vaccination were evaluated. Vaccination of piglets failed to induce an active immune response. Vaccination of sows induced a significant increase in anti-S. suis antibodies, mainly composed of IgG1. However, isotype switching was modulated by the S. suis serotype included in the vaccine formulation. Despite this antibody increase in vaccinated sows, transfer of maternal immunity to piglets was not different from the control group (i.e., piglets from non-vaccinated sows). Notably, levels of maternal antibodies in piglets were already very high with marked opsonophagocytosis capacity at one week of age, independently of the vaccination program. However, their levels decreased by three weeks of age, indicating possible absence of antibodies in the post-weaning high-risk period. These observations correlated with lack of clinical protection in the farm. Overall, a piglet or a sow vaccination program herein mostly failed to induce lasting protection in nursery piglets. An improvement of vaccine formulation or an optimized program may be required.
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161
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Davis JS, Ferreira D, Paige E, Gedye C, Boyle M. Infectious Complications of Biological and Small Molecule Targeted Immunomodulatory Therapies. Clin Microbiol Rev 2020; 33:e00035-19. [PMID: 32522746 PMCID: PMC7289788 DOI: 10.1128/cmr.00035-19] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The past 2 decades have seen a revolution in our approach to therapeutic immunosuppression. We have moved from relying on broadly active traditional medications, such as prednisolone or methotrexate, toward more specific agents that often target a single receptor, cytokine, or cell type, using monoclonal antibodies, fusion proteins, or targeted small molecules. This change has transformed the treatment of many conditions, including rheumatoid arthritis, cancers, asthma, and inflammatory bowel disease, but along with the benefits have come risks. Contrary to the hope that these more specific agents would have minimal and predictable infectious sequelae, infectious complications have emerged as a major stumbling block for many of these agents. Furthermore, the growing number and complexity of available biologic agents makes it difficult for clinicians to maintain current knowledge, and most review articles focus on a particular target disease or class of agent. In this article, we review the current state of knowledge about infectious complications of biologic and small molecule immunomodulatory agents, aiming to create a single resource relevant to a broad range of clinicians and researchers. For each of 19 classes of agent, we discuss the mechanism of action, the risk and types of infectious complications, and recommendations for prevention of infection.
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Affiliation(s)
- Joshua S Davis
- Department of Infectious Diseases and Immunology, John Hunter Hospital, Newcastle, NSW, Australia
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
| | - David Ferreira
- School of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Emma Paige
- Department of Infectious Diseases, Alfred Hospital, Melbourne, VIC, Australia
| | - Craig Gedye
- School of Medicine, University of New South Wales, Sydney, NSW, Australia
- Department of Oncology, Calvary Mater Hospital, Newcastle, NSW, Australia
| | - Michael Boyle
- Department of Infectious Diseases and Immunology, John Hunter Hospital, Newcastle, NSW, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
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162
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Zhang MM, Huang RYC, Beno BR, Deyanova EG, Li J, Chen G, Gross ML. Epitope and Paratope Mapping of PD-1/Nivolumab by Mass Spectrometry-Based Hydrogen-Deuterium Exchange, Cross-linking, and Molecular Docking. Anal Chem 2020; 92:9086-9094. [PMID: 32441507 DOI: 10.1021/acs.analchem.0c01291] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Programmed cell death-1 (PD-1), an antigen co-receptor on cell surfaces, is one of the conspicuous immune checkpoints. Nivolumab, a monoclonal antibody therapeutic approved by the FDA, binds to PD-1 and efficiently blocks its pathways. In this study, an integrated approach was developed to map the epitope/paratope of PD-1/nivolumab. The approach includes hydrogen-deuterium exchange mass spectrometry (HDX-MS) followed by electron-transfer dissociation (ETD), chemical cross-linking, and molecular docking. HDX-ETD offers some binding-site characterization with amino acid resolution. Chemical cross-linking provides complementary information on one additional epitope (i.e., the BC-loop) and a potential paratope at the N-terminus of the heavy chain. Furthermore, cross-linking identifies another loop region (i.e., the C'D-loop) that undergoes a remote conformational change. The distance restraints derived from the cross-links enable building high-confidence models of PD-1/nivolumab, evaluated with respect to a resolved crystal structure. This integrated strategy is an opportunity to characterize comprehensively other antigen-antibody interactions, to enable the understanding of binding mechanisms, and to design future antibody therapeutics.
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Affiliation(s)
- Mengru Mira Zhang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Brett R Beno
- Molecular Structure & Design, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Ekaterina G Deyanova
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Jing Li
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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163
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Azcárate IG, Marín-García P, Abad P, Pérez-Benavente S, Paz-Artal E, Reche PA, Fobil JN, Rubio JM, Diez A, Puyet A, Bautista JM. Plasmodium falciparum immunodominant IgG epitopes in subclinical malaria. Sci Rep 2020; 10:9398. [PMID: 32523082 PMCID: PMC7287129 DOI: 10.1038/s41598-020-66384-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/18/2020] [Indexed: 01/30/2023] Open
Abstract
Incomplete non-sterile immunity to malaria is attained in endemic regions after recurrent infections by a large percentage of the adult population, who carry the malaria parasite asymptomatically. Although blood-stage Plasmodium falciparum rapidly elicits IgG responses, the target antigens of partially protective and non-protective IgG antibodies as well as the basis for the acquisition of these antibodies remain largely unknown. We performed IgG-immunomics to screen for P. falciparum antigens and to identify epitopes associated with exposure and clinical disease. Sera from malaria cases identified five prevalent antigens recognized by all analyzed patients' IgGs. Epitope mapping of them, using adult and children sera samples from an endemic malaria region in Ghana segregated into patients with positive or negative subclinical detection of P. falciparum, revealed binding specificity for two 20-mer immunodominant antigenic regions within the START-related lipid transfer protein and the protein disulfide isomerase PDI8. These 20-mer epitopes challenged with sera samples from children under 5 years old displayed specific IgG binding in those with detectable parasitemia, even at subclinical level. These results suggest that humoral response against START and PDI8 antigens may be triggered at submicroscopic parasitemia levels in children and may eventually be used to differentially diagnose subclinical malaria in children.
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Affiliation(s)
- Isabel G Azcárate
- Department of Biochemistry and Molecular Biology and Research Institute Hospital 12 de Octubre (Imas12), Universidad Complutense de Madrid, 28040, Madrid, Spain.,Isabel G. Azcárate, Faculty of Health Sciences, Rey Juan Carlos University, Alcorcón, 28922, Madrid, Spain
| | | | - Paloma Abad
- Department of Biochemistry and Molecular Biology and Research Institute Hospital 12 de Octubre (Imas12), Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Susana Pérez-Benavente
- Department of Biochemistry and Molecular Biology and Research Institute Hospital 12 de Octubre (Imas12), Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Estela Paz-Artal
- Immunodeficiency and Transplant Immunology Unit, Research Institute Hospital 12 de Octubre (Imas12), 28041, Madrid, Spain
| | - Pedro A Reche
- Faculty of Medicine, Department of Immunology, Ophthalmology and ORL, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Julius N Fobil
- Department of Biological, Environmental & Occupational Health Sciences, School of Public Health, College of Health Sciences, University of Ghana, P.O. Box LG 13, Legon, Ghana
| | - José M Rubio
- Malaria & Emerging Parasitic Diseases Laboratory, National Centre of Microbiology. Instituto de Salud Carlos III, 28220, Majadahonda, Spain
| | - Amalia Diez
- Department of Biochemistry and Molecular Biology and Research Institute Hospital 12 de Octubre (Imas12), Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Antonio Puyet
- Department of Biochemistry and Molecular Biology and Research Institute Hospital 12 de Octubre (Imas12), Universidad Complutense de Madrid, 28040, Madrid, Spain.
| | - José M Bautista
- Department of Biochemistry and Molecular Biology and Research Institute Hospital 12 de Octubre (Imas12), Universidad Complutense de Madrid, 28040, Madrid, Spain.
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164
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Mohsin AZ, Sukor R, Selamat J, Meor Hussin AS, Ismail IH, Jambari NN, Mustaffa-Kamal F. Generation of High Affinity Anti-Peptide Polyclonal Antibodies Recognizing Goat α s1-Casein. Molecules 2020; 25:E2622. [PMID: 32516919 PMCID: PMC7321099 DOI: 10.3390/molecules25112622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
The chemical, technological and allergy properties of goat's milk are significantly affected by the level of αs1-casein. Detection and quantification of αs1-casein requires high-specificity methods to overcome high-sequence similarity between this protein and others in the casein family. Unavailability of antibodies with high affinity and specificity towards goat αs1-casein hinders the development of immuno-based analytical methods such as enzyme-linked immunosorbent assay (ELISA) and biosensors. Here, we report the generation of polyclonal antibodies (or immunoglobulins, IgGs) raised towards goat αs1-casein N- (Nter) and C-terminal (Cter) peptide sequences. The Nter and Cter peptides of goat αs1-casein were immunized in rabbits for the generation of antisera, which were purified using protein G affinity chromatography. The binding affinity of the antisera and purified IgGs were tested and compared using indirect ELISA, where peptide-BSA conjugates and goat αs1-casein were used as the coating antigens. The Nter antiserum displayed higher titer than Cter antiserum, at 1/64,000 and 1/32,000 dilutions, respectively. The purification step further yielded 0.5 mg/mL of purified IgGs from 3 mL of antisera. The purified Nter IgG showed a significantly (p < 0.05) higher binding affinity towards peptide-BSA and goat αs1-casein, with lower Kd value at 5.063 × 10-3 μM compared to 9.046 × 10-3 μM for the Cter IgG. A cross-reactivity test showed that there was no binding in neither Nter nor Cter IgGs towards protein extracts from the milk of cow, buffalo, horse and camel. High-quality antibodies generated will allow further development of immuno-based analytical methods and future in vitro studies to be conducted on goat αs1-casein.
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Affiliation(s)
- Aliah Zannierah Mohsin
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
| | - Rashidah Sukor
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Jinap Selamat
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | | | | | - Nuzul Noorahya Jambari
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia; (A.Z.M.); (J.S.); (N.N.J.)
- Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
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165
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Damen LAA, van de Westerlo EMA, Versteeg EMM, van Wessel T, Daamen WF, van Kuppevelt TH. Construction and evaluation of an antibody phage display library targeting heparan sulfate. Glycoconj J 2020; 37:445-455. [PMID: 32468289 PMCID: PMC7329785 DOI: 10.1007/s10719-020-09925-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/30/2020] [Accepted: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Heparan sulfate (HS) is a linear polysaccharide with high structural diversity. Different HS epitopes have been detected and localized using single chain variable fragment (scFv) antibodies from a ‘single pot’ phage display library containing a randomized complementarity determining region of the heavy chain (CDR3). In this study, we created a new library containing anti-HS scFvs that all harbor a dp-38 heavy chain segment where the CDR3 region was engineered to contain the XBBXBX heparin binding consensus site (X = any amino acid, B = R, K or H). The library contained ~1.73 × 106 unique antibodies and was biopanned against HS from several sources. The selected antibodies were sequenced and chemically/immunohistologically characterized. A number of 67 anti-HS scFv antibodies were selected, of which 31 contained a XBBXBX CDR3 sequence. There was a clear preference for glycine at the first and proline at the fourth position of the CDR3. The sequence GZZP(R/K)X (Z = R, K or H, but may also contain N, S, or Q) was unusually overrepresented. Selected antibodies reacted with HS/heparin, but not with other glycosaminoglycans. Antibodies reacted differentially with respect to N-, 2-O, or 6-O-desulfated heparin preparations, and showed distinct topologies of HS epitopes in rat kidney sections. The library may be instrumental in the selection of a large pool of HS epitope-specific antibodies, and - since all antibodies differ only in their 6 amino acid CDR region - may be a tool for a rational design of antibodies recognizing specific HS sulfation patterns.
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Affiliation(s)
- Lars A A Damen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Els M A van de Westerlo
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Elly M M Versteeg
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Thierry van Wessel
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Willeke F Daamen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.
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166
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Marks C, Deane CM. How repertoire data are changing antibody science. J Biol Chem 2020; 295:9823-9837. [PMID: 32409582 DOI: 10.1074/jbc.rev120.010181] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Antibodies are vital proteins of the immune system that recognize potentially harmful molecules and initiate their removal. Mammals can efficiently create vast numbers of antibodies with different sequences capable of binding to any antigen with high affinity and specificity. Because they can be developed to bind to many disease agents, antibodies can be used as therapeutics. In an organism, after antigen exposure, antibodies specific to that antigen are enriched through clonal selection, expansion, and somatic hypermutation. The antibodies present in an organism therefore report on its immune status, describe its innate ability to deal with harmful substances, and reveal how it has previously responded. Next-generation sequencing technologies are being increasingly used to query the antibody, or B-cell receptor (BCR), sequence repertoire, and the amount of BCR data in public repositories is growing. The Observed Antibody Space database, for example, currently contains over a billion sequences from 68 different studies. Repertoires are available that represent both the naive state (i.e. antigen-inexperienced) and that after immunization. This wealth of data has created opportunities to learn more about our immune system. In this review, we discuss the many ways in which BCR repertoire data have been or could be exploited. We highlight its utility for providing insights into how the naive immune repertoire is generated and how it responds to antigens. We also consider how structural information can be used to enhance these data and may lead to more accurate depictions of the sequence space and to applications in the discovery of new therapeutics.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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167
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Rizzardi K, Åkerlund T, Norén T, Matussek A. Impact of ribotype on Clostridioides difficile diagnostics. Eur J Clin Microbiol Infect Dis 2020; 39:847-853. [PMID: 31884555 PMCID: PMC7182543 DOI: 10.1007/s10096-019-03772-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022]
Abstract
This study investigates the performance of diagnostic methods for detection of Clostridioides difficile infection in Sweden, including impact of PCR ribotype on diagnostic performance. Between 2011 and 2016, a total of 17,878 stool samples from 26 laboratories were tested by either well-type enzyme immunoassays (EIAs), membrane bound EIAs, cell cytotoxicity neutralization assay (CTA), or nucleic acid amplification tests (NAATs) and subsequently cultured for C. difficile. Roughly half of the samples (9454/17878) were subjected to diagnostic testing both on the fecal sample and on the 1323 isolated C. difficile strains. All C. difficile isolates were typed by PCR ribotyping, and the isolates were classified as toxigenic or non-toxigenic based on the empirical knowledge of the association between toxin-positivity and ribotype. The overall sensitivity, specificity, and positive and negative predictive values were highest for NAATs and membrane EIAs. Ribotype-specific sensitivity varied greatly between methods and ribotypes. All methods had 100% sensitivity against ribotype 027 and 013. For other types, the sensitivity ranged from 33 to 85% in fecal samples and from 78 to 100% on isolates. For the most prevalent ribotypes (014, 020, and 001), the sensitivity varied between 38 and 100% in the fecal samples, with the lowest sensitivity observed for well-type EIAs and CTA. The large variation in diagnostic sensitivity implies that type distribution significantly affects the outcome when evaluating diagnostic performance. Furthermore, performing comparative studies of diagnostic tests in settings with high prevalence of ribotype 027 will overestimate the general performance of diagnostic tests.
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Affiliation(s)
- Kristina Rizzardi
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden.
| | - Thomas Åkerlund
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Torbjörn Norén
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Andreas Matussek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska University Hospital, Huddinge, Sweden
- Karolinska University Laboratory, Solna, Stockholm, Sweden
- Department of Laboratory Medicine, Jönköping, Jönköping County, Sweden
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168
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Makabe K. Molecular basis of flexible peptide recognition by an antibody. J Biochem 2020; 167:343-345. [PMID: 32027351 DOI: 10.1093/jb/mvaa017] [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: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/12/2022] Open
Abstract
Antibodies can recognize various types of antigens with high specificity and affinity and peptide is one of their major targets. Understanding an antibody's molecular recognition mechanism for peptide is important for developing clones with a higher specificity and affinity. Here, the author reviews recent progresses in flexible peptide recognition by an antibody using several biophysical techniques, including X-ray crystallography, molecular dynamics simulations and calorimetric measurements. A set of two reports highlight the importance of intramolecular hydrogen bonds that form in an unbound flexible state. Such intramolecular hydrogen bonds restrict the fluctuation of the peptide and reduce the conformational entropy, resulting in the destabilization of the unbound state and increasing the binding affinity by increasing the free energy change. These detailed analyses will aid in the antibody design in the future.
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Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
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169
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Yoo DK, Lee SR, Jung Y, Han H, Lee HK, Han J, Kim S, Chae J, Ryu T, Chung J. Machine Learning-Guided Prediction of Antigen-Reactive In Silico Clonotypes Based on Changes in Clonal Abundance through Bio-Panning. Biomolecules 2020; 10:E421. [PMID: 32182714 PMCID: PMC7175295 DOI: 10.3390/biom10030421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
c-Met is a promising target in cancer therapy for its intrinsic oncogenic properties. However, there are currently no c-Met-specific inhibitors available in the clinic. Antibodies blocking the interaction with its only known ligand, hepatocyte growth factor, and/or inducing receptor internalization have been clinically tested. To explore other therapeutic antibody mechanisms like Fc-mediated effector function, bispecific T cell engagement, and chimeric antigen T cell receptors, a diverse panel of antibodies is essential. We prepared a chicken immune scFv library, performed four rounds of bio-panning, obtained 641 clones using a high-throughput clonal retrieval system (TrueRepertoireTM, TR), and found 149 antigen-reactive scFv clones. We also prepared phagemid DNA before the start of bio-panning (round 0) and, after each round of bio-panning (round 1-4), performed next-generation sequencing of these five sets of phagemid DNA, and identified 860,207 HCDR3 clonotypes and 443,292 LCDR3 clonotypes along with their clonal abundance data. We then established a TR data set consisting of antigen reactivity for scFv clones found in TR analysis and the clonal abundance of their HCDR3 and LCDR3 clonotypes in five sets of phagemid DNA. Using the TR data set, a random forest machine learning algorithm was trained to predict the binding properties of in silico HCDR3 and LCDR3 clonotypes. Subsequently, we synthesized 40 HCDR3 and 40 LCDR3 clonotypes predicted to be antigen reactive (AR) and constructed a phage-displayed scFv library called the AR library. In parallel, we also prepared an antigen non-reactive (NR) library using 10 HCDR3 and 10 LCDR3 clonotypes predicted to be NR. After a single round of bio-panning, we screened 96 randomly-selected phage clones from the AR library and found out 14 AR scFv clones consisting of 5 HCDR3 and 11 LCDR3 AR clonotypes. We also screened 96 randomly-selected phage clones from the NR library, but did not identify any AR clones. In summary, machine learning algorithms can provide a method for identifying AR antibodies, which allows for the characterization of diverse antibody libraries inaccessible by traditional methods.
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Affiliation(s)
- Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Seung Ryul Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yushin Jung
- Celemics, Inc., 131 Gasandigital 1-ro, Geumcheon-gu, Seoul 08506, Korea
| | - Haejun Han
- Celemics, Inc., 131 Gasandigital 1-ro, Geumcheon-gu, Seoul 08506, Korea
| | - Hwa Kyoung Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jerome Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Soohyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jisu Chae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Taehoon Ryu
- Celemics, Inc., 131 Gasandigital 1-ro, Geumcheon-gu, Seoul 08506, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
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170
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Zelazowska MA, Dong Q, Plummer JB, Zhong Y, Liu B, Krug LT, McBride KM. Gammaherpesvirus-infected germinal center cells express a distinct immunoglobulin repertoire. Life Sci Alliance 2020; 3:3/3/e201900526. [PMID: 32029571 PMCID: PMC7012147 DOI: 10.26508/lsa.201900526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
Germinal center B cells infected with gammaherpesvirus display altered repertoire with biased usage of lambda light chain and skewed utilization of IGHV genes. The gammaherpesviruses (γHVs), human Kaposi sarcoma-associated herpesvirus (KSHV), EBV, and murine γHV68 are prevalent infections associated with lymphocyte pathologies. After primary infection, EBV and γHV68 undergo latent expansion in germinal center (GC) B cells and persists in memory cells. The GC reaction evolves and selects antigen-specific B cells for memory development but whether γHV passively transients or manipulates this process in vivo is unknown. Using the γHV68 infection model, we analyzed the Ig repertoire of infected and uninfected GC cells from individual mice. We found that infected cells displayed the hallmarks of affinity maturation, hypermutation, and isotype switching but underwent clonal expansion. Strikingly, infected cells displayed distinct repertoire, not found in uninfected cells, with recurrent utilization of certain Ig heavy V segments including Ighv10-1. In a manner observed with KSHV, γHV68 infected cells also displayed lambda light chain bias. Thus, γHV68 subverts GC selection to expand in a specific B cell subset during the process that develops long-lived immunologic memory.
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Affiliation(s)
- Monika A Zelazowska
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Qiwen Dong
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA.,Graduate Program of Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Joshua B Plummer
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Yi Zhong
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Laurie T Krug
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Kevin M McBride
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
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171
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Mendoza MN, Jian M, King MT, Brooks CL. Role of a noncanonical disulfide bond in the stability, affinity, and flexibility of a VHH specific for the Listeria virulence factor InlB. Protein Sci 2020; 29:1004-1017. [PMID: 31981247 DOI: 10.1002/pro.3831] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/29/2022]
Abstract
A distinguishing feature of camel (Camelus dromedarius) VHH domains are noncanonical disulfide bonds between CDR1 and CDR3. The disulfide bond may provide an evolutionary advantage, as one of the cysteines in the bond is germline encoded. It has been hypothesized that this additional disulfide bond may play a role in binding affinity by reducing the entropic penalty associated with immobilization of a long CDR3 loop upon antigen binding. To examine the role of a noncanonical disulfide bond on antigen binding and the biophysical properties of a VHH domain, we have used the VHH R303, which binds the Listeria virulence factor InlB as a model. Using site directed mutagenesis, we produced a double mutant of R303 (C33A/C102A) to remove the extra disulfide bond of the VHH R303. Antigen binding was not affected by loss of the disulfide bond, however the mutant VHH displayed reduced thermal stability (Tm = 12°C lower than wild-type), and a loss of the ability to fold reversibly due to heat induced aggregation. X-ray structures of the mutant alone and in complex with InlB showed no major changes in the structure. B-factor analysis of the structures suggested that the loss of the disulfide bond elicited no major change on the flexibility of the CDR loops, and revealed no evidence of loop immobilization upon antigen binding. These results suggest that the noncanonical disulfide bond found in camel VHH may have evolved to stabilize the biophysical properties of the domain, rather than playing a significant role in antigen binding.
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Affiliation(s)
- Matthew N Mendoza
- Department of Chemistry, California State University Fresno, Fresno, California
| | - Mike Jian
- Department of Chemistry, California State University Fresno, Fresno, California
| | - Moeko T King
- Department of Chemistry, California State University Fresno, Fresno, California
| | - Cory L Brooks
- Department of Chemistry, California State University Fresno, Fresno, California
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172
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Kadonosono T, Kizaka-Kondoh S. [Semi-rational Design of Target-binding Small Proteins for Cancer Treatment]. YAKUGAKU ZASSHI 2020; 140:159-162. [PMID: 32009038 DOI: 10.1248/yakushi.19-00187-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Small proteins that have a high affinity for cancer cell surface markers can be promising cheap alternatives to antibodies (antibody mimetics). Various types of antibody mimetics have thus been extensively developed. We recently found that a target-binding peptide binds to its target molecule more strongly when it is structurally constrained. To apply this finding to the development of chemically synthesizable small antibody mimetics, we have established an efficient method of creating such proteins, named fluctuation-regulated affinity proteins (FLAPs). To identify desirable scaffolds, first, 13 human proteins (46-104 aa) were selected from the Protein Data Bank. Then, thirteen graft acceptor (GA) sites that efficiently immobilize the grafted peptide structure were identified from six small protein scaffolds using molecular dynamics simulation. To assess the designed antibody mimetics in vitro, human epidermal growth factor receptor 2 (HER2)-binding peptides were selected from the anti-HER2 antibody drugs trastuzumab and pertuzumab by calculating the binding energy, and these were then grafted into the GA sites of scaffolds to create 65 FLAP candidates. The FLAP candidates were expressed in bacteria as fusion proteins with Renilla luciferase (Rluc), and their relative binding affinity to HER2 was easily determined by measuring the Rluc bioluminescence intensity without protein purification. Finally, four out of the 65 showed specific binding to HER2 with a dissociation constant (KD) of 24-65 nM, and these were used for the detection of HER2-expressing cancer cells. Our design strategy will promote the development of antibody mimetics for the effective treatment of cancers and other diseases.
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173
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Marques AC, Costa PJ, Velho S, Amaral MH. Functionalizing nanoparticles with cancer-targeting antibodies: A comparison of strategies. J Control Release 2020; 320:180-200. [PMID: 31978444 DOI: 10.1016/j.jconrel.2020.01.035] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/17/2020] [Accepted: 01/18/2020] [Indexed: 01/07/2023]
Abstract
Standard cancer therapies sometimes fail to deliver chemotherapeutic drugs to tumor cells in a safe and effective manner. Nanotechnology takes the lead in providing new therapeutic options for cancer due to major potential for selective targeting and controlled drug release. Antibodies and antibody fragments are attracting much attention as a source of targeting ligands to bind specific receptors that are overexpressed on cancer cells. Therefore, researchers are devoting time and effort to develop targeting strategies based on nanoparticles functionalized with antibodies, which hold great promise to enhance therapeutic efficacy and circumvent severe side effects. Several methods have been described to immobilize antibodies on the surface of nanoparticles. However, selecting the most appropriate for each application is challenging but also imperative to preserve antigen binding ability and yield stable antibody-conjugated nanoparticles. From this perspective, we aim to provide considerable knowledge on the most widely used methods of functionalization that can be helpful for decision-making and design of conjugation protocols as well. This review summarizes adsorption, covalent conjugation (carbodiimide, maleimide and "click" chemistries) and biotin-avidin interaction, while discussing the advantages, limitations and relevant therapeutic approaches currently under investigation.
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Affiliation(s)
- A C Marques
- UCIBIO, REQUIMTE, MEDTECH, Laboratory of Pharmaceutical Technology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto (FFUP), R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - P J Costa
- UCIBIO, REQUIMTE, MEDTECH, Laboratory of Pharmaceutical Technology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto (FFUP), R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - S Velho
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, R. Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
| | - M H Amaral
- UCIBIO, REQUIMTE, MEDTECH, Laboratory of Pharmaceutical Technology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto (FFUP), R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
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174
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Shine PV, Shankar KM, Abhiman B, Sudheer NS, Patil R. Epitope mapping of the White Spot Syndrome Virus (WSSV) VP28 monoclonal antibody through combined in silico and in vitro analysis reveals the potential antibody binding site. Mol Cell Probes 2020; 50:101508. [PMID: 31935436 DOI: 10.1016/j.mcp.2020.101508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/23/2019] [Accepted: 01/10/2020] [Indexed: 01/18/2023]
Abstract
White Spot Syndrome Virus (WSSV) infecting shrimp is an enveloped double-stranded DNA virus. The WSSV is a member of the genus Whispovirus. The envelope protein VP28 is the most investigated protein of WSSV. In the present study, the epitope mapping of the monoclonal antibody (MAb) C-33 was carried out. Based on the epitope mapping results, an antigen-antibody interaction model was derived. Peptide scanning and confirmation of epitopes of MAb C-33 were carried out using the sequence data. The MAb was reactive to the epitope of both recombinant VP28 and the whole virus. The results of the study indicated the presence of an epitope region. The epitope region is found positioned within two peptides, covering 13 amino acids. Framework and CDR (complementarity determining regions) of heavy and light chain (VH & VL) sequences showed identity to germline immunoglobulin sequences. The Web Antibody Modelling (WAM) selected for further evaluation based on a comparative analysis of WAM and Rosetta server-generated models of the Fv region. The docking study using WAM generated model revealed that the residues from LEU98 to GLY105 are active in antibody binding. The findings of this study could form a structural basis for further research in VP28 based diagnostics and therapeutics or vaccine discovery.
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Affiliation(s)
- P V Shine
- Aquatic Animal Health Laboratory, Department of Aquaculture, College of Fisheries, Mangalore, India
| | - K M Shankar
- Aquatic Animal Health Laboratory, Department of Aquaculture, College of Fisheries, Mangalore, India.
| | - B Abhiman
- Aquatic Animal Health Laboratory, Department of Aquaculture, College of Fisheries, Mangalore, India
| | - N S Sudheer
- Central Institute of Brackishwater Aquaculture, Chennai, India
| | - R Patil
- Aquatic Animal Health Laboratory, Department of Aquaculture, College of Fisheries, Mangalore, India
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175
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020. [PMID: 32983137 DOI: 10.3389/fimmu.2020.01986/bibtex] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage-derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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176
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Papageorgiou L, Maroulis D, Chrousos GP, Eliopoulos E, Vlachakis D. Antibody Clustering Using a Machine Learning Pipeline that Fuses Genetic, Structural, and Physicochemical Properties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1194:41-58. [PMID: 32468522 DOI: 10.1007/978-3-030-32622-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibody V domain clustering is of paramount importance to a repertoire of immunology-related areas. Although several approaches have been proposed for antibody clustering, still no consensus has been reached. Numerous attempts use information from genes, protein sequences, 3D structures, and 3D surfaces in an effort to elucidate unknown action mechanisms directly related to their function and to either link them directly to diseases or drive the discovery of new medicines, such as antibody drug conjugates (ADC). Herein, we describe a new V domain antibody clustering method based on the comparison of the interaction sites between each antibody and its antigen. A more specific clustering analysis of the antibody's V domain was provided using deep learning and data mining techniques. The multidimensional information was extracted from the structural resolved antibodies when they were captured to interact with other proteins. The available 3D structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how antibody V domains recognize antigens as well as about which amino acids are involved in the recognition. As such, the antibody surface holds information about antigens' folding that reside with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, we propose a new simple philosophy to transform the conserved framework (fragment regions, complementarity-determining regions) of antibody V domain in a binary form using structural features of antibody-antigen interactions, toward identifying new antibody signatures in V domain binding activity. Finally, an advanced three-level hybrid classification scheme has been set for clustering antibodies in subgroups, which can combine the information from the protein sequences, the three-dimensional structures, and specific "key patterns" of recognized interactions. The clusters provide multilevel information about antibodies and antibody-antigen complexes.
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Affiliation(s)
- Louis Papageorgiou
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece.,Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitris Maroulis
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Chrousos
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Elias Eliopoulos
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece. .,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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177
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Abstract
In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an integral role in the armamentarium of immune defense against various pathogens. After an antigenic challenge, antibodies are secreted by differentiated B cells called plasma cells. Antibodies have two predominant roles that involve specific binding to antigens to launch an immune response, along with activation of other components of the immune system to fight pathogens. The ability of immunoglobulins to fight against innumerable and diverse pathogens lies in their intrinsic ability to discriminate between different antigens. Due to this specificity and high affinity for their antigens, antibodies have been a valuable and indispensable tool in research, diagnostics and therapy. Although seemingly a simple maneuver, the association between an antibody and its antigen, to make an antigen-antibody complex, is comprised of myriads of non-covalent interactions. Amino acid residues on the antigen binding site, the epitope, and on the antibody binding site, the paratope, intimately contribute to the energetics needed for the antigen-antibody complex stability. Structural biology methods to study antigen-antibody complexes are extremely valuable tools to visualize antigen-antibody interactions in detail; this helps to elucidate the basis of molecular recognition between an antibody and its specific antigen. The main scope of this chapter is to discuss the structure and function of different classes of antibodies and the various aspects of antigen-antibody interactions including antigen-antibody interfaces-with a special focus on paratopes, complementarity determining regions (CDRs) and other non-CDR residues important for antigen binding and recognition. Herein, we also discuss methods used to study antigen-antibody complexes, antigen recognition by antibodies, types of antigens in complexes, and how antigen-antibody complexes play a role in modern day medicine and human health. Understanding the molecular basis of antigen binding and recognition by antibodies helps to facilitate the production of better and more potent antibodies for immunotherapy, vaccines and various other applications.
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Affiliation(s)
- A Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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178
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Karadag M, Arslan M, Kaleli NE, Kalyoncu S. Physicochemical determinants of antibody-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:85-114. [PMID: 32312427 DOI: 10.1016/bs.apcsb.2019.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antibodies are specialized proteins generated by immune system for high specificity and affinity binding to target antigens. Because of their essential roles in immune system, antibodies have been successfully developed and engineered as biopharmaceuticals for treatment of various diseases. Analysis of antibody-protein interactions is always required to get detailed information on effectivity of such antibody-based therapeutics. Although physicochemical rules cannot be generalized for every antibody-protein interaction, there are some features which should be taken into account during antibody development and engineering efforts. In this chapter, physicochemical analysis of antibody paratope-protein epitope interactions will be discussed to highlight important characteristics. First, paratope and non-paratope regions of antibodies will be described and important roles of these regions on binding and biophysical features of antibodies will be discussed. Then, general features of epitope regions of protein antigens will be introduced along with several computational/experimental tools to identify them. Lastly, a rising star of antibody biopharmaceuticals, nanobodies, will be described to show importance of next-generation antibody fragment based biopharmaceuticals in drug development.
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Affiliation(s)
- Murat Karadag
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
| | - Nazli Eda Kaleli
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
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179
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Popa SC, Shin JA. The Intrinsically Disordered Loop in the USF1 bHLHZ Domain Modulates Its DNA-Binding Sequence Specificity in Hereditary Asthma. J Phys Chem B 2019; 123:9862-9871. [PMID: 31670516 DOI: 10.1021/acs.jpcb.9b06719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
USF1, a basic region/helix-loop-helix/leucine zipper (bHLHZ) transcription factor, binds to the E-box in the PAI-1 (plasminogen activator inhibitor) promoter. Two alleles containing the E-box control PAI-1 transcription; these alleles are termed "4G" and "5G" based on the G tract flanking E-box. USF1-governed transcription of PAI-1 is elevated in heritable asthma sufferers: the 4G/4G genotype has the highest plasma levels of PAI-1. While USF1 uses its basic region to bind E-box, we found that it uses its 12 amino-acid loop to recognize the flanking sequence and discern the single-nucleotide difference between the alleles. We used the bacterial one-hybrid and electrophoretic mobility shift assays to assess protein-DNA recognition, and circular dichroism to examine protein secondary structure. We mutated Ser233 and Thr234 in the USF1 bHLHZ loop to Ala to generate S233A and T234A. Interestingly, USF1 bHLHZ, S233A, and T234A prefer the 5G sequence (USF1 bHLHZ Kd values 4.1 ± 0.3 nM and 7.0 ± 0.4 nM for 5G and 4G, respectively), whereas studies in stimulated human mast cells showed a preference for 4G. We replaced the 8 amino-acid loop of transcription factor Max bHLHZ with the 12 amino-acid USF1 loop: this mutant now distinguishes the 4G/5G polymorphism-while Max bHLHZ does not-confirming that USF1 differentiation of the 4G/5G is driven by the loop.
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Affiliation(s)
- Serban C Popa
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
| | - Jumi A Shin
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
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180
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Ambrosetti F, Jiménez-García B, Roel-Touris J, Bonvin AMJJ. Modeling Antibody-Antigen Complexes by Information-Driven Docking. Structure 2019; 28:119-129.e2. [PMID: 31727476 DOI: 10.1016/j.str.2019.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/03/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
Antibodies are Y-shaped proteins essential for immune response. Their capability to recognize antigens with high specificity makes them excellent therapeutic targets. Understanding the structural basis of antibody-antigen interactions is therefore crucial for improving our ability to design efficient biological drugs. Computational approaches such as molecular docking are providing a valuable and fast alternative to experimental structural characterization for these complexes. We investigate here how information about complementarity-determining regions and binding epitopes can be used to drive the modeling process, and present a comparative study of four different docking software suites (ClusPro, LightDock, ZDOCK, and HADDOCK) providing specific options for antibody-antigen modeling. Their performance on a dataset of 16 complexes is reported. HADDOCK, which includes information to drive the docking, is shown to perform best in terms of both success rate and quality of the generated models in both the presence and absence of information about the epitope on the antigen.
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Affiliation(s)
- Francesco Ambrosetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00184 Rome, Italy; Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Brian Jiménez-García
- Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jorge Roel-Touris
- Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Faculty of Science - Chemistry, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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181
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Wong WK, Leem J, Deane CM. Comparative Analysis of the CDR Loops of Antigen Receptors. Front Immunol 2019; 10:2454. [PMID: 31681328 PMCID: PMC6803477 DOI: 10.3389/fimmu.2019.02454] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022] Open
Abstract
The adaptive immune system uses two main types of antigen receptors: T-cell receptors (TCRs) and antibodies. While both proteins share a globally similar β-sandwich architecture, TCRs are specialized to recognize peptide antigens in the binding groove of the major histocompatibility complex, while antibodies can bind an almost infinite range of molecules. For both proteins, the main determinants of target recognition are the complementarity-determining region (CDR) loops. Five of the six CDRs adopt a limited number of backbone conformations, known as the "canonical classes"; the remaining CDR (β3in TCRs and H3 in antibodies) is more structurally diverse. In this paper, we first update the definition of canonical forms in TCRs, build an auto-updating sequence-based prediction tool (available at http://opig.stats.ox.ac.uk/resources) and demonstrate its application on large scale sequencing studies. Given the global similarity of TCRs and antibodies, we then examine the structural similarity of their CDRs. We find that TCR and antibody CDRs tend to have different length distributions, and where they have similar lengths, they mostly occupy distinct structural spaces. In the rare cases where we found structural similarity, the underlying sequence patterns for the TCR and antibody version are different. Finally, where multiple structures have been solved for the same CDR sequence, the structural variability in TCR loops is higher than that in antibodies, suggesting TCR CDRs are more flexible. These structural differences between TCR and antibody CDRs may be important to their different biological functions.
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182
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Mahajan S, Yan Z, Jespersen MC, Jensen KK, Marcatili P, Nielsen M, Sette A, Peters B. Benchmark datasets of immune receptor-epitope structural complexes. BMC Bioinformatics 2019; 20:490. [PMID: 31601176 PMCID: PMC6785892 DOI: 10.1186/s12859-019-3109-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/20/2019] [Indexed: 02/05/2023] Open
Abstract
Background The development of accurate epitope prediction tools is important in facilitating disease diagnostics, treatment and vaccine development. The advent of new approaches making use of antibody and TCR sequence information to predict receptor-specific epitopes have the potential to transform the epitope prediction field. Development and validation of these new generation of epitope prediction methods would benefit from regularly updated high-quality receptor-antigen complex datasets. Results To address the need for high-quality datasets to benchmark performance of these new generation of receptor-specific epitope prediction tools, a webserver called SCEptRe (Structural Complexes of Epitope-Receptor) was created. SCEptRe extracts weekly updated 3D complexes of antibody-antigen, TCR-pMHC and MHC-ligand from the Immune Epitope Database and clusters them based on antigen, receptor and epitope features to generate benchmark datasets. SCEptRe also provides annotated information such as CDR sequences and VDJ genes on the receptors. Users can generate custom datasets based by selecting thresholds for structural quality and clustering parameters (e.g. resolution, R-free factor, antigen or epitope sequence identity) based on their need. Conclusions SCEptRe provides weekly updated, user-customized comprehensive benchmark datasets of immune receptor-epitope structural complexes. These datasets can be used to develop and benchmark performance of receptor-specific epitope prediction tools in the future. SCEptRe is freely accessible at http://tools.iedb.org/sceptre.
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Affiliation(s)
- Swapnil Mahajan
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
| | - Zhen Yan
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | | | | | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Department of Medicine, University of California, San Diego, CA, 92093, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Department of Medicine, University of California, San Diego, CA, 92093, USA
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183
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Designing and Modeling of Multi-epitope Proteins for Diagnosis of Toxocara canis Infection. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09940-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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184
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Krawczyk K, Raybould MIJ, Kovaltsuk A, Deane CM. Looking for therapeutic antibodies in next-generation sequencing repositories. MAbs 2019; 11:1197-1205. [PMID: 31216939 PMCID: PMC6748601 DOI: 10.1080/19420862.2019.1633884] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 12/20/2022] Open
Abstract
Recently it has become possible to query the great diversity of natural antibody repertoires using next-generation sequencing (NGS). These methods are capable of producing millions of sequences in a single experiment. Here we compare clinical-stage therapeutic antibodies to the ~1b sequences from 60 independent sequencing studies in the Observed Antibody Space database, which includes antibody sequences from NGS analysis of immunoglobulin gene repertoires. Of 242 post-Phase 1 antibodies, we found 16 with sequence identity matches of 95% or better for both heavy and light chains. There are also 54 perfect matches to therapeutic CDR-H3 regions in the NGS outputs, suggesting a nontrivial amount of convergence between naturally observed sequences and those developed artificially. This has potential implications for both the legal protection of commercial antibodies and the discovery of antibody therapeutics.
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185
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Ahamadi-Fesharaki R, Fateh A, Vaziri F, Solgi G, Siadat SD, Mahboudi F, Rahimi-Jamnani F. Single-Chain Variable Fragment-Based Bispecific Antibodies: Hitting Two Targets with One Sophisticated Arrow. Mol Ther Oncolytics 2019; 14:38-56. [PMID: 31011631 PMCID: PMC6463744 DOI: 10.1016/j.omto.2019.02.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite the success of monoclonal antibodies (mAbs) to treat some disorders, the monospecific molecular entity of mAbs as well as the presence of multiple factors and pathways involved in the pathogenesis of disorders, such as various malignancies, infectious diseases, and autoimmune disorders, and resistance to therapy have restricted the therapeutic efficacy of mAbs in clinical use. Bispecific antibodies (bsAbs), by concurrently recognizing two targets, can partly circumvent these problems. Serial killing of tumor cells by bsAb-redirected T cells, simultaneous blocking of two antigens involved in the HIV-1 infection, and concurrent targeting of the activating and inhibitory receptors on B cells to modulate autoimmunity are part of the capabilities of bsAbs. After designing and developing a large number of bsAbs for years, catumaxomab, a full-length bsAb targeting EpCAM and CD3, was approved in 2009 to treat EpCAM-positive carcinomas besides blinatumomab, a bispecific T cell engager antibody targeting CD19 and CD3, which was approved in 2014 to treat relapsed or refractory acute lymphoblastic leukemia. Furthermore, approximately 60 bsAbs are under investigation in clinical trials. The current review aims at portraying different formats of the single-chain variable fragment (scFv)-based bsAbs and shedding light on the scFv-based bsAbs in preclinical development, different phases of clinical trials, and the market.
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Affiliation(s)
- Raoufeh Ahamadi-Fesharaki
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ghasem Solgi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Davar Siadat
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rahimi-Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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186
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Bobkov V, Arimont M, Zarca A, De Groof TWM, van der Woning B, de Haard H, Smit MJ. Antibodies Targeting Chemokine Receptors CXCR4 and ACKR3. Mol Pharmacol 2019; 96:753-764. [PMID: 31481460 DOI: 10.1124/mol.119.116954] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/03/2019] [Indexed: 12/19/2022] Open
Abstract
Dysregulation of the chemokine system is implicated in a number of autoimmune and inflammatory diseases, as well as cancer. Modulation of chemokine receptor function is a very promising approach for therapeutic intervention. Despite interest from academic groups and pharmaceutical companies, there are currently few approved medicines targeting chemokine receptors. Monoclonal antibodies (mAbs) and antibody-based molecules have been successfully applied in the clinical therapy of cancer and represent a potential new class of therapeutics targeting chemokine receptors belonging to the class of G protein-coupled receptors (GPCRs). Besides conventional mAbs, single-domain antibodies and antibody scaffolds are also gaining attention as promising therapeutics. In this review, we provide an extensive overview of mAbs, single-domain antibodies, and other antibody fragments targeting CXCR4 and ACKR3, formerly referred to as CXCR7. We discuss their unique properties and advantages over small-molecule compounds, and also refer to the molecules in preclinical and clinical development. We focus on single-domain antibodies and scaffolds and their utilization in GPCR research. Additionally, structural analysis of antibody binding to CXCR4 is discussed. SIGNIFICANCE STATEMENT: Modulating the function of GPCRs, and particularly chemokine receptors, draws high interest. A comprehensive review is provided for monoclonal antibodies, antibody fragments, and variants directed at CXCR4 and ACKR3. Their advantageous functional properties, versatile applications as research tools, and use in the clinic are discussed.
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Affiliation(s)
- Vladimir Bobkov
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
| | - Marta Arimont
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
| | - Aurélien Zarca
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
| | - Timo W M De Groof
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
| | - Bas van der Woning
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
| | - Hans de Haard
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
| | - Martine J Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (V.B., M.A., A.Z., T.W.M.D.G., M.J.S.); and argenx BVBA, Zwijnaarde, Belgium (V.B., B.W., H.H.)
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187
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Sun W, Yang Z, Lin H, Liu M, Zhao C, Hou X, Hu Z, Cui B. Improvement in affinity and thermostability of a fully human antibody against interleukin-17A by yeast-display technology and CDR grafting. Acta Pharm Sin B 2019; 9:960-972. [PMID: 31649846 PMCID: PMC6804450 DOI: 10.1016/j.apsb.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/24/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022] Open
Abstract
Monoclonal antibodies (mAbs) are widely used in many fields due to their high specificity and ability to recognize a broad range of antigens. IL-17A can induce a rapid inflammatory response both alone and synergistically with other proinflammatory cytokines. Accumulating evidence suggests that therapeutic intervention of IL-17A signaling offers an attractive treatment option for autoimmune diseases and cancer. Here, we present a combinatorial approach for optimizing the affinity and thermostability of a novel anti-hIL-17A antibody. From a large naïve phage-displayed library, we isolated the anti-IL-17A mAb 7H9 that can neutralize the effects of recombinant human IL-17A. However, the modest neutralization potency and poor thermostability limit its therapeutic applications. In vitro affinity optimization was then used to generate 8D3 by using yeast-displayed random mutagenesis libraries. This resulted in four key amino acid changes and provided an approximately 15-fold potency increase in a cell-based neutralization assay. Complementarity-determining regions (CDRs) of 8D3 were further grafted onto the stable framework of the huFv 4D5 to improve thermostability. The resulting hybrid antibody 9NT/S has superior stabilization and affinities beyond its original antibody. Human fibrosarcoma cell-based assays and in vivo analyses in mice indicated that the anti-IL-17A antibody 9NT/S efficiently inhibited the secretion of IL-17A-induced proinflammatory cytokines. Therefore, this lead anti-IL-17A mAb might be used as a potential best-in-class candidate for treating IL-17A related diseases.
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Key Words
- AIN457, secukinumab
- Antibody engineering
- Antibody maturation
- CDR grafting
- CDRs, complementarity-determining regions
- FACS, fluorescent-activated cell sorting
- HC, heavy chain
- HRP, horse radish peroxidase
- KD, dissociation constant
- Koff, the dissociation rate constant
- Kon, the association rate constant
- LC, light chain
- LY2439821, ixekizumab
- MACS, magnetic-activated cell sorting
- MFI, mean fluorescence intensity
- Monoclonal antibody
- Phage display
- VH, the variable regions of heavy chains
- VL, the variable regions of light chains
- YSD, yeast surface display
- Yeast surface display
- mAbs, monoclonal antibodies
- scFv, single-chain variable fragment
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Affiliation(s)
| | | | | | | | | | | | | | - Bing Cui
- Corresponding author. Tel./fax: +86 10 83165034.
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188
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Abstract
Antibodies are large proteins generated in vivo to bind specifically to a wide spectrum of targets ranging from biological to environmental molecules. They play a vital role in research, diagnostics, sensing, and therapeutic applications. Over the past few decades, advancements have been made to improve the performance of antibodies, specifically in the area of immunosensors. However, there has been an urgent need for alternative high-quality recognition probes that can be produced synthetically in bulk quantity to ensure better reproducibility and lower cost, as well as avoiding the need of using animals in the production process. Aptamers are synthetic nucleic acid single-stranded (ss) DNAs or RNAs that can bind with high affinity and specificity to their targets. They can be generated via in vitro section protocol, known as systematic evolution of ligands by exponential enrichment (SELEX). The advantages of aptamers promoted their successful incorporation in several signal transduction schemes, some of which reached the commercial market for point-of-care and in-field applications. This chapter describes the two types of affinity reagents: antibodies and aptamers, and their methods of production, advantages, and limitations. The focus will be directed at their incorporation in analytical transduction methods and how aptamer molecular size as well as unique conformational change upon target binding has triggered the evolution of new sensing methods.
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Affiliation(s)
- Omar A. Alsager
- National Center for Irradiation Technology, Nuclear Science Research Institute, King Abdulaziz City for Science and Technology P.O. Box 6086 Riyadh 11442 Saudi Arabia
| | - Shimaa Eissa
- Department of Chemistry, Alfaisal University Al Zahrawi Street, Al Maather, Al Takhassusi Rd Riyadh 11533 Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University Al Zahrawi Street, Al Maather, Al Takhassusi Rd Riyadh 11533 Saudi Arabia
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189
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Kim JW, Kim S, Jang YH, Lim KI, Lee WH. Attomolar detection of virus by liquid coplanar-gate graphene transistor on plastic. NANOTECHNOLOGY 2019; 30:345502. [PMID: 30865941 DOI: 10.1088/1361-6528/ab0f52] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The direct method of detecting a virus with extremely low concentration is recommended for the diagnosis of viral disease. In this study, coplanar-gate graphene field-effect transistors (GFETs) were built on flexible polyethylene terephthalate substrates for the attomolar detection of a virus. The GFETs exhibited a very low detection limit of 47.8 aM with relatively low source/drain voltage due to aqueous dielectric media which stabilizes viruses and antibodies for specific bonding. The antibody as a probe molecule was decorated on a graphene surface using 1-pyrenebutanoic acid succinimidyl ester that had previously been immobilized on a graphene surface. The Dirac point voltage shifted downward after dropping the virus solution, due to the electrostatic gating effect of graphene in the antigen (namely, virus)-antibody complex. The virus detection platform used in this study is expected to be beneficial for direct diagnosis in saline environments, since the performances of GFETs were not significantly affected by the presence of Na+ and Cl-. Furthermore, since our flexible and transparent virus sensors can be used in a wearable device, they provide a simple and fast method for diagnosing viruses.
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Affiliation(s)
- Jin Woo Kim
- Department of Organic and Nano System Engineering, Konkuk University, Seoul 05029, Republic of Korea
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190
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Schmelter C, Fomo KN, Perumal N, Manicam C, Bell K, Pfeiffer N, Grus FH. Synthetic Polyclonal-Derived CDR Peptides as an Innovative Strategy in Glaucoma Therapy. J Clin Med 2019; 8:jcm8081222. [PMID: 31443184 PMCID: PMC6723090 DOI: 10.3390/jcm8081222] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/30/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022] Open
Abstract
The pathogenesis of glaucoma is strongly associated with the occurrence of autoimmune-mediated loss of retinal ganglion cells (RGCs) and additionally, recent evidence shows that specific antibody-derived signature peptides are significantly differentially expressed in sera of primary-open angle glaucoma patients (POAG) compared to healthy controls. Synthetically antibody-derived peptides can modulate various effector functions of the immune system and act as antimicrobial or antiviral molecules. In an ex vivo adolescent glaucoma model, this study, for the first time, demonstrates that polyclonal-derived complementarity-determining regions (CDRs) can significantly increase the survival rate of RGCs (p = 0.013). We subsequently performed affinity capture experiments that verified the mitochondrial serine protease HTRA2 (gene name: HTRA2) as a high-affinity retinal epitope target of CDR1 sequence motif ASGYTFTNYGLSWVR. Quantitative proteomic analysis of the CDR-treated retinal explants revealed increased expression of various anti-apoptotic and anti-oxidative proteins (e.g., VDAC2 and TXN) compared to untreated controls (p < 0.05) as well as decreased expression levels of cellular stress response markers (e.g., HSPE1 and HSP90AA1). Mitochondrial dysfunction, the protein ubiquitination pathway and oxidative phosphorylation were annotated as the most significantly affected signaling pathways and possibly can be traced back to the CDR-induced inhibition or modulation of the master regulator HTRA2. These findings emphasize the great potential of synthetic polyclonal-derived CDR peptides as therapeutic agents in future glaucoma therapy and provide an excellent basis for affinity-based biomarker discovery purposes.
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Affiliation(s)
- Carsten Schmelter
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Kristian Nzogang Fomo
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Natarajan Perumal
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Caroline Manicam
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Katharina Bell
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Norbert Pfeiffer
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Franz H Grus
- Department of Experimental and Translational Ophthalmology, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany.
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191
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Wang Q, Chen Y, Park J, Liu X, Hu Y, Wang T, McFarland K, Betenbaugh MJ. Design and Production of Bispecific Antibodies. Antibodies (Basel) 2019; 8:antib8030043. [PMID: 31544849 PMCID: PMC6783844 DOI: 10.3390/antib8030043] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/18/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023] Open
Abstract
With the current biotherapeutic market dominated by antibody molecules, bispecific antibodies represent a key component of the next-generation of antibody therapy. Bispecific antibodies can target two different antigens at the same time, such as simultaneously binding tumor cell receptors and recruiting cytotoxic immune cells. Structural diversity has been fast-growing in the bispecific antibody field, creating a plethora of novel bispecific antibody scaffolds, which provide great functional variety. Two common formats of bispecific antibodies on the market are the single-chain variable fragment (scFv)-based (no Fc fragment) antibody and the full-length IgG-like asymmetric antibody. Unlike the conventional monoclonal antibodies, great production challenges with respect to the quantity, quality, and stability of bispecific antibodies have hampered their wider clinical application and acceptance. In this review, we focus on these two major bispecific types and describe recent advances in the design, production, and quality of these molecules, which will enable this important class of biologics to reach their therapeutic potential.
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Affiliation(s)
- Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yiqun Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jaeyoung Park
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xiao Liu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yifeng Hu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tiexin Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kevin McFarland
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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192
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Carvalho MB, Molina F, Felicori LF. Yvis: antibody high-density alignment visualization and analysis platform with an integrated database. Nucleic Acids Res 2019; 47:W490-W495. [PMID: 31106372 PMCID: PMC6602444 DOI: 10.1093/nar/gkz387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 11/18/2022] Open
Abstract
As antibodies are a very important tool for diagnosis, therapy, and experimental biology, a large number of antibody structures and sequences have become available in recent years. Therefore, tools that allow the analysis, comparison, and visualization of this large amount of antibody data are crucially needed. We developed the antibody high-density alignment visualization and analysis (Yvis) platform to provide an innovative, robust and high-density data visualization of antibody sequence alignments, called Collier de Diamants. The Yvis platform also provides an integrated structural database, which is updated weekly, and many different search and filter options. This platform can help to formulate hypotheses concerning the key residues in antibody structures or interactions to improve the understanding of antibody properties. The Yvis platform is available at http://bioinfo.icb.ufmg.br/yvis/.
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Affiliation(s)
- Milene B Carvalho
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Departamento de Ciência da Computação, Universidade Federal de São João del Rei, São João del Rei, Minas Gerais, 36301-360, Brazil
| | - Franck Molina
- Sys2diag, UMR9005 CNRS Alcediag, Montpellier 34184, France
| | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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193
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Yanaka S, Yogo R, Inoue R, Sugiyama M, Itoh SG, Okumura H, Miyanoiri Y, Yagi H, Satoh T, Yamaguchi T, Kato K. Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations. Antibodies (Basel) 2019; 8:antib8030039. [PMID: 31544845 PMCID: PMC6784063 DOI: 10.3390/antib8030039] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
The Fc portion of immunoglobulin G (IgG) is a horseshoe-shaped homodimer, which interacts with various effector proteins, including Fcγ receptors (FcγRs). These interactions are critically dependent on the pair of N-glycans packed between the two CH2 domains. Fucosylation of these N-glycans negatively affects human IgG1-FcγRIIIa interaction. The IgG1-Fc crystal structures mostly exhibit asymmetric quaternary conformations with divergent orientations of CH2 with respect to CH3. We aimed to provide dynamic views of IgG1-Fc by performing long-timescale molecular dynamics (MD) simulations, which were experimentally validated by small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our simulation results indicated that the dynamic conformational ensembles of Fc encompass most of the previously reported crystal structures determined in both free and complex forms, although the major Fc conformers in solution exhibited almost symmetric, stouter quaternary structures, unlike the crystal structures. Furthermore, the MD simulations suggested that the N-glycans restrict the motional freedom of CH2 and endow quaternary-structure plasticity through multiple intramolecular interaction networks. Moreover, the fucosylation of these N-glycans restricts the conformational freedom of the proximal tyrosine residue of functional importance, thereby precluding its interaction with FcγRIIIa. The dynamic views of Fc will provide opportunities to control the IgG interactions for developing therapeutic antibodies.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Satoru G Itoh
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Takumi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan.
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194
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Kim J, Yang J, Kim YB, Lee HJ, Kim S, Poo H. Development of a Specific CHIKV-E2 Monoclonal Antibody for Chikungunya Diagnosis. Virol Sin 2019; 34:563-571. [PMID: 31214999 DOI: 10.1007/s12250-019-00135-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/26/2019] [Indexed: 01/18/2023] Open
Abstract
Chikungunya fever is a vector-borne viral disease transmitted to humans by chikungunya virus (CHIKV)-infected mosquitoes. There have been many outbreaks of CHIKV infection worldwide, and the virus poses ongoing risks to global health. To prevent and control CHIKV infection, it is important to improve the current CHIKV diagnostic approaches to allow for the detection of low CHIKV concentrations and to correctly distinguish CHIKV infections from those due to other mosquito-transmitted viruses, including dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV). Here, we produced monoclonal antibodies (mAbs) against the CHIKV envelope 2 protein (CHIKV-E2) and compared their sensitivity and specificity with commercially available mAbs using enzyme-linked immunosorbent assays (ELISA). Two anti-CHIKV-E2 mAbs, 19-1 and 21-1, showed higher binding affinities to CHIKV-E2 protein than the commercial mAbs did. In particular, the 19-1 mAb had the strongest binding affinity to inactivated CHIKV. Moreover, the 19-1 mAb had very little cross-reactivity with other mosquito-borne viruses, such as ZIKV, JEV, and DENV. These results suggest that the newly produced anti-CHIKV-E2 mAb, 19-1, could be used for CHIKV diagnostic approaches.
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Affiliation(s)
- Jaemoo Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jihyun Yang
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Young Bong Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.,Department of Bio-Industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hee-Jung Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sehyun Kim
- Department of Bio-Industrial Technologies, Konkuk University, Seoul, 05029, Republic of Korea
| | - Haryoung Poo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Department of Biosystems and Bioengineering, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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195
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Recombinant Antibodies against Mycolactone. Toxins (Basel) 2019; 11:toxins11060346. [PMID: 31212961 PMCID: PMC6628451 DOI: 10.3390/toxins11060346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022] Open
Abstract
In the past, it has proved challenging to generate antibodies against mycolactone, the primary lipidic toxin A of Mycobacterium ulcerans causing Buruli ulcer, due to its immunosuppressive properties. Here we show that in vitro display, comprising both phage and yeast display, can be used to select antibodies recognizing mycolactone from a large human naïve phage antibody library. Ten different antibodies were isolated, and hundreds more identified by next generation sequencing. These results indicate the value of in vitro display methods to generate antibodies against difficult antigenic targets such as toxins, which cannot be used for immunization unless inactivated by structural modification. The possibility to easily generate anti-mycolactone antibodies is an exciting prospect for the development of rapid and simple diagnostic/detection methods.
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196
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Hirokawa M, Fujishima N, Togashi M, Saga A, Omokawa A, Saga T, Moritoki Y, Ueki S, Takahashi N, Kitaura K, Suzuki R. High-throughput sequencing of IgG B-cell receptors reveals frequent usage of the rearranged IGHV4-28/IGHJ4 gene in primary immune thrombocytopenia. Sci Rep 2019; 9:8645. [PMID: 31201346 PMCID: PMC6570656 DOI: 10.1038/s41598-019-45264-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022] Open
Abstract
Primary immune thrombocytopenia (ITP) is an acquired form of thrombocytopenia caused by IgG anti-platelet autoantibodies and represents an organ-specific autoimmune disorder. Although the glycoprotein (GP)IIb/IIIa and GPIb/IX have been shown to be targets for autoantibodies, the antigen specificity of autoantibodies is not fully elucidated. To identify the characteristics of IgG B-cell receptor (BCR) repertoires in ITP, we took advantage of adaptor-ligation PCR and high-throughput DNA sequencing methods for analyzing the clone-based repertoires of IgG-expressing peripheral blood B cells. A total of 2,009,943 in-frame and 315,469 unique reads for IGH (immunoglobulin heavy) were obtained from twenty blood samples. Comparison of the IGHV repertoires between patients and controls revealed an increased usage of IGHV4–28 in ITP patients. One hundred eighty-six distinct IGHV4–28-carrying sequences were identified in ITP patients and the majority of these clones used an IGHJ4 segment. The IGHV4–28/IGHJ4-carrying B-cell clones were found in all ITP patients. Oligoclonal expansions of IGHV4–28/IGHJ4-carrying B cells were accompanied by multiple related clones with single amino substitution in the CDR3 region suggesting somatic hypermutation. Taken together, the expansion of IGHV4–28/IGHJ4-carrying IgG-expressing B cells in ITP may be the result of certain antigenic pressure and may provide a clue for the immune pathophysiology of ITP.
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Affiliation(s)
- Makoto Hirokawa
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan.
| | - Naohito Fujishima
- Division of Blood Transfusion, Akita University Hospital, Akita, Japan.,Department of Hematology, Nephrology and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Masaru Togashi
- Department of Hematology, Nephrology and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Akiko Saga
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Ayumi Omokawa
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Tomoo Saga
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Yuki Moritoki
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Shigeharu Ueki
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Naoto Takahashi
- Department of Hematology, Nephrology and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | | | - Ryuji Suzuki
- Repertoire Genesis Incorporation, Ibaraki, Japan.,Department of Rheumatology and Clinical Immunology, Clinical Research Center for Allergy and Rheumatology, Sagamihara National Hospital, Sagamihara, Japan
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197
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Marchan J. In silico identification of epitopes present in human heat shock proteins (HSPs) overexpressed by tumour cells. J Immunol Methods 2019; 471:34-45. [PMID: 31129262 DOI: 10.1016/j.jim.2019.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/03/2019] [Accepted: 05/22/2019] [Indexed: 11/26/2022]
Abstract
Although many of heat shock proteins (HSPs) are crucial in homeostasis due to their role in maintaining cellular proteostasis by the integration of two pivotal processes-folding and degradation, several decades of cancer proteomics suggest that HSPs may improve cancer establishment and progression. Therefore, it is imperative to explore how these molecules impact patient outcomes and whether their interaction with the immune systems improves the protumour or antitumour environment. Here, using an immunoinformatics approach were investigated the best probable epitopes from ten HSPs (HSP90α, HSP90β, HSPA1A, HSPA1L, HSPA2, HSPA5, HSPA6, HSPB1, HSPB5 and HSP60/HSP10). To achieve this aim, antigenicity, immunogenicity (prediction of continuous and discontinuous B cell epitopes, binding peptides to HLA class I and HLA class II, and overlapping epitopes), analysis of conservancy and population coverage, and prediction of IgE epitopes were evaluated. According to the physicochemical properties used for their prediction (hydrophilicity, flexibility, accessibility and antigenicity propensity), ten continuous epitopes (one per HSPs) were considered as the best and also several regions of each molecule were identified as B discontinuous epitopes. Interestingly, peptides of HSP90β, HSPA2, HSPB1, and HSPB5 were predicted as both continuous and discontinuous B cell epitopes. For all the HSPs evaluated were identified potential overlapping epitopes ("NTFYSNKEI", "TTYSCVGVF", "TADRWRVSL", "VKHFSPEEL" and "CEFQDAYVL"). Moreover, these peptides were negative for IgE epitopes and showed a large coverage in the human population (HLA-A*02, HLA-B*15, HLA-C*03, and HLA-C*12). Taken together, these data indicate that such epitopes may activate both the humoral and cell-mediated response, and thus serve as therapeutic targets for cancer. However, it must be assessed their efficacy and safety in vitro and in vivo before their translation in clinical trials.
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Affiliation(s)
- Jose Marchan
- Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.
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198
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Cheng ZX, Ang WL, Bonanni A. Electroactive Nanocarbon Can Simultaneously Work as Platform and Signal Generator for Label‐Free Immunosensing. ChemElectroChem 2019. [DOI: 10.1002/celc.201900577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Zhao Xuan Cheng
- Division of Chemistry & Biological Chemistry School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371
| | - Wei Li Ang
- Division of Chemistry & Biological Chemistry School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371
| | - Alessandra Bonanni
- Division of Chemistry & Biological Chemistry School of Physical and Mathematical SciencesNanyang Technological University Singapore 637371
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199
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Gjetting T, Gad M, Fröhlich C, Lindsted T, Melander MC, Bhatia VK, Grandal MM, Dietrich N, Uhlenbrock F, Galler GR, Strandh M, Lantto J, Bouquin T, Horak ID, Kragh M, Pedersen MW, Koefoed K. Sym021, a promising anti-PD1 clinical candidate antibody derived from a new chicken antibody discovery platform. MAbs 2019; 11:666-680. [PMID: 31046547 PMCID: PMC6601539 DOI: 10.1080/19420862.2019.1596514] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Discovery of therapeutic antibodies is a field of intense development, where immunization of rodents remains a major source of antibody candidates. However, high orthologue protein sequence homology between human and rodent species disfavors generation of antibodies against functionally conserved binding epitopes. Chickens are phylogenetically distant from mammals. Since chickens generate antibodies from a restricted set of germline genes, the possibility of adapting the Symplex antibody discovery platform to chicken immunoglobulin genes and combining it with high-throughput humanization of antibody frameworks by “mass complementarity-determining region grafting” was explored. Hence, wild type chickens were immunized with an immune checkpoint inhibitor programmed cell death 1 (PD1) antigen, and a repertoire of 144 antibodies was generated. The PD1 antibody repertoire was successfully humanized, and we found that most humanized antibodies retained affinity largely similar to that of the parental chicken antibodies. The lead antibody Sym021 blocked PD-L1 and PD-L2 ligand binding, resulting in elevated T-cell cytokine production in vitro. Detailed epitope mapping showed that the epitope recognized by Sym021 was unique compared to the clinically approved PD1 antibodies pembrolizumab and nivolumab. Moreover, Sym021 bound human PD1 with a stronger affinity (30 pM) compared to nivolumab and pembrolizumab, while also cross-reacting with cynomolgus and mouse PD1. This enabled direct testing of Sym021 in the syngeneic mouse in vivo cancer models and evaluation of preclinical toxicology in cynomolgus monkeys. Preclinical in vivo evaluation in various murine and human tumor models demonstrated a pronounced anti-tumor effect of Sym021, supporting its current evaluation in a Phase 1 clinical trial. Abbreviations: ADCC, antibody-dependent cellular cytotoxicity; CD, cluster of differentiation; CDC, complement-dependent cytotoxicity; CDR, complementarity determining region; DC, dendritic cell; ELISA, enzyme-linked immunosorbent assay; FACS, fluorescence activated cell sorting; FR, framework region; GM-CSF, granulocyte-macrophage colony-stimulating factor; HRP, horseradish peroxidase; IgG, immunoglobulin G; IL, interleukin; IFN, interferon; mAb, monoclonal antibody; MLR, mixed lymphocyte reaction; NK, natural killer; PBMC, peripheral blood mono-nuclear cell; PD1, programmed cell death 1; PDL1, programmed cell death ligand 1; RT-PCR, reverse transcription polymerase chain reaction; SEB, Staphylococcus Enterotoxin B; SPR, surface Plasmon Resonance; VL, variable part of light chain; VH, variable part of heavy chain
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Affiliation(s)
- Torben Gjetting
- a Antibody Discovery, Antibody Discovery , Ballerup , Denmark
| | - Monika Gad
- b Cancer Biology and Immunology, Symphogen A/S , Ballerup , Denmark
| | | | - Trine Lindsted
- b Cancer Biology and Immunology, Symphogen A/S , Ballerup , Denmark
| | | | - Vikram K Bhatia
- a Antibody Discovery, Antibody Discovery , Ballerup , Denmark
| | | | | | | | | | - Magnus Strandh
- a Antibody Discovery, Antibody Discovery , Ballerup , Denmark
| | - Johan Lantto
- d Global Research and Development, Symphogen A/S , Ballerup , Denmark
| | - Thomas Bouquin
- a Antibody Discovery, Antibody Discovery , Ballerup , Denmark
| | - Ivan D Horak
- d Global Research and Development, Symphogen A/S , Ballerup , Denmark
| | - Michael Kragh
- c Antibody Pharmacology, Symphogen A/S , Ballerup , Denmark
| | | | - Klaus Koefoed
- a Antibody Discovery, Antibody Discovery , Ballerup , Denmark
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200
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Bridging Vaccine-Induced HIV-1 Neutralizing and Effector Antibody Responses in Rabbit and Rhesus Macaque Animal Models. J Virol 2019; 93:JVI.02119-18. [PMID: 30842326 PMCID: PMC6498063 DOI: 10.1128/jvi.02119-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/20/2019] [Indexed: 12/13/2022] Open
Abstract
Nonneutralizing antibody functions have been associated with reduced infection risk, or control of virus replication, for HIV-1 and related viruses. It is therefore critical to evaluate development of these responses throughout all stages of preclinical testing. Rabbits are conventionally used to evaluate the ability of vaccine candidates to safely elicit antibodies that bind and neutralize HIV-1. However, it remained unexplored how effectively rabbits model the development of nonneutralizing antibody responses in primates. We administered identical HIV-1 vaccine regimens to rabbits and rhesus macaques and performed detailed comparisons of vaccine-induced antibody responses. We demonstrated that nonneutralizing HIV-specific antibody responses can be studied in the rabbit model and have identified aspects of these responses that are common, and those that are unique, to rabbits and rhesus macaques. Our findings will help determine how to best utilize preclinical rabbit and rhesus macaque models to accelerate HIV vaccine candidate testing in human trials. Studies in animal models are essential prerequisites for clinical trials of candidate HIV vaccines. Small animals, such as rabbits, are used to evaluate promising strategies prior to further immunogenicity and efficacy testing in nonhuman primates. Our goal was to determine how HIV-specific vaccine-elicited antibody responses, epitope specificity, and Fc-mediated functions in the rabbit model can predict those in the rhesus macaque (RM) model. Detailed comparisons of the HIV-1-specific IgG response were performed on serum from rabbits and RM given identical modified vaccinia virus Ankara-prime/gp120-boost immunization regimens. We found that vaccine-induced neutralizing antibody, gp120-binding antibody levels and immunodominant specificities, antibody-dependent cellular phagocytosis of HIV-1 virions, and antibody-dependent cellular cytotoxicity (ADCC) responses against gp120-coated target cells were similar in rabbits and RM. However, we also identified characteristics of humoral immunity that differed across species. ADCC against HIV-infected target cells was elicited in rabbits but not in RM, and we observed differences among subdominantly targeted epitopes. Human Fc receptor binding assays and analysis of antibody-cell interactions indicated that rabbit vaccine-induced antibodies effectively recruited and activated human natural killer cells, while vaccine-elicited RM antibodies were unable to activate either human or RM NK cells. Thus, our data demonstrate that both Fc-independent and Fc-dependent functions of rabbit antibodies can be measured with commonly used in vitro assays; however, the ability of immunogenicity studies performed in rabbits to predict responses in RM will vary depending on the particular immune parameter of interest. IMPORTANCE Nonneutralizing antibody functions have been associated with reduced infection risk, or control of virus replication, for HIV-1 and related viruses. It is therefore critical to evaluate development of these responses throughout all stages of preclinical testing. Rabbits are conventionally used to evaluate the ability of vaccine candidates to safely elicit antibodies that bind and neutralize HIV-1. However, it remained unexplored how effectively rabbits model the development of nonneutralizing antibody responses in primates. We administered identical HIV-1 vaccine regimens to rabbits and rhesus macaques and performed detailed comparisons of vaccine-induced antibody responses. We demonstrated that nonneutralizing HIV-specific antibody responses can be studied in the rabbit model and have identified aspects of these responses that are common, and those that are unique, to rabbits and rhesus macaques. Our findings will help determine how to best utilize preclinical rabbit and rhesus macaque models to accelerate HIV vaccine candidate testing in human trials.
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