1
|
Lyu Y, He R, Hu J, Wang C, Gong X. Prediction of the tetramer protein complex interaction based on CNN and SVM. Front Genet 2023; 14:1076904. [PMID: 36777731 PMCID: PMC9909274 DOI: 10.3389/fgene.2023.1076904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions play an important role in life activities. The study of protein-protein interactions helps to better understand the mechanism of protein complex interaction, which is crucial for drug design, protein function annotation and three-dimensional structure prediction of protein complexes. In this paper, we study the tetramer protein complex interaction. The research has two parts: The first part is to predict the interaction between chains of the tetramer protein complex. In this part, we proposed a feature map to represent a sample generated by two chains of the tetramer protein complex, and constructed a Convolutional Neural Network (CNN) model to predict the interaction between chains of the tetramer protein complex. The AUC value of testing set is 0.6263, which indicates that our model can be used to predict the interaction between chains of the tetramer protein complex. The second part is to predict the tetramer protein complex interface residue pairs. In this part, we proposed a Support Vector Machine (SVM) ensemble method based on under-sampling and ensemble method to predict the tetramer protein complex interface residue pairs. In the top 10 predictions, when at least one protein-protein interaction interface is correctly predicted, the accuracy of our method is 82.14%. The result shows that our method is effective for the prediction of the tetramer protein complex interface residue pairs.
Collapse
Affiliation(s)
- Yanfen Lyu
- Department of Mathematics and PhysicsScience and Engineering, Hebei University of Engineering, Handan, China
| | - Ruonan He
- School of Information, Renmin University of China, Beijing, China
| | - Jingjing Hu
- Department of Mathematics and PhysicsScience and Engineering, Hebei University of Engineering, Handan, China
| | - Chunxia Wang
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China,*Correspondence: Chunxia Wang, ; Xinqi Gong,
| | - Xinqi Gong
- Mathematical Intelligence Application Lab, Institute for Mathematical Sciences, School of Math, Renmin University of China, Beijing, China,Beijing Academy of Artificial Intelligence, Beijing, China,*Correspondence: Chunxia Wang, ; Xinqi Gong,
| |
Collapse
|
2
|
Musnier A, Bourquard T, Vallet A, Mathias L, Bruneau G, Ayoub MA, Travert O, Corde Y, Gallay N, Boulo T, Cortes S, Watier H, Crépieux P, Reiter E, Poupon A. A New in Silico Antibody Similarity Measure Both Identifies Large Sets of Epitope Binders with Distinct CDRs and Accurately Predicts Off-Target Reactivity. Int J Mol Sci 2022; 23:ijms23179765. [PMID: 36077163 PMCID: PMC9456297 DOI: 10.3390/ijms23179765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
Developing a therapeutic antibody is a long, tedious, and expensive process. Many obstacles need to be overcome, such as biophysical properties (issues of solubility, stability, weak production yields, etc.), as well as cross-reactivity and subsequent toxicity, which are major issues. No in silico method exists today to solve such issues. We hypothesized that if we were able to properly measure the similarity between the CDRs of antibodies (Ab) by considering not only their evolutionary proximity (sequence identity) but also their structural features, we would be able to identify families of Ab recognizing similar epitopes. As a consequence, Ab within the family would share the property to recognize their targets, which would allow (i) to identify off-targets and forecast the cross-reactions, and (ii) to identify new Ab specific for a given target. Testing our method on 238D2, an antagonistic anti-CXCR4 nanobody, we were able to find new nanobodies against CXCR4 and to identify influenza hemagglutinin as an off-target of 238D2.
Collapse
Affiliation(s)
- Astrid Musnier
- MAbSilico, 1 Impasse du Palais, 37000 Tours, France
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Thomas Bourquard
- MAbSilico, 1 Impasse du Palais, 37000 Tours, France
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Amandine Vallet
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
- Synthélis, BIOPOLIS, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Laetitia Mathias
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Gilles Bruneau
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Mohammed Akli Ayoub
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Ophélie Travert
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | | | - Nathalie Gallay
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Thomas Boulo
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
| | - Sandra Cortes
- Synthélis, BIOPOLIS, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Hervé Watier
- Centre Hospitalier Régional Universitaire de Tours, Université de Tours, EA 7501, 37032 Tours, France
| | - Pascale Crépieux
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
- Inria, Inria Saclay-Île-de-France, 91120 Palaiseau, France
| | - Eric Reiter
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
- Inria, Inria Saclay-Île-de-France, 91120 Palaiseau, France
| | - Anne Poupon
- Physiologie de la Reproduction et des Comportements, INRAE UMR-0085, CNRS UMR-7247, Université de Tours, 37380 Nouzilly, France
- Inria, Inria Saclay-Île-de-France, 91120 Palaiseau, France
- Correspondence:
| |
Collapse
|
3
|
A Two-Layer SVM Ensemble-Classifier to Predict Interface Residue Pairs of Protein Trimers. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25194353. [PMID: 32977371 PMCID: PMC7582526 DOI: 10.3390/molecules25194353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/29/2022]
Abstract
Study of interface residue pairs is important for understanding the interactions between monomers inside a trimer protein–protein complex. We developed a two-layer support vector machine (SVM) ensemble-classifier that considers physicochemical and geometric properties of amino acids and the influence of surrounding amino acids. Different descriptors and different combinations may give different prediction results. We propose feature combination engineering based on correlation coefficients and F-values. The accuracy of our method is 65.38% in independent test set, indicating biological significance. Our predictions are consistent with the experimental results. It shows the effectiveness and reliability of our method to predict interface residue pairs of protein trimers.
Collapse
|
4
|
Wiehe K, Nicely NI, Lockwood B, Kuraoka M, Anasti K, Arora S, Bowman CM, Stolarchuk C, Parks R, Lloyd KE, Xia SM, Duffy R, Shen X, Kyratsous CA, Macdonald LE, Murphy AJ, Scearce RM, Moody MA, Alam SM, Verkoczy L, Tomaras GD, Kelsoe G, Haynes BF. Immunodominance of Antibody Recognition of the HIV Envelope V2 Region in Ig-Humanized Mice. THE JOURNAL OF IMMUNOLOGY 2016; 198:1047-1055. [PMID: 28011932 DOI: 10.4049/jimmunol.1601640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/18/2016] [Indexed: 12/13/2022]
Abstract
In the RV144 gp120 HIV vaccine trial, decreased transmission risk was correlated with Abs that reacted with a linear epitope at a lysine residue at position 169 (K169) in the HIV-1 envelope (Env) V2 region. The K169 V2 response was restricted to Abs bearing Vλ rearrangements that expressed aspartic acid/glutamic acid in CDR L2. The AE.A244 gp120 in AIDSVAX B/E also bound to the unmutated ancestor of a V2-glycan broadly neutralizing Ab, but this Ab type was not induced in the RV144 trial. In this study, we sought to determine whether immunodominance of the V2 linear epitope could be overcome in the absence of human Vλ rearrangements. We immunized IgH- and Igκ-humanized mice with the AE.A244 gp120 Env. In these mice, the V2 Ab response was focused on a linear epitope that did not include K169. V2 Abs were isolated that used the same human VH gene segment as an RV144 V2 Ab but paired with a mouse λ L chain. Structural characterization of one of these V2 Abs revealed how the linear V2 epitope could be engaged, despite the lack of aspartic acid/glutamic acid encoded in the mouse repertoire. Thus, despite the absence of the human Vλ locus in these humanized mice, the dominance of Vλ pairing with human VH for HIV-1 Env V2 recognition resulted in human VH pairing with mouse λ L chains instead of allowing otherwise subdominant V2-glycan broadly neutralizing Abs to develop.
Collapse
Affiliation(s)
- Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710; .,Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Bradley Lockwood
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | | | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Sabrina Arora
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Cindy M Bowman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Christina Stolarchuk
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Ryan Duffy
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | | | | | | | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710.,Department of Immunology, Duke University, Durham, NC 27710.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710; and
| | - Laurent Verkoczy
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710; and
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710.,Department of Immunology, Duke University, Durham, NC 27710
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710.,Department of Immunology, Duke University, Durham, NC 27710
| |
Collapse
|
5
|
Jones TD, Carter PJ, Plückthun A, Vásquez M, Holgate RGE, Hötzel I, Popplewell AG, Parren PWHI, Enzelberger M, Rademaker HJ, Clark MR, Lowe DC, Dahiyat BI, Smith V, Lambert JM, Wu H, Reilly M, Haurum JS, Dübel S, Huston JS, Schirrmann T, Janssen RAJ, Steegmaier M, Gross JA, Bradbury ARM, Burton DR, Dimitrov DS, Chester KA, Glennie MJ, Davies J, Walker A, Martin S, McCafferty J, Baker MP. The INNs and outs of antibody nonproprietary names. MAbs 2016; 8:1-9. [PMID: 26716992 PMCID: PMC4966553 DOI: 10.1080/19420862.2015.1114320] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
An important step in drug development is the assignment of an International Nonproprietary Name (INN) by the World Health Organization (WHO) that provides healthcare professionals with a unique and universally available designated name to identify each pharmaceutical substance. Monoclonal antibody INNs comprise a –mab suffix preceded by a substem indicating the antibody type, e.g., chimeric (-xi-), humanized (-zu-), or human (-u-). The WHO publishes INN definitions that specify how new monoclonal antibody therapeutics are categorized and adapts the definitions to new technologies. However, rapid progress in antibody technologies has blurred the boundaries between existing antibody categories and created a burgeoning array of new antibody formats. Thus, revising the INN system for antibodies is akin to aiming for a rapidly moving target. The WHO recently revised INN definitions for antibodies now to be based on amino acid sequence identity. These new definitions, however, are critically flawed as they are ambiguous and go against decades of scientific literature. A key concern is the imposition of an arbitrary threshold for identity against human germline antibody variable region sequences. This leads to inconsistent classification of somatically mutated human antibodies, humanized antibodies as well as antibodies derived from semi-synthetic/synthetic libraries and transgenic animals. Such sequence-based classification implies clear functional distinction between categories (e.g., immunogenicity). However, there is no scientific evidence to support this. Dialog between the WHO INN Expert Group and key stakeholders is needed to develop a new INN system for antibodies and to avoid confusion and miscommunication between researchers and clinicians prescribing antibodies.
Collapse
Affiliation(s)
- Tim D Jones
- a Antitope Ltd. (part of Abzena Plc.), Babraham Research Campus , Cambridge CB22 3AT , UK
| | - Paul J Carter
- b Genentech Inc., 1 DNA Way , South San Francisco , CA 94080 , USA
| | - Andreas Plückthun
- c Department of Biochemistry , University of Zurich , Zurich CH-8057 , Switzerland
| | - Max Vásquez
- d Adimab LLC., 7 Lucent Drive , Lebanon , NH 03766 , USA
| | - Robert G E Holgate
- a Antitope Ltd. (part of Abzena Plc.), Babraham Research Campus , Cambridge CB22 3AT , UK
| | - Isidro Hötzel
- b Genentech Inc., 1 DNA Way , South San Francisco , CA 94080 , USA
| | | | - Paul W H I Parren
- f Genmab, PO Box 85199, 3508 AD , Utrecht , The Netherlands.,g Leiden University Medical Center, Department of Immunohematology and Blood Transfusion , Leiden University Medical Center , Albinusdreef 2, 2333 ZA Leiden , The Netherlands
| | - Markus Enzelberger
- h MorphoSys AG., Lena-Christ-Str. 48, 82152 Martinsried/Planegg , Germany
| | | | - Michael R Clark
- i Clark Antibodies Ltd., 11 Wellington Street , Cambridge CB1 1HW , UK
| | - David C Lowe
- j MedImmune Ltd., Milstein Building, Granta Park , Cambridge CB21 6GH , UK
| | | | | | - John M Lambert
- m ImmunoGen Inc., 830 Winter Street , Waltham , MA 02451-1477 , USA
| | - Herren Wu
- n MedImmune., One MedImmune Way , Gaithersburg , MD 20878 , USA
| | - Mary Reilly
- o Opsona Therapeutics Ltd., 2nd Floor, Ashford House , Tara Street , Dublin 2 , Ireland
| | - John S Haurum
- p F-Star Biotechnology Ltd., Babraham Research Campus , Cambridge CB22 3AT , UK
| | - Stefan Dübel
- q Technische Universität Braunschweig., Institute of Biochemistry, Biotechnology and Bioinformatics Spielmannstr. 7 , 38106 Braunschweig , Germany
| | - James S Huston
- r The Antibody Society & Huston BioConsulting LLC. , 270 Pleasant Street #A206, Watertown , MA 02472 , USA
| | | | | | - Martin Steegmaier
- u Roche Pharmaceutical Research and Early Development,. Large Molecule Research, Roche Innovation Center Penzberg , 82377 Penzberg , Germany
| | - Jane A Gross
- v Emergent BioSolutions. , 2401 4th Avenue, Suite 1050, Seattle , WA 98121 , USA
| | - Andrew R M Bradbury
- w Biosciences Division., MS-M888, TA-43, HRL-1, Building 1, Los Alamos National Laboratory , Los Alamos , NM 87545 , USA
| | - Dennis R Burton
- x The Scripps Research Institute., 10550 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Dimiter S Dimitrov
- y Protein Interactions Section., Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute , Frederick , MD 21702 , USA
| | - Kerry A Chester
- z UCL Cancer Institute., 72 Huntley Street , London WC1E 6BT , UK
| | - Martin J Glennie
- aa Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton General Hospital , Southampton , Hampshire SO16 6YD , UK
| | - Julian Davies
- ab Lilly Biotechnology Center San Diego , CA 92121 , USA
| | - Adam Walker
- ac GSK., Addenbrooke's Centre for Clinical Investigation, Addenbrooke's Hospital, Hills Road , Cambridge , CB2 2GG , UK
| | - Steve Martin
- ad GSK, Medicines Research Centre, Gunnels Wood Road , Stevenage , Herts , SG1 2NY , UK
| | - John McCafferty
- ae Iontas Ltd., Babraham Research Campus , Cambridge CB22 3AT , UK
| | - Matthew P Baker
- a Antitope Ltd. (part of Abzena Plc.), Babraham Research Campus , Cambridge CB22 3AT , UK
| |
Collapse
|
6
|
Haji-Ghassemi O, Müller-Loennies S, Rodriguez T, Brade L, Grimmecke HD, Brade H, Evans SV. The Combining Sites of Anti-lipid A Antibodies Reveal a Widely Utilized Motif Specific for Negatively Charged Groups. J Biol Chem 2016; 291:10104-18. [PMID: 26933033 DOI: 10.1074/jbc.m115.712448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/29/2023] Open
Abstract
Lipopolysaccharide dispersed in the blood by Gram-negative bacteria can be a potent inducer of septic shock. One research focus has been based on antibody sequestration of lipid A (the endotoxic principle of LPS); however, none have been successfully developed into a clinical treatment. Comparison of a panel of anti-lipid A antibodies reveals highly specific antibodies produced through distinct germ line precursors. The structures of antigen-binding fragments for two homologous mAbs specific for lipid A, S55-3 and S55-5, have been determined both in complex with lipid A disaccharide backbone and unliganded. These high resolution structures reveal a conserved positively charged pocket formed within the complementarity determining region H2 loops that binds the terminal phosphates of lipid A. Significantly, this motif occurs in unrelated antibodies where it mediates binding to negatively charged moieties through a range of epitopes, including phosphorylated peptides used in diagnostics and therapeutics. S55-3 and S55-5 have combining sites distinct from anti-lipid A antibodies previously described (as a result of their separate germ line origin), which are nevertheless complementary both in shape and charge to the antigen. S55-3 and S55-5 display similar avidity toward lipid A despite possessing a number of different amino acid residues in their combining sites. Binding of lipid A occurs independent of the acyl chains, although the GlcN-O6 attachment point for the core oligosaccharide is buried in the combining site, which explains their inability to recognize LPS. Despite their lack of therapeutic potential, the observed motif may have significant immunological implications as a tool for engineering recombinant antibodies.
Collapse
Affiliation(s)
- Omid Haji-Ghassemi
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Sven Müller-Loennies
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Teresa Rodriguez
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Lore Brade
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Hans-Dieter Grimmecke
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Helmut Brade
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, Borstel D-23845, Germany
| | - Stephen V Evans
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| |
Collapse
|
7
|
Caoili SEC. An integrative structure-based framework for predicting biological effects mediated by antipeptide antibodies. J Immunol Methods 2015; 427:19-29. [PMID: 26410103 DOI: 10.1016/j.jim.2015.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/30/2015] [Accepted: 09/20/2015] [Indexed: 01/18/2023]
Abstract
A general framework is presented for predicting quantitative biological effects mediated by antipeptide antibodies, primarily on the basis of antigen structure (possibly featuring intrinsic disorder) analyzed to estimate epitope-paratope binding affinities, which in turn is considered within the context of dose-response relationships as regards antibody concentration. This is illustrated mainly using an approach based on protein structural energetics, whereby expected amounts of solvent-accessible surface area buried upon epitope-paratope binding are related to the corresponding binding affinity, which is estimated from putative B-cell epitope structure with implicit treatment of paratope structure, for antipeptide antibodies either reacting with peptides or cross-reacting with cognate protein antigens. Key methods described are implemented in SAPPHIRE/SUITE (Structural-energetic Analysis Program for Predicting Humoral Immune Response Epitopes/SAPPHIRE User Interface Tool Ensemble; publicly accessible via http://freeshell.de/~badong/suite.htm). Representative results thus obtained are compared with published experimental data on binding affinities and quantitative biological effects, with special attention to loss of paratope sidechain conformational entropy (neglected in previous analyses) and in light of key in-vivo constraints on antigen-antibody binding affinity and antibody-mediated effects. Implications for further refinement of B-cell epitope prediction methods are discussed as regards envisioned biomedical applications including the development of prophylactic and therapeutic antibodies, peptide-based vaccines and immunodiagnostics.
Collapse
Affiliation(s)
- Salvador Eugenio C Caoili
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines.
| |
Collapse
|
8
|
Feil SC, Holien JK, Morton CJ, Hancock NC, Thompson PE, Parker MW. Discovery of Phosphodiesterase-4 Inhibitors: Serendipity and Rational Drug Design. Aust J Chem 2014. [DOI: 10.1071/ch14397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phosphodiesterase 4 (PDE4), the primary cyclic AMP-hydrolysing enzyme in cells, is a promising drug target for a wide range of mental disorders including Alzheimer's and Huntington's diseases, schizophrenia, and depression, plus a range of inflammatory diseases including chronic obstructive pulmonary disease, asthma, and rheumatoid arthritis. However, targeting PDE4 is complicated by the fact that the enzyme is encoded by four very closely related genes, together with 20 distinct isoforms as a result of mRNA splicing, and inhibition of some of these isoforms leads to intolerable side effects in clinical trials. With almost identical active sites between the isoforms, X-ray crystallography has played a critical role in the discovery and development of safer PDE4 inhibitors. Here we describe our discovery of a novel class of highly potent PDE4 via a ‘virtuous’ cycle of structure-based drug design and serendipity.
Collapse
|
9
|
Antibodies that bind complex glycosaminoglycans accumulate in the Golgi. Proc Natl Acad Sci U S A 2013; 110:11958-63. [PMID: 23818632 DOI: 10.1073/pnas.1308620110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Light (L) chains that edit anti-DNA heavy (H) chains rescue B-cell development by suppressing DNA binding. However, exceptional editor L chains allow B cells to reach splenic compartments even though their B-cell receptors remain autoreactive. Such incompletely edited B cells express multireactive antibodies that accumulate in the Golgi and are released as insoluble, amyloid-like immune complexes. Here, we examine examples of incomplete editing from the analysis of variable to joining (VJ) gene junction of the variable (Vλx) editor L chain. When paired with the anti-DNA heavy chain, VH56R, the Vλx variants yield antibodies with differing specificities, including glycosaminoglycan reactivity. Our results implicate these specificities in the evasion of receptor editing through intracellular sequestration of IgM and the release of insoluble IgM complexes. Our findings can be extrapolated to human L chains and have implications for understanding a latent component of the Ig repertoire that could exert pathogenic and protective functions.
Collapse
|
10
|
Klein FAC, Zeder-Lutz G, Cousido-Siah A, Mitschler A, Katz A, Eberling P, Mandel JL, Podjarny A, Trottier Y. Linear and extended: a common polyglutamine conformation recognized by the three antibodies MW1, 1C2 and 3B5H10. Hum Mol Genet 2013; 22:4215-23. [PMID: 23777629 DOI: 10.1093/hmg/ddt273] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A long-standing pathomechanistic model proposes that the polyglutamine (polyQ)-length-dependent toxicity threshold observed in all polyQ diseases is triggered by a conformational change within the monomer that occurs only above a certain polyQ length. If true, this yet undefined and elusive mutant-specific toxic conformation would constitute a direct therapeutic target. Three anti-polyQ antibodies-MW1, 1C2 and 3B5H10-have been extensively used to probe the conformation of polyQ. The crystal structure of the MW1 epitope reveals a linear, non-pathogenic polyQ. In contrast, although the detailed structure of its epitope is unknown, the 3B5H10 antibody is widely advertised and used as a conformational antibody that recognizes the toxic conformation of expanded polyQ. We solved the crystal structure of the 1C2 antigen-binding domain (1C2-Fab) and performed a direct comparison between the 1C2, MW1 and 3B5H10 structures. The MW1 and 1C2 antibodies have similar sequences and structures, consistent with their binding to short polyQ and their polyQ length-discrimination properties. Unexpectedly, the 3B5H10 antibody also shares striking features with MW1 and 1C2, which prompted us to revisit its binding properties. We show that the 3B5H10 epitope is actually a short, non-pathogenic polyQ. All three antibodies MW1, 1C2 and 3B5H10 interact similarly with polyQ of various lengths, and bind small polyQ epitopes in similar linear and extended conformations. Together with studies published during the recent years, our work argues against the hypothesis that a mutant-specific conformation in monomeric polyQ molecules is the toxic entity responsible for polyQ diseases.
Collapse
Affiliation(s)
- Fabrice A C Klein
- Present address: Computational Chemistry and Biology Group-DETEMA, Facultad de Química, UdelaR, Isidoro de María 1620 piso 3, CC1157, Montevideo, Uruguay
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Nankervis JL, Feil SC, Hancock NC, Zheng Z, Ng HL, Morton CJ, Holien JK, Ho PW, Frazzetto MM, Jennings IG, Manallack DT, John Martin T, Thompson PE, Parker MW. Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2. Bioorg Med Chem Lett 2011; 21:7089-93. [DOI: 10.1016/j.bmcl.2011.09.109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/21/2011] [Accepted: 09/21/2011] [Indexed: 12/21/2022]
|