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Ghosh M, Rana S. The anaphylatoxin C5a: Structure, function, signaling, physiology, disease, and therapeutics. Int Immunopharmacol 2023; 118:110081. [PMID: 36989901 DOI: 10.1016/j.intimp.2023.110081] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
The complement system is one of the oldest known tightly regulated host defense systems evolved for efficiently functioning cell-based immune systems and antibodies. Essentially, the complement system acts as a pivot between the innate and adaptive arms of the immune system. The complement system collectively represents a cocktail of ∼50 cell-bound/soluble glycoproteins directly involved in controlling infection and inflammation. Activation of the complement cascade generates complement fragments like C3a, C4a, and C5a as anaphylatoxins. C5a is the most potent proinflammatory anaphylatoxin, which is involved in inflammatory signaling in a myriad of tissues. This review provides a comprehensive overview of human C5a in the context of its structure and signaling under several pathophysiological conditions, including the current and future therapeutic applications targeting C5a.
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Affiliation(s)
- Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha 752050, India.
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2
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Cawez F, Mercuri PS, Morales-Yãnez FJ, Maalouf R, Vandevenne M, Kerff F, Guérin V, Mainil J, Thiry D, Saulmont M, Vanderplasschen A, Lafaye P, Aymé G, Bogaerts P, Dumoulin M, Galleni M. Development of Nanobodies as Theranostic Agents against CMY-2-Like Class C β-Lactamases. Antimicrob Agents Chemother 2023; 67:e0149922. [PMID: 36892280 PMCID: PMC10112224 DOI: 10.1128/aac.01499-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/24/2023] [Indexed: 03/10/2023] Open
Abstract
Three soluble single-domain fragments derived from the unique variable region of camelid heavy-chain antibodies (VHHs) against the CMY-2 β-lactamase behaved as inhibitors. The structure of the complex VHH cAbCMY-2(254)/CMY-2 showed that the epitope is close to the active site and that the CDR3 of the VHH protrudes into the catalytic site. The β-lactamase inhibition pattern followed a mixed profile with a predominant noncompetitive component. The three isolated VHHs recognized overlapping epitopes since they behaved as competitive binders. Our study identified a binding site that can be targeted by a new class of β-lactamase inhibitors designed on the sequence of the paratope. Furthermore, the use of mono- or bivalent VHH and rabbit polyclonal anti-CMY-2 antibodies enables the development of the first generation of enzyme-linked immunosorbent assay (ELISA) for the detection of CMY-2 produced by CMY-2-expressing bacteria, irrespective of resistotype.
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Affiliation(s)
- Frédéric Cawez
- InBioS, Center for Protein Engineering, Biological Macromolecules, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Paola Sandra Mercuri
- InBioS, Center for Protein Engineering, Biological Macromolecules, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Francisco Javier Morales-Yãnez
- InBioS, Center for Protein Engineering, NEPTUNS, Department of Life Sciences, University of Liège, Liège, Belgium
- ALPANANO, Center for Protein Engineering & FARAH, University of Liège, Liège, Belgium
| | - Rita Maalouf
- InBioS, Center for Protein Engineering, NEPTUNS, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Marylène Vandevenne
- InBios, Center for Protein Engineering, ROBOTEIN, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Frederic Kerff
- InBioS, Center for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Virginie Guérin
- Bacteriology, FARAH and Faculty of Veterinary Medicine, Department of Infectious and Parasitic Diseases, University of Liège, Liège, Belgium
| | - Jacques Mainil
- Bacteriology, FARAH and Faculty of Veterinary Medicine, Department of Infectious and Parasitic Diseases, University of Liège, Liège, Belgium
| | - Damien Thiry
- Bacteriology, FARAH and Faculty of Veterinary Medicine, Department of Infectious and Parasitic Diseases, University of Liège, Liège, Belgium
| | - Marc Saulmont
- Regional Animal Health and Identification Association (ARSIA), Ciney, Belgium
| | - Alain Vanderplasschen
- ALPANANO, Center for Protein Engineering & FARAH, University of Liège, Liège, Belgium
- Immunology-Vaccinology, FARAH and Faculty of Veterinary Medicine, Department of Infectious and Parasitic Diseases, University of Liège, Liège, Belgium
| | - Pierre Lafaye
- Institut Pasteur, Université Paris Cité, CNRS UMR 328, Paris, France
| | - Gabriel Aymé
- Institut Pasteur, Université Paris Cité, CNRS UMR 328, Paris, France
| | - Pierre Bogaerts
- National Reference Center for Antibiotic-Resistant Gram-Negative Bacilli, Department of Clinical Microbiology, CHU UCL Namur, Yvoir, Belgium
| | - Mireille Dumoulin
- InBioS, Center for Protein Engineering, NEPTUNS, Department of Life Sciences, University of Liège, Liège, Belgium
- ALPANANO, Center for Protein Engineering & FARAH, University of Liège, Liège, Belgium
| | - Moreno Galleni
- InBioS, Center for Protein Engineering, Biological Macromolecules, Department of Life Sciences, University of Liège, Liège, Belgium
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3
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Mittal L, Tonk R, Awasthi A, Asthana S. Traversing through the Dynamic Protein-Protein Interaction Landscape and Conformational Plasticity of PD-1 for Small-Molecule Discovery. J Med Chem 2022; 65:5941-5953. [PMID: 35420421 DOI: 10.1021/acs.jmedchem.2c00176] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Monoclonal antibodies (mAbs) blocking the PD-1/PD-L1 interface have shown remarkable success in treating malignancies, but they may also initiate lethal immune-related adverse events. Small molecules may circumvent the mAb limitations; however, none has entered clinical trials targeting PD-1. Its complex protein-protein interaction interfaces necessitate an atomic-level understanding of recognition and binding mechanisms. Hence, we have aimed to highlight the PD-1's sequence-structure-dynamic-function link with its cognate ligands and diversely reported inhibitors. We focus primarily on the anti-PD-1 mAbs, their mode of actions, and interactions with PD-1 epitopes. The comparison of co-crystals showed that these ligands/inhibitors harness the PD-1's conformational plasticity and structural determinants differentially. The relationship between modulator binding patterns and biological activity is demonstrated using interaction fingerprinting of all reported human PD-1 co-crystals. The significant dynamical events and hot-spot residues underpinned from crystallographic wealth and computational studies have been highlighted to expedite small-molecule discovery.
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Affiliation(s)
- Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Haryana 121001, India.,Delhi Pharmaceutical Sciences and Research University (DPSRU), Delhi 110017, India
| | - Rajiv Tonk
- Delhi Pharmaceutical Sciences and Research University (DPSRU), Delhi 110017, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute (THSTI), Haryana 121001, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Haryana 121001, India
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4
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Peltomaa R, Barderas R, Benito-Peña E, Moreno-Bondi MC. Recombinant antibodies and their use for food immunoanalysis. Anal Bioanal Chem 2022; 414:193-217. [PMID: 34417836 PMCID: PMC8380008 DOI: 10.1007/s00216-021-03619-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022]
Abstract
Antibodies are widely employed as biorecognition elements for the detection of a plethora of compounds including food and environmental contaminants, biomarkers, or illicit drugs. They are also applied in therapeutics for the treatment of several disorders. Recent recommendations from the EU on animal protection and the replacement of animal-derived antibodies by non-animal-derived ones have raised a great controversy in the scientific community. The application of recombinant antibodies is expected to achieve a high growth rate in the years to come thanks to their versatility and beneficial characteristics in comparison to monoclonal and polyclonal antibodies, such as stability in harsh conditions, small size, relatively low production costs, and batch-to-batch reproducibility. This review describes the characteristics, advantages, and disadvantages of recombinant antibodies including antigen-binding fragments (Fab), single-chain fragment variable (scFv), and single-domain antibodies (VHH) and their application in food analysis with especial emphasis on the analysis of biotoxins, antibiotics, pesticides, and foodborne pathogens. Although the wide application of recombinant antibodies has been hampered by a number of challenges, this review demonstrates their potential for the sensitive, selective, and rapid detection of food contaminants.
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Affiliation(s)
- Riikka Peltomaa
- Department of Life Sciences, University of Turku, 20014, Turku, Finland
- Turku Collegium for Science and Medicine, University of Turku, 20014, Turku, Finland
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Elena Benito-Peña
- Department of Analytical Chemistry, Universidad Complutense de Madrid, 28040, Madrid, Spain.
| | - María C Moreno-Bondi
- Department of Analytical Chemistry, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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5
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Van Holsbeeck K, Martins JC, Ballet S. Downsizing antibodies: Towards complementarity-determining region (CDR)-based peptide mimetics. Bioorg Chem 2021; 119:105563. [PMID: 34942468 DOI: 10.1016/j.bioorg.2021.105563] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022]
Abstract
Monoclonal antibodies emerged as an important therapeutic drug class with remarkable specificity and binding affinity. Nonetheless, these heterotetrameric immunoglobulin proteins come with high manufacturing and therapeutic costs which can take extraordinary proportions, besides other limitations such as their limited in cellulo access imposed by their molecular size (ca. 150 kDa). These drawbacks stimulated the development of downsized functional antibody fragments (ca. 15-50 kDa), together with smaller synthetic peptides (ca. 1-3 kDa) derived from the antibodies' crucial complementarity-determining regions (CDR). Despite the general lack of success in the literal translation of CDR loops in peptide mimetics, rational structure-based and computational approaches have shown their potential for obtaining functional CDR-based peptide mimetics. In this review, we describe the efforts made in the development of antibody and nanobody paratope-derived peptide mimetics with particular focus on the used design strategies, in addition to highlighting the challenges associated with their development.
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Affiliation(s)
- Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; NMR and Structure Analysis Unit, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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6
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Olson KM, Traynor JR, Alt A. Allosteric Modulator Leads Hiding in Plain Site: Developing Peptide and Peptidomimetics as GPCR Allosteric Modulators. Front Chem 2021; 9:671483. [PMID: 34692635 PMCID: PMC8529114 DOI: 10.3389/fchem.2021.671483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Allosteric modulators (AMs) of G-protein coupled receptors (GPCRs) are desirable drug targets because they can produce fewer on-target side effects, improved selectivity, and better biological specificity (e.g., biased signaling or probe dependence) than orthosteric drugs. An underappreciated source for identifying AM leads are peptides and proteins-many of which were evolutionarily selected as AMs-derived from endogenous protein-protein interactions (e.g., transducer/accessory proteins), intramolecular receptor contacts (e.g., pepducins or extracellular domains), endogenous peptides, and exogenous libraries (e.g., nanobodies or conotoxins). Peptides offer distinct advantages over small molecules, including high affinity, good tolerability, and good bioactivity, and specific disadvantages, including relatively poor metabolic stability and bioavailability. Peptidomimetics are molecules that combine the advantages of both peptides and small molecules by mimicking the peptide's chemical features responsible for bioactivity while improving its druggability. This review 1) discusses sources and strategies to identify peptide/peptidomimetic AMs, 2) overviews strategies to convert a peptide lead into more drug-like "peptidomimetic," and 3) critically analyzes the advantages, disadvantages, and future directions of peptidomimetic AMs. While small molecules will and should play a vital role in AM drug discovery, peptidomimetics can complement and even exceed the advantages of small molecules, depending on the target, site, lead, and associated factors.
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Affiliation(s)
- Keith M. Olson
- Department of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, United States
| | - John R. Traynor
- Department of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Andrew Alt
- Department of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
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7
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Murali R, Zhang H, Cai Z, Lam L, Greene M. Rational Design of Constrained Peptides as Protein Interface Inhibitors. Antibodies (Basel) 2021; 10:antib10030032. [PMID: 34449551 PMCID: PMC8395526 DOI: 10.3390/antib10030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
The lack of progress in developing targeted therapeutics directed at protein–protein complexes has been due to the absence of well-defined ligand-binding pockets and the extensive intermolecular contacts at the protein–protein interface. Our laboratory has developed approaches to dissect protein–protein complexes focusing on the superfamilies of erbB and tumor necrosis factor (TNF) receptors by the combined use of structural biology and computational biology to facilitate small molecule development. We present a perspective on the development and application of peptide inhibitors as well as immunoadhesins to cell surface receptors performed in our laboratory.
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Affiliation(s)
- Ramachandran Murali
- Cedars-Sinai Medical Center, Department of Biomedical Science, Research Division of Immunology, Los Angeles, CA 90211, USA
- Correspondence: (R.M.); (M.G.)
| | - Hongtao Zhang
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
| | - Zheng Cai
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
| | - Lian Lam
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
| | - Mark Greene
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.Z.); (Z.C.); (L.L.)
- Correspondence: (R.M.); (M.G.)
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8
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Korie NPU, Tandoh KZ, Kwofie SK, Quaye O. Therapeutic potential of HIV-1 entry inhibitor peptidomimetics. Exp Biol Med (Maywood) 2021; 246:1060-1068. [PMID: 33596698 PMCID: PMC8113741 DOI: 10.1177/1535370221990870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) infection remains a public health concern globally. Although great strides in the management of HIV-1 have been achieved, current highly active antiretroviral therapy is limited by multidrug resistance, prolonged use-related effects, and inability to purge the HIV-1 latent pool. Even though novel therapeutic options with HIV-1 broadly neutralizing antibodies (bNAbs) are being explored, the scalability of bNAbs is limited by economic cost of production and obligatory requirement for parenteral administration. However, these limitations can be addressed by antibody mimetics/peptidomimetics of HIV-1 bNAbs. In this review we discuss the limitations of HIV-1 bNAbs as HIV-1 entry inhibitors and explore the potential therapeutic use of antibody mimetics/peptidomimetics of HIV-1 entry inhibitors as an alternative for HIV-1 bNAbs. We highlight the reduced cost of production, high specificity, and oral bioavailability of peptidomimetics compared to bNAbs to demonstrate their suitability as candidates for novel HIV-1 therapy and conclude with some perspectives on future research toward HIV-1 novel drug discovery.
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Affiliation(s)
- Nneka PU Korie
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
| | - Kwesi Z Tandoh
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
| | - Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
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Murali R. Perspective on Crystallographic Studies of Antibody Structures. Monoclon Antib Immunodiagn Immunother 2020; 39:195-198. [PMID: 33156727 DOI: 10.1089/mab.2020.0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In the past 50 years, there has been a great progress made in understanding and deploying antibodies in biology, medicine, and therapy. In this study, a brief overview is presented on how the crystal structures of antibody fragments guided therapeutic strategies emanating from our laboratories along with some historical perspective.
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Affiliation(s)
- Ramachandran Murali
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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10
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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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Konieczna I, Relich I, Durajski M, Lechowicz L, Chrapek M, Gaweda J, Fraczyk J, Kaminski ZJ. Novel tool in rheumatoid arthritis diagnosis-The usage of urease flap region peptidomimetics. J Pept Sci 2018; 24:e3084. [PMID: 29870122 DOI: 10.1002/psc.3084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 12/18/2022]
Abstract
Rheumatoid arthritis (RA) is an autoimmune inflammatory disease. Early diagnosis can prevent joint erosion. However, available biomarkers do not always allow for clear distinction between RA and non-RA individuals. It has become known that bacteria/viruses are among the environmental triggers that initiate RA via multiple molecular mechanisms. Thus, to better understand the role of bacteria in RA, we synthetized 6 peptidomimetics of bacterial ureases' flap region. These peptides were then used to distinguish RA patients from healthy people sera by immunoblotting. Most patients' sera were bound to peptidomimetic characteristic for Enterobacter sp. and Klebsiella sp. flap urease. We also found similarities between peptidomimetic sequence and human proteins connected with RA. This pilot study suggests that bacteria may trigger RA via mechanism of molecular mimicry of urease to host proteins and ureases flap peptidomimetics may be potential candidate as a new additional diagnostic test.
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Affiliation(s)
- Iwona Konieczna
- Department of Microbiology, Jan Kochanowski University, Swietokrzyska 15, 25-406, Kielce, Poland
| | - Inga Relich
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Maciej Durajski
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Lukasz Lechowicz
- Department of Microbiology, Jan Kochanowski University, Swietokrzyska 15, 25-406, Kielce, Poland
| | - Magdalena Chrapek
- Department of Probability and Statistics, Jan Kochanowski University, Swietokrzyska 15, 25-406, Kielce, Poland
| | - Jozef Gaweda
- Swietokrzyskie Rheumatology Center, St. Luke Specialized Hospital, Gimnazjalna 41B, 26-200, Konskie, Poland
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
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12
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Munikumar M, Krishna VS, Reddy VS, Rajeswari B, Sriram D, Rao MV. In silico design of small peptides antagonist against leptin receptor for the treatment of obesity and its associated immune-mediated diseases. J Mol Graph Model 2018; 82:20-36. [PMID: 29649778 DOI: 10.1016/j.jmgm.2018.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
Excess adiposity in obese inhibits negatively impacts immune function and host defence. Obesity is characterized by a state of low-grade, chronic inflammation in addition to disturbed levels of circulating nutrients and metabolic hormones. The impact of metabolic abnormalities on obesity-related co-morbidities has undergone intense scrutiny over the past decades. Thus, treatment of obesity and its associated immune-mediated diseases is challenging due to impaired function of leptin system. These disorders are managed through antibiotics and by cytokines replacement. However, the effectiveness of cytokines coupled to the complexity of the cytokine network leads to severe side-effects, which can still occur after careful preclinical evaluation. In addition, synthetic immunotherapeutics carry a degree of risk, time-consuming and expensive. Hence, the complexity of existing therapy and adverse effects emphasizes the need for an alternative approach for the management of immune dysfunction associated with obesity. Computer-aided small molecule antibody technology has been successful in the design of novel biologicals for the diagnosis of diseases and therapeutic interventions. In this study, the crystal structure of leptin receptor (LEPR) complex with monoclonal antibody (9F8 Fab) was explored to predict Ag-Ab interactions using bioinformatics tools. The LEPR of complementarity-determining region (CDR) loops were mutated with published positive control residues of Ser, Thr, Tyr, Trp, and Phe to design a set of 678 peptides which were evaluated through Ag-peptide docking, binding free-energies, and interaction energies. Thus, hypothesized novel peptides can be explored as clinically applicable antagonists for the treatment of obesity and associated immune-mediated diseases.
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Affiliation(s)
- Manne Munikumar
- Biomedical Informatics Center (BMIC), National Institute of Nutrition, Indian Council of Medical Research (ICMR), Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India.
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Ranga Reddy, 500078, India
| | | | - Bolla Rajeswari
- Biomedical Informatics Center (BMIC), National Institute of Nutrition, Indian Council of Medical Research (ICMR), Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Ranga Reddy, 500078, India
| | - Mendu Vishnuvardhana Rao
- National Institute of Medical Statistics, Indian Council of Medical Research, (ICMR), Ansari Nagar, New Delhi, 110029, India
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13
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Okochi M, Muto M, Yanai K, Tanaka M, Onodera T, Wang J, Ueda H, Toko K. Array-Based Rational Design of Short Peptide Probe-Derived from an Anti-TNT Monoclonal Antibody. ACS COMBINATORIAL SCIENCE 2017; 19:625-632. [PMID: 28845964 DOI: 10.1021/acscombsci.7b00035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complementarity-determining regions (CDRs) are sites on the variable chains of antibodies responsible for binding to specific antigens. In this study, a short peptide probe for recognition of 2,4,6-trinitrotoluene (TNT), was identified by testing sequences derived from the CDRs of an anti-TNT monoclonal antibody. The major TNT-binding site in this antibody was identified in the heavy chain CDR3 by antigen docking simulation and confirmed by an immunoassay using a spot-synthesis based peptide array comprising amino acid sequences of six CDRs in the variable region. A peptide derived from heavy chain CDR3 (RGYSSFIYWF) bound to TNT with a dissociation constant of 1.3 μM measured by surface plasmon resonance. Substitution of selected amino acids with basic residues increased TNT binding while substitution with acidic amino acids decreased affinity, an isoleucine to arginine change showed the greatest improvement of 1.8-fold. The ability to create simple peptide binders of volatile organic compounds from sequence information provided by the immune system in the creation of an immune response will be beneficial for sensor developments in the future.
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Affiliation(s)
- Mina Okochi
- Department
of Chemical Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
- JST, ImPACT, Sanban-cho
5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masaki Muto
- Department
of Chemical Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
- JST, ImPACT, Sanban-cho
5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Kentaro Yanai
- Department
of Chemical Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Masayoshi Tanaka
- Department
of Chemical Science and Engineering, School of Materials and Chemical
Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
- JST, ImPACT, Sanban-cho
5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Takeshi Onodera
- JST, ImPACT, Sanban-cho
5, Chiyoda-ku, Tokyo 102-0075, Japan
- Research
and Development Center for Taste and Odor Sensing, Kyushu University, Fukuoka, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Jin Wang
- JST, ImPACT, Sanban-cho
5, Chiyoda-ku, Tokyo 102-0075, Japan
- Research
and Development Center for Taste and Odor Sensing, Kyushu University, Fukuoka, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroshi Ueda
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-18, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Kiyoshi Toko
- JST, ImPACT, Sanban-cho
5, Chiyoda-ku, Tokyo 102-0075, Japan
- Research
and Development Center for Taste and Odor Sensing, Kyushu University, Fukuoka, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
- Graduate
School of Information Science and Electrical Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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14
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Yu X, Yang YP, Dikici E, Deo SK, Daunert S. Beyond Antibodies as Binding Partners: The Role of Antibody Mimetics in Bioanalysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:293-320. [PMID: 28375702 PMCID: PMC5895458 DOI: 10.1146/annurev-anchem-061516-045205] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence of novel binding proteins or antibody mimetics capable of binding to ligand analytes in a manner analogous to that of the antigen-antibody interaction has spurred increased interest in the biotechnology and bioanalytical communities. The goal is to produce antibody mimetics designed to outperform antibodies with regard to binding affinities, cellular and tumor penetration, large-scale production, and temperature and pH stability. The generation of antibody mimetics with tailored characteristics involves the identification of a naturally occurring protein scaffold as a template that binds to a desired ligand. This scaffold is then engineered to create a superior binder by first creating a library that is then subjected to a series of selection steps. Antibody mimetics have been successfully used in the development of binding assays for the detection of analytes in biological samples, as well as in separation methods, cancer therapy, targeted drug delivery, and in vivo imaging. This review describes recent advances in the field of antibody mimetics and their applications in bioanalytical chemistry, specifically in diagnostics and other analytical methods.
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Affiliation(s)
- Xiaowen Yu
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Yu-Ping Yang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Sapna K Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
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15
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Abstract
In spite of their widespread applications as therapeutic, diagnostic, and detection agents, the limitations of polyclonal and monoclonal antibodies have enthused scientists to plan for next-generation biomedical agents, the so-called antibody mimetics, which offer many advantages compared to traditional antibodies. Antibody mimetics could be designed through protein-directed evolution or fusion of complementarity-determining regions with intervening framework regions. In the recent decade, extensive progress has been made in exploiting human, butterfly (Pieris brassicae), and bacterial systems to design and select mimetics using display technologies. Notably, some of the mimetics have made their way to market. Numerous limitations lie ahead in developing mimetics for different biomedical usage, particularly for which conventional antibodies are ineffective. This chapter presents a brief overview of the current characteristics, construction, and applications of antibody mimetics.
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16
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McEnaney PJ, Fitzgerald KJ, Zhang AX, Douglass EF, Shan W, Balog A, Kolesnikova MD, Spiegel DA. Chemically synthesized molecules with the targeting and effector functions of antibodies. J Am Chem Soc 2014; 136:18034-43. [PMID: 25514603 PMCID: PMC4291750 DOI: 10.1021/ja509513c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 12/21/2022]
Abstract
This article reports the design, synthesis, and evaluation of a novel class of molecules of intermediate size (approximately 7000 Da), which possess both the targeting and effector functions of antibodies. These compounds—called synthetic antibody mimics targeting prostate cancer (SyAM-Ps)—bind simultaneously to prostate-specific membrane antigen and Fc gamma receptor I, thus eliciting highly selective cancer cell phagocytosis. SyAMs have the potential to combine the advantages of both small-molecule and biologic therapies, and may address many drawbacks associated with available treatments for cancer and other diseases.
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Affiliation(s)
- Patrick J McEnaney
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06511, United States
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17
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Baloch AR, Baloch AW, Sutton BJ, Zhang X. Antibody mimetics: promising complementary agents to animal-sourced antibodies. Crit Rev Biotechnol 2014; 36:268-75. [PMID: 25264572 DOI: 10.3109/07388551.2014.958431] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite their wide use as therapeutic, diagnostic and detection agents, the limitations of polyclonal and monoclonal antibodies have inspired scientists to design the next generation biomedical agents, so-called antibody mimetics that offer many advantages over conventional antibodies. Antibody mimetics can be constructed by protein-directed evolution or fusion of complementarity-determining regions through intervening framework regions. Substantial progress in exploiting human, butterfly (Pieris brassicae) and bacterial systems to design and select mimetics using display technologies has been made in the past 10 years, and one of these mimetics [Kalbitor® (Dyax)] has made its way to market. Many challenges lie ahead to develop mimetics for various biomedical applications, especially those for which conventional antibodies are ineffective, and this review describes the current characteristics, construction and applications of antibody mimetics compared to animal-sourced antibodies. The possible limitations of mimetics and future perspectives are also discussed.
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Affiliation(s)
- Abdul Rasheed Baloch
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
| | - Abdul Wahid Baloch
- b Department of Plant Breeding and Genetics , Sindh Agriculture University , Tandojam , Pakistan , and
| | - Brian J Sutton
- c Randall Division of Cell and Molecular Biophysics, King's College London , London , UK
| | - Xiaoying Zhang
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
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