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Eronen V, Tullila A, Iljin K, Rouvinen J, Nevanen TK, Hakulinen N. Structural insight to elucidate the binding specificity of the anti-cortisol Fab fragment with glucocorticoids. J Struct Biol 2023; 215:107966. [PMID: 37100101 DOI: 10.1016/j.jsb.2023.107966] [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: 02/16/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023]
Abstract
Cortisol is a steroid hormone that is produced by the adrenal gland. It is a primary stress hormone that increases glucose levels in the blood stream. High concentrations of cortisol in the body can be used as a biomarker for acute and chronic stress and related mental and physiological disorders. Therefore, the accurate quantification of cortisol levels in body fluids is essential for clinical diagnosis. In this article, we describe the isolation of recombinant anti-cortisol antibodies with high affinity for cortisol and discover their cross-reactivity with other glucocorticoids. To describe the cortisol binding site and elucidate the structural basis for the binding specificity, the high-resolution crystal structures of the anti-cortisol (17) Fab fragment in the absence of glucocorticoid (2.00 Å) and the presence of cortisol (2.26 Å), corticosterone (1.86 Å), cortisone (1.85 Å) and prednisolone (2.00 Å) were determined. To our knowledge, this is the first determined crystal structure of a cortisol-specific antibody. The recognition of cortisol is driven by hydrophobic interactions and hydrogen bonding at the protein-ligand interface coupled with a conformational transition. Comparison of ligand-free and ligand-bound structures showed that the side chains of residues Tyr58-H and Arg56-H can undergo local conformational changes at the binding site, most likely prior to the binding event via a conformational selection mechanism. Compared to other anti-steroid antibody-antigen complexes, (17) Fab possesses a structurally unique steroid binding site, as the H3 loop from the CDR area has only a minor contribution, but framework residues have a prominent contribution to hapten binding.
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Affiliation(s)
- Veikko Eronen
- Department of Chemistry, University of Eastern Finland, PO BOX 111, 80100 Joensuu, Finland
| | - Antti Tullila
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, 02150, Espoo, Finland; Current address Aidian Oy, Finland. Koivu-Mankkaantie 6 B, 02101, Espoo
| | - Kristiina Iljin
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, PO BOX 111, 80100 Joensuu, Finland
| | - Tarja K Nevanen
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO BOX 111, 80100 Joensuu, Finland
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2
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Tit-Oon P, Tharakaraman K, Artpradit C, Godavarthi A, Sungkeeree P, Sasisekharan V, Kerdwong J, Miller NL, Mahajan B, Khongmanee A, Ruchirawat M, Sasisekharan R, Fuangthong M. Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking. Sci Rep 2020; 10:18256. [PMID: 33106487 PMCID: PMC7588459 DOI: 10.1038/s41598-020-75056-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Nipah Virus (NiV) has been designated as a priority disease with an urgent need for therapeutic development by World Health Organization. The monoclonal antibody m102.4 binds to the immunodominant NiV receptor-binding glycoprotein (GP), and potently neutralizes NiV, indicating its potential as a therapeutic agent. Although the co-crystal structure of m102.3, an m102.4 derivative, in complex with the GP of the related Hendra Virus (HeV) has been solved, the structural interaction between m102.4 and NiV is uncharacterized. Herein, we used structure-guided alanine-scanning mutagenesis to map the functional epitope and paratope residues that govern the antigen-antibody interaction. Our results revealed that the binding of m102.4 is mediated predominantly by two residues in the HCDR3 region, which is unusually small for an antibody-antigen interaction. We performed computational docking to generate a structural model of m102.4-NiV interaction. Our model indicates that m102.4 targets the common hydrophobic central cavity and a hydrophilic rim on the GP, as observed for the m102.3-HeV co-crystal, albeit with Fv orientation differences. In summary, our study provides insight into the m102.4-NiV interaction, demonstrating that structure-guided alanine-scanning and computational modeling can serve as the starting point for additional antibody reengineering (e.g. affinity maturation) to generate potential therapeutic candidates.
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Affiliation(s)
- Phanthakarn Tit-Oon
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Kannan Tharakaraman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Abhinav Godavarthi
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Yale University, New Haven, CT, 06520, USA
| | - Pareenart Sungkeeree
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Varun Sasisekharan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Jarunee Kerdwong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Nathaniel Loren Miller
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bhuvna Mahajan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Amnart Khongmanee
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Mayuree Fuangthong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
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Yang KA, Chun H, Zhang Y, Pecic S, Nakatsuka N, Andrews AM, Worgall TS, Stojanovic MN. High-Affinity Nucleic-Acid-Based Receptors for Steroids. ACS Chem Biol 2017; 12:3103-3112. [PMID: 29083858 DOI: 10.1021/acschembio.7b00634] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Artificial receptors for hydrophobic molecules usually have moderate affinities and limited selectivities. We describe three new classes of high affinity hydrophobic receptors for nonaromatic steroids based on deoxyribonucleotides, obtained through five high stringency selections coupled with tailored counter-selections. The isolation of multiple classes of high affinity steroid receptors demonstrates the surprising breadth of moderately sized hydrophobic binding motifs (<40 nucleotides) available to natural nucleic acids. Studies of interactions with analogs indicate that two classes, four-way junctions and 4XGN motifs, comprise receptors with shapes that prevent binding of specific steroid conjugates used in counter-selections. Furthermore, they strongly prefer nonhydroxylated steroid cores, which is typical for hydrophobic receptors. The third new class accommodates hydroxyl groups in high-affinity, high-selectivity binding pockets, thus reversing the preferences of the first two classes. The high-affinity binding of aptamers to targets efficiently inhibits double-helix formation in the presence of the complementary oligonucleotides. The high affinity of some of these receptors and tailored elimination of binding through counter-selections ensures that these new aptamers will enable clinical chemistry applications.
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Affiliation(s)
| | - Hyosun Chun
- School
of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
| | | | | | - Nako Nakatsuka
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Anne M. Andrews
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience
and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, California 90095, United States
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4
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Eichinger A, Neumaier I, Pschenitza M, Niessner R, Knopp D, Skerra A. Enge molekulare Erkennung von Benzo[ a
]pyren durch einen hochaffinen Antikörper. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Andreas Eichinger
- Munich Center for Integrated Protein Science (CIPS-M) und Lehrstuhl für Biologische Chemie; Technische Universität München; 85354 Freising, Weihenstephan Deutschland
| | - Irmgard Neumaier
- Munich Center for Integrated Protein Science (CIPS-M) und Lehrstuhl für Biologische Chemie; Technische Universität München; 85354 Freising, Weihenstephan Deutschland
| | - Michael Pschenitza
- Lehrstuhl für Analytische Chemie; Technische Universität München; 81377 München Deutschland
| | - Reinhard Niessner
- Lehrstuhl für Analytische Chemie; Technische Universität München; 81377 München Deutschland
| | - Dietmar Knopp
- Lehrstuhl für Analytische Chemie; Technische Universität München; 81377 München Deutschland
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CIPS-M) und Lehrstuhl für Biologische Chemie; Technische Universität München; 85354 Freising, Weihenstephan Deutschland
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Eichinger A, Neumaier I, Pschenitza M, Niessner R, Knopp D, Skerra A. Tight Molecular Recognition of Benzo[a]pyrene by a High-Affinity Antibody. Angew Chem Int Ed Engl 2017; 56:10592-10597. [PMID: 28603847 DOI: 10.1002/anie.201703893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/26/2017] [Indexed: 01/19/2023]
Abstract
Benzo[a]pyrene, which is produced during the incomplete combustion of organic material, is an abundant noxious pollutant because of its carcinogenic metabolic degradation products. The high-affinity (KD ≈3 nm) monoclonal antibody 22F12 allows facile bioanalytical quantification of benzo[a]pyrene even in complex matrices. We report the functional and X-ray crystallographic analysis of 22F12 in complex with 3-hydroxybenzo[a]pyrene after cloning of the V-genes and production as a recombinant Fab fragment. The polycyclic aromatic hydrocarbon is bound in a deep pocket between the light and heavy chains, surrounded mainly by aromatic and aliphatic amino acid side chains. Interestingly, the hapten-antibody interface is less densely packed than expected and reveals polar, H-bond-like interactions with the polycyclic aromatic π-electron system, which may allow the antibody to maintain a large, predominantly hydrophobic binding site in an aqueous environment while providing sufficient complementarity to its ligand.
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Affiliation(s)
- Andreas Eichinger
- Munich Center for Integrated Protein Science, CIPS-M, und Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Weihenstephan, Germany
| | - Irmgard Neumaier
- Munich Center for Integrated Protein Science, CIPS-M, und Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Weihenstephan, Germany
| | - Michael Pschenitza
- Lehrstuhl für Analytische Chemie, Technische Universität München, 81377, München, Germany
| | - Reinhard Niessner
- Lehrstuhl für Analytische Chemie, Technische Universität München, 81377, München, Germany
| | - Dietmar Knopp
- Lehrstuhl für Analytische Chemie, Technische Universität München, 81377, München, Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science, CIPS-M, und Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Weihenstephan, Germany
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6
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Klas K, Tsukamoto S, Sherman DH, Williams RM. Natural Diels-Alderases: Elusive and Irresistable. J Org Chem 2016; 80:11672-85. [PMID: 26495876 DOI: 10.1021/acs.joc.5b01951] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eight examples of biosynthetic pathways wherein a natural enzyme has been identified and claimed to function as a catalyst for the [4 + 2] cycloaddition reaction, namely, Diels-Alderases, are briefly reviewed. These are discussed in the context of the mechanistic challenges associated with the technical difficulty of proving that the net formal [4 + 2] cycloaddition under study indeed proceeds through a synchronous mechanism and that the putative biosynthetic enzyme deploys the pericyclic transition state required for a Diels-Alder cycloaddition reaction.
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Affiliation(s)
- Kimberly Klas
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80524, United States
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Kumamoto 862-0973, Japan
| | - David H Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Microbiology & Immunology, and Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Robert M Williams
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80524, United States.,University of Colorado Cancer Center , Aurora, Colorado 80045, United States
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7
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Niemi MH, Takkinen K, Amundsen LK, Söderlund H, Rouvinen J, Höyhtyä M. The testosterone binding mechanism of an antibody derived from a naïve human scFv library. J Mol Recognit 2011; 24:209-19. [PMID: 21360611 DOI: 10.1002/jmr.1039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A testosterone binding scFv antibody was isolated from a naïve human library with a modest size of 10(8) clones. The crystal structure of the Fab fragment form of the 5F2 antibody clone complexed with testosterone determined at 1.5 Å resolution shows that the hapten is bound deeply in the antibody binding pocket. In addition to the interactions with framework residues only CDR-L3 and CDR-H3 loops interact with testosterone and the heavy chain forms the majority of the contacts with the hapten. The testosterone binding site of the 5F2 antibody with a high abundance of aromatic amino acid residues shows similarity with an in vitro affinity matured antibody having around 300 times higher affinity. The moderate affinity of the 5F2 antibody originates from the different orientation of the hapten and few light chain contacts. This is the first three-dimensional structure of a human steroid hormone binding antibody that has been isolated from a naïve human repertoire.
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Affiliation(s)
- Merja H Niemi
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
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8
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Kar P, Lipowsky R, Knecht V. Importance of Polar Solvation for Cross-Reactivity of Antibody and Its Variants with Steroids. J Phys Chem B 2011; 115:7661-9. [DOI: 10.1021/jp201538t] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Parimal Kar
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Volker Knecht
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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