1
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Ghosh R, Thomas DS, Arcot J. Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies. Foods 2023; 12:foods12030575. [PMID: 36766105 PMCID: PMC9914923 DOI: 10.3390/foods12030575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Ligand-receptor molecular recognition is the basis of biological processes. The Saturation Transfer Difference-NMR (STD-NMR) technique has been recently used to gain qualitative and quantitative information about physiological interactions at an atomic resolution. The molecular recognition patterns between the cyanocobalamin (CNBL)/aqua cobalamin (OHBL) and different plant and animal proteins were investigated via STD-NMR supplemented by molecular docking. This study demonstrates that myoglobin has the highest binding affinity and that gluten has the lowest affinity. Casein also shows a higher binding affinity for cyanocobalamin when compared with that of plant-based proteins. STD-NMR results showed the moderate binding capability of casein with both CNBL and OHBL. Computer simulation confirmed the recognition mode in theory and was compared with the experiments. This work is beneficial for understanding the binding affinity and biological action of cyanocobalamin and will attract researchers to use NMR technology to link the chemical and physiological properties of nutrients.
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Affiliation(s)
- Ruchira Ghosh
- Food and Health, School of Chemical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Jayashree Arcot
- Food and Health, School of Chemical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: ; Tel.: +61-293855360
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2
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Dey A, Mitra D, Rachineni K, Khatri LR, Paithankar H, Vajpai N, Kumar A. Mapping of Methyl Epitopes of a Peptide-Drug with Its Receptor by 2D STDD-Methyl TROSY NMR Spectroscopy. Chembiochem 2022; 23:e202200489. [PMID: 36227643 DOI: 10.1002/cbic.202200489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/13/2022] [Indexed: 01/25/2023]
Abstract
The current trend in the biopharmaceutical market has boosted the development and production of biological drugs with high efficacy and fidelity for receptor binding. While high-resolution structural insights into binding epitopes of the receptor are indispensable for better therapeutic design, it is tedious and costly. In this work, we develop a protocol by integrating two well-known NMR-based solution-state methods. Saturation transfer double-difference with methyl-TROSY (STDD-Methyl TROSY NMR) was used to probe methyl binding epitopes of the ligand in a label-free environment. This study was carried out with Human insulin as a model peptide drug, with the insulin growth factor receptor (IGFR), which is an off-target receptor for insulin. Methyl epitopes identified from STDD-Methyl TROSY NMR spectroscopy were validated through the HADDOCK platform to generate a drug-receptor model. Since this method can be applied at natural abundance, it has the potential to screen a large set of peptide-drug interactions for optimum receptor binding. Thus, we propose STDD-Methyl TROSY NMR spectroscopy as a technique for rapid screening of biologics for the development of optimized biopharmaceutics.
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Affiliation(s)
- Anomitra Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, 400076, India
| | - Debarghya Mitra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, 400076, India
| | - Kavitha Rachineni
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, 400076, India
| | - Lakshya Raj Khatri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, 400076, India
| | - Harshad Paithankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, 400076, India
| | - Navratna Vajpai
- Biocon Biologics Limited, Biocon Park (SEZ), Bommasandra-Jigani Link Road, Bangalore, 560099, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai Mumbai, 400076, India
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3
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Unione L, Moure MJ, Lenza MP, Oyenarte I, Ereño‐Orbea J, Ardá A, Jiménez‐Barbero J. The SARS-CoV-2 Spike Glycoprotein Directly Binds Exogeneous Sialic Acids: A NMR View. Angew Chem Int Ed Engl 2022; 61:e202201432. [PMID: 35191576 PMCID: PMC9074024 DOI: 10.1002/anie.202201432] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 01/07/2023]
Abstract
The interaction of the SARS CoV2 spike glycoprotein with two sialic acid-containing trisaccharides (α2,3 and α2,6 sialyl N-acetyllactosamine) has been demonstrated by NMR. The NMR-based distinction between the signals of those sialic acids in the glycans covalently attached to the spike protein and those belonging to the exogenous α2,3 and α2,6 sialyl N-acetyllactosamine ligands has been achieved by synthesizing uniformly 13 C-labelled trisaccharides at the sialic acid and galactose moieties. STD-1 H,13 C-HSQC NMR experiments elegantly demonstrate the direct interaction of the sialic acid residues of both trisaccharides with additional participation of the galactose moieties, especially for the α2,3-linked analogue. Additional experiments with the spike protein in the presence of a specific antibody for the N-terminal domain and with the isolated receptor binding and N-terminal domains of the spike protein unambiguously show that the sialic acid binding site is located at the N-terminal domain.
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Affiliation(s)
- Luca Unione
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
| | - María J. Moure
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
| | - Maria Pia Lenza
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
| | - Iker Oyenarte
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
| | - June Ereño‐Orbea
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
- IkerbasqueBasque Foundation for ScienceMaria Diaz de Haro 348013 BilbaoBizkaiaSpain
| | - Ana Ardá
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
- IkerbasqueBasque Foundation for ScienceMaria Diaz de Haro 348013 BilbaoBizkaiaSpain
| | - Jesús Jiménez‐Barbero
- CICbioGUNEBasque Research & Technology Alliance (BRTA)Bizkaia Technology Park, Building 80048162 DerioBizkaiaSpain
- IkerbasqueBasque Foundation for ScienceMaria Diaz de Haro 348013 BilbaoBizkaiaSpain
- Department of Organic ChemistryII Faculty of Science and Technology University of the Basque Country, EHU-UPV48940LeioaSpain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias (CIBERES)28029MadridSpain
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4
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Unione L, Moure MJ, Lenza MP, Oyenarte I, Ereño‐Orbea J, Ardá A, Jiménez‐Barbero J. The SARS‐CoV‐2 Spike Glycoprotein Directly Binds Exogeneous Sialic Acids: A NMR View. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Luca Unione
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
| | - María J. Moure
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
| | - Maria Pia Lenza
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
| | - Iker Oyenarte
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
| | - June Ereño‐Orbea
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
- Ikerbasque Basque Foundation for Science Maria Diaz de Haro 3 48013 Bilbao Bizkaia Spain
| | - Ana Ardá
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
- Ikerbasque Basque Foundation for Science Maria Diaz de Haro 3 48013 Bilbao Bizkaia Spain
| | - Jesús Jiménez‐Barbero
- CICbioGUNE Basque Research & Technology Alliance (BRTA) Bizkaia Technology Park, Building 800 48162 Derio Bizkaia Spain
- Ikerbasque Basque Foundation for Science Maria Diaz de Haro 3 48013 Bilbao Bizkaia Spain
- Department of Organic Chemistry II Faculty of Science and Technology University of the Basque Country, EHU-UPV 48940 Leioa Spain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias (CIBERES) 28029 Madrid Spain
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5
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Soares CO, Grosso AS, Ereño-Orbea J, Coelho H, Marcelo F. Molecular Recognition Insights of Sialic Acid Glycans by Distinct Receptors Unveiled by NMR and Molecular Modeling. Front Mol Biosci 2021; 8:727847. [PMID: 34869580 PMCID: PMC8634706 DOI: 10.3389/fmolb.2021.727847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
All cells are decorated with a highly dense and complex structure of glycan chains, which are mostly attached to proteins and lipids. In this context, sialic acids are a family of nine-carbon acidic monosaccharides typically found at the terminal position of glycan chains, modulating several physiological and pathological processes. Sialic acids have many structural and modulatory roles due to their negative charge and hydrophilicity. In addition, the recognition of sialic acid glycans by mammalian cell lectins, such as siglecs, has been described as an important immunological checkpoint. Furthermore, sialic acid glycans also play a pivotal role in host-pathogen interactions. Various pathogen receptors exposed on the surface of viruses and bacteria are responsible for the binding to sialic acid sugars located on the surface of host cells, becoming a critical point of contact in the infection process. Understanding the molecular mechanism of sialic acid glycans recognition by sialic acid-binding proteins, present on the surface of pathogens or human cells, is essential to realize the biological mechanism of these events and paves the way for the rational development of strategies to modulate sialic acid-protein interactions in diseases. In this perspective, nuclear magnetic resonance (NMR) spectroscopy, assisted with molecular modeling protocols, is a versatile and powerful technique to investigate the structural and dynamic aspects of glycoconjugates and their interactions in solution at the atomic level. NMR provides the corresponding ligand and protein epitopes, essential for designing and developing potential glycan-based therapies. In this review, we critically discuss the current state of knowledge about the structural features behind the molecular recognition of sialic acid glycans by different receptors, naturally present on human cells or pathogens, disclosed by NMR spectroscopy and molecular modeling protocols.
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Affiliation(s)
- Cátia Oliveira Soares
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Ana Sofia Grosso
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - June Ereño-Orbea
- CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Technology Park, Bilbao, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Helena Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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6
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Zhao X, Meng X, Ragauskas AJ, Lai C, Ling Z, Huang C, Yong Q. Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques. Biotechnol Adv 2021; 54:107830. [PMID: 34480987 DOI: 10.1016/j.biotechadv.2021.107830] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/07/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.
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Affiliation(s)
- Xiaoxue Zhao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Renewable Carbon, Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA; Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chenhuan Lai
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Ling
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China
| | - Caoxing Huang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Qiang Yong
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Department of Bioengineering, Nanjing Forestry University, Nanjing 210037, China.
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7
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Lal K, Bermeo R, Cramer J, Vasile F, Ernst B, Imberty A, Bernardi A, Varrot A, Belvisi L. Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia*. Chemistry 2021; 27:10341-10348. [PMID: 33769626 PMCID: PMC8360069 DOI: 10.1002/chem.202100252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Indexed: 12/12/2022]
Abstract
Burkholderia cenocepacia is an opportunistic Gram‐negative bacterium that causes infections in patients suffering from chronic granulomatous diseases and cystic fibrosis. It displays significant morbidity and mortality due to extreme resistance to almost all clinically useful antibiotics. The bacterial lectin BC2L‐C expressed in B. cenocepacia is an interesting drug target involved in bacterial adhesion and subsequent deadly infection to the host. We solved the first high resolution crystal structure of the apo form of the lectin N‐terminal domain (BC2L‐C‐nt) and compared it with the ones complexed with carbohydrate ligands. Virtual screening of a small fragment library identified potential hits predicted to bind in the vicinity of the fucose binding site. A series of biophysical techniques and X‐ray crystallographic screening were employed to validate the interaction of the hits with the protein domain. The X‐ray structure of BC2L‐C‐nt complexed with one of the identified active fragments confirmed the ability of the site computationally identified to host drug‐like fragments. The fragment affinity could be determined by titration microcalorimetry. These structure‐based strategies further provide an opportunity to elaborate the fragments into high affinity anti‐adhesive glycomimetics, as therapeutic agents against B. cenocepacia.
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Affiliation(s)
- Kanhaya Lal
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, I-20133, Milano, Italy.,Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Rafael Bermeo
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, I-20133, Milano, Italy.,Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Jonathan Cramer
- University of Basel, Department of Pharmaceutical Sciences, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Francesca Vasile
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, I-20133, Milano, Italy
| | - Beat Ernst
- University of Basel, Department of Pharmaceutical Sciences, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Anna Bernardi
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, I-20133, Milano, Italy
| | - Annabelle Varrot
- Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Laura Belvisi
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, I-20133, Milano, Italy
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8
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Gramlich M, Hays HCW, Crichton S, Kaiser PD, Heine A, Schneiderhan-Marra N, Rothbauer U, Stoll D, Maier S, Zeck A. HDX-MS for Epitope Characterization of a Therapeutic ANTIBODY Candidate on the Calcium-Binding Protein Annexin-A1. Antibodies (Basel) 2021; 10:11. [PMID: 33808657 PMCID: PMC8006148 DOI: 10.3390/antib10010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/15/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Annexin-A1 (ANXA1) belongs to a class of highly homologous Ca2+-dependent phospholipid-binding proteins. Its structure consists of a core region composed of four homologous repeats arranged in a compact, hydrolysis-resistant structure and an N-terminal region with a Ca2+-dependent conformation. ANXA1 is involved in several processes, including cell proliferation, apoptosis, metastasis, and the inflammatory response. Therefore, the development of antibodies blocking selected regions on ANXA1 holds great potential for the development of novel therapeutics treating inflammatory and cancer diseases. Here, we report the interaction site between an ANXA1-specific antibody known to inhibit T cell activation without adverse cytotoxic effects and ANXA1 using amide hydrogen-deuterium exchange mass spectrometry (HDX-MS). For the epitope determination, we applied two bottom-up HDX-MS approaches with pepsin digestion in solution and immobilized on beads. Both strategies revealed the interaction region within domain III of ANXA1 in Ca2+-bound conformation. The antibody-binding region correlates with the hydrophobic binding pocket of the N-terminal domain formed in the absence of calcium. This study demonstrates that even cryptic and flexible binding regions can be studied by HDX-MS, allowing a fast and efficient determination of the binding sites of antibodies which will help to define a mode of action profile for their use in therapy.
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Affiliation(s)
- Marius Gramlich
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Henry C. W. Hays
- Medannex Ltd., 1 Lochrin Square, Fountainbridge, Edinburgh EH3 9QA, UK; (H.C.W.H.); (S.C.)
| | - Scott Crichton
- Medannex Ltd., 1 Lochrin Square, Fountainbridge, Edinburgh EH3 9QA, UK; (H.C.W.H.); (S.C.)
| | - Philipp D. Kaiser
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Anne Heine
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Nicole Schneiderhan-Marra
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Geschwister-Scholl-Platz, 72074 Tuebingen, Germany
| | - Dieter Stoll
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
- Department of Life Sciences, University of Applied Sciences Albstadt-Sigmaringen, Anton-Guentherstr. 51, 72488 Sigmaringen, Germany
| | - Sandra Maier
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Anne Zeck
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
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9
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Monaco S, Walpole S, Doukani H, Nepravishta R, Martínez‐Bailén M, Carmona AT, Ramos‐Soriano J, Bergström M, Robina I, Angulo J. Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B. Chemistry 2020; 26:10024-10034. [PMID: 32449563 PMCID: PMC7496166 DOI: 10.1002/chem.202001723] [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: 04/08/2020] [Revised: 05/08/2020] [Indexed: 11/30/2022]
Abstract
Ligand-based NMR techniques to study protein-ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.
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Affiliation(s)
- Serena Monaco
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Samuel Walpole
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Hassan Doukani
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Ridvan Nepravishta
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Biochemistry & Molecular BiologySealy Center for Structural Biology & Molecular BiophysicsUniversity of Texas Medical Branch301 University BlvdGalvestonTX77555-1068USA
| | | | - Ana T. Carmona
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Javier Ramos‐Soriano
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Maria Bergström
- Department of Chemistry and Biomedical SciencesLinnaeus University391 82KalmarSweden
| | - Inmaculada Robina
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Jesus Angulo
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
- Instituto de Investigaciones Químicas (CSIC-US)Avda. Américo Vespucio, 4941092SevillaSpain
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10
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Mateos B, Sealey‐Cardona M, Balazs K, Konrat J, Staffler G, Konrat R. NMR Characterization of Surface Receptor Protein Interactions in Live Cells Using Methylcellulose Hydrogels. Angew Chem Int Ed Engl 2020; 59:3886-3890. [PMID: 31721390 PMCID: PMC7065066 DOI: 10.1002/anie.201913585] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/11/2019] [Indexed: 01/29/2023]
Abstract
Interactions of transmembrane receptors with their extracellular ligands are essential for cellular communication and signaling and are therefore a major focus in drug discovery programs. The transition from in vitro to live cell interaction studies, however, is typically a bottleneck in many drug discovery projects due to the challenge of obtaining atomic-resolution information under near-physiological conditions. Although NMR spectroscopy is ideally suited to overcome this limitation, several experimental impairments are still present. Herein, we propose the use of methylcellulose hydrogels to study extracellular proteins and their interactions with plasma membrane receptors. This approach reduces cell sedimentation, prevents the internalization of membrane receptors, and increases cell survival, while retaining the free tumbling of extracellular proteins.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
| | - Marco Sealey‐Cardona
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
- Present address: Calyxha Biotechnologies GmbHKarl-Farkas-Gasse 221030ViennaAustria
| | | | - Judith Konrat
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
| | | | - Robert Konrat
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
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11
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Mateos B, Sealey‐Cardona M, Balazs K, Konrat J, Staffler G, Konrat R. NMR Characterization of Surface Receptor Protein Interactions in Live Cells Using Methylcellulose Hydrogels. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
| | - Marco Sealey‐Cardona
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
- Present address: Calyxha Biotechnologies GmbH Karl-Farkas-Gasse 22 1030 Vienna Austria
| | - Katja Balazs
- AFFiRiS AG Karl-Farkas-Gasse 22 1030 Vienna Austria
| | - Judith Konrat
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
| | | | - Robert Konrat
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
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12
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Bhattacharyya D, Mohite GM, Krishnamoorthy J, Gayen N, Mehra S, Navalkar A, Kotler SA, Ratha BN, Ghosh A, Kumar R, Garai K, Mandal AK, Maji SK, Bhunia A. Lipopolysaccharide from Gut Microbiota Modulates α-Synuclein Aggregation and Alters Its Biological Function. ACS Chem Neurosci 2019; 10:2229-2236. [PMID: 30855940 DOI: 10.1021/acschemneuro.8b00733] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Altered intestinal permeability has been correlated with Parkinson's pathophysiology in the enteric nervous system, before manifestations in the central nervous system (CNS). The inflammatory endotoxin or lipopolysaccharide (LPS) released by gut bacteria is known to modulate α-synuclein amyloidogenesis through the formation of intermediate nucleating species. Here, biophysical techniques in conjunction with microscopic images revealed the molecular interaction between lipopolysaccharide and α-synuclein that induce rapid nucleation events. This heteromolecular interaction stabilizes the α-helical intermediates in the α-synuclein aggregation pathway. Multitude NMR studies probed the residues involved in the LPS-binding structural motif that modulates the nucleating forms, affecting the cellular internalization and associated cytotoxicity. Collectively, our data characterizes this heteromolecular interaction associated with an alternative pathway in Parkinson's disease progression.
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Affiliation(s)
| | - Ganesh M. Mohite
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | | | - Nilanjan Gayen
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Samuel A. Kotler
- Laboratory of Chemical Physics, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bhisma N. Ratha
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Anirban Ghosh
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Kanchan Garai
- TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Hyderabad 500075, India
| | - Atin K. Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400076, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
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13
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Roy D, Bhattacharyya D, Bhunia A. Do Catechins (ECG and EGCG) Bind to the Same Site as Thioflavin T (ThT) in Amyloid Fibril? Answer From Saturation Transfer Difference NMR. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Dipanwita Roy
- Department of Biophysics, Bose Institute, Kolkata, WB, India
| | | | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, WB, India
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14
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Nepravishta R, Walpole S, Tailford L, Juge N, Angulo J. Deriving Ligand Orientation in Weak Protein-Ligand Complexes by DEEP-STD NMR Spectroscopy in the Absence of Protein Chemical-Shift Assignment. Chembiochem 2018; 20:340-344. [PMID: 30379391 PMCID: PMC6468252 DOI: 10.1002/cbic.201800568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 01/07/2023]
Abstract
Differential epitope mapping saturation transfer difference (DEEP‐STD) NMR spectroscopy is a recently developed powerful approach for elucidating the structure and pharmacophore of weak protein–ligand interactions, as it reports key information on the orientation of the ligand and the architecture of the binding pocket.1 The method relies on selective saturation of protein residues in the binding site and the generation of a differential epitope map by observing the ligand, which depicts the nature of the protein residues making contact with the ligand in the bound state. Selective saturation requires knowledge of the chemical‐shift assignment of the protein residues, which can be obtained either experimentally by NMR spectroscopy or predicted from 3D structures. Herein, we propose a simple experimental procedure to expand the DEEP‐STD NMR methodology to protein–ligand cases in which the spectral assignment of the protein is not available. This is achieved by experimentally identifying the chemical shifts of the residues present in binding hot‐spots on the surface of the receptor protein by using 2D NMR experiments combined with a paramagnetic probe.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Louise Tailford
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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15
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Hamark C, Pendrill R, Landström J, Dotson Fagerström A, Sandgren M, Ståhlberg J, Widmalm G. Enantioselective Binding of Propranolol and Analogues Thereof to Cellobiohydrolase Cel7A. Chemistry 2018; 24:17975-17985. [PMID: 30255965 DOI: 10.1002/chem.201803104] [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: 06/18/2018] [Indexed: 12/28/2022]
Abstract
At the catalytic site for the hydrolysis of cellulose the enzyme cellobiohydrolase Cel7A binds the enantiomers of the adrenergic beta-blocker propranolol with different selectivity. Methyl-to-hydroxymethyl group modifications of propranolol, which result in higher affinity and improved selectivity, were herein studied by 1 H,1 H and 1 H,13 C scalar spin-spin coupling constants as well as utilizing the nuclear Overhauser effect (NOE) in conjunction with molecular dynamics simulations of the ligands per se, which showed the presence of all-antiperiplanar conformations, except for the one containing a vicinal oxygen-oxygen arrangement governed by the gauche effect. For the ligand-protein complexes investigated by NMR spectroscopy using, inter alia, transferred NOESY and saturation-transfer difference (STD) NMR experiments the S-isomers were shown to bind with a higher affinity and a conformation similar to that preferred in solution, in contrast to the R-isomer. The fact that the S-form of the propranolol enantiomer is pre-arranged for binding to the protein is also observed for a crystal structure of dihydroxy-(S)-propranolol and Cel7A presented herein. Whereas the binding of propranolol is entropy driven, the complexation with the dihydroxy analogue is anticipated to be favored also by an enthalpic term, such as for its enantiomer, that is, dihydroxy-(R)-propranolol, because hydrogen-bond donation replaces the corresponding bonding from hydroxyl groups in glucosyl residues of the natural substrate. In addition to a favorable entropy component, albeit lesser in magnitude, this represents an effect of enthalpy-to-entropy compensation in ligand-protein interactions.
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Affiliation(s)
- Christoffer Hamark
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Jens Landström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | | | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 75007, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 75007, Uppsala, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
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16
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Watt JE, Hughes GR, Walpole S, Monaco S, Stephenson GR, Bulman Page PC, Hemmings AM, Angulo J, Chantry A. Discovery of Small Molecule WWP2 Ubiquitin Ligase Inhibitors. Chemistry 2018; 24:17677-17680. [PMID: 30207403 DOI: 10.1002/chem.201804169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 12/20/2022]
Abstract
We have screened small molecule libraries specifically for inhibitors that target WWP2, an E3 ubiquitin ligase associated with tumour outgrowth and spread. Selected hits demonstrated dose-dependent WWP2 inhibition, low micromolar IC50 values, and inhibition of PTEN substrate-specific ubiquitination. Binding to WWP2 was confirmed by ligand-based NMR spectroscopy. Furthermore, we used a combination of STD NMR, the recently developed DEEP-STD NMR approach, and docking calculations, to propose for the first time an NMR-validated 3D molecular model of a WWP2-inhibitor complex. These first generation WWP2 inhibitors provide a molecular framework for informing organic synthetic approaches to improve activity and selectivity.
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Affiliation(s)
- Jessica E Watt
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Gregory R Hughes
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | | | - Andrew M Hemmings
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Chantry
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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