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(12) United States Patent (10) Patent No.: US 8,877,688 B2 Vasquez Et Al
US008877688B2 (12) United States Patent (10) Patent No.: US 8,877,688 B2 Vasquez et al. (45) Date of Patent: *Nov. 4, 2014 (54) RATIONALLY DESIGNED, SYNTHETIC (56) References Cited ANTIBODY LIBRARIES AND USES THEREFOR U.S. PATENT DOCUMENTS 4.946,778 A 8, 1990 Ladner et al. (75) Inventors: Maximiliano Vasquez, Palo Alto, CA 5,118,605 A 6/1992 Urdea (US); Michael Feldhaus, Grantham, NH 5,223,409 A 6/1993 Ladner et al. 5,283,173 A 2f1994 Fields et al. (US); Tillman U. Gerngross, Hanover, 5,380,833. A 1, 1995 Urdea NH (US); K. Dane Wittrup, Chestnut 5,525.490 A 6/1996 Erickson et al. Hill, MA (US) 5,530,101 A 6/1996 Queen et al. 5,565,332 A 10/1996 Hoogenboom et al. (73) Assignee: Adimab, LLC, Lebanon, NH (US) 5,571,698 A 11/1996 Ladner et al. 5,618,920 A 4/1997 Robinson et al. (*) Notice: Subject to any disclaimer, the term of this 5,658,727 A 8, 1997 Barbas et al. patent is extended or adjusted under 35 (Continued) U.S.C. 154(b) by 747 days. FOREIGN PATENT DOCUMENTS This patent is Subject to a terminal dis claimer. DE 19624562 A1 1, 1998 WO WO-88.01649 A1 3, 1988 (21) Appl. No.: 12/404,059 (Continued) OTHER PUBLICATIONS (22) Filed: Mar 13, 2009 Rader et al. (Jul. 21, 1998) Proceedings of the National Academy of (65) Prior Publication Data Sciences USA vol. 95 pp. 8910 to 8915.* US 201O/OO5638.6 A1 Mar. 4, 2010 (Continued) Primary Examiner — Heather Calamita Related U.S. -
Phage Display Libraries for Antibody Therapeutic Discovery and Development
antibodies Review Phage Display Libraries for Antibody Therapeutic Discovery and Development Juan C. Almagro 1,2,* , Martha Pedraza-Escalona 3, Hugo Iván Arrieta 3 and Sonia Mayra Pérez-Tapia 3 1 GlobalBio, Inc., 320, Cambridge, MA 02138, USA 2 UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico 3 CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico * Correspondence: [email protected] Received: 24 June 2019; Accepted: 15 August 2019; Published: 23 August 2019 Abstract: Phage display technology has played a key role in the remarkable progress of discovering and optimizing antibodies for diverse applications, particularly antibody-based drugs. This technology was initially developed by George Smith in the mid-1980s and applied by John McCafferty and Gregory Winter to antibody engineering at the beginning of 1990s. Here, we compare nine phage display antibody libraries published in the last decade, which represent the state of the art in the discovery and development of therapeutic antibodies using phage display. We first discuss the quality of the libraries and the diverse types of antibody repertoires used as substrates to build the libraries, i.e., naïve, synthetic, and semisynthetic. Second, we review the performance of the libraries in terms of the number of positive clones per panning, hit rate, affinity, and developability of the selected antibodies. Finally, we highlight current opportunities and challenges pertaining to phage display platforms and related display technologies. -
The Generation of Synthetic Antibody Reagents for Clostridium Difficile Toxins
The Generation of Synthetic Antibody Reagents for Clostridium difficile Toxins by Sylvia Cien Man Wong A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Sylvia Wong 2013 The Generation of Synthetic Antibody Reagents for Clostridium difficile Toxins Sylvia Cien Man Wong Master of Science Graduate Department of Molecular Genetics University of Toronto 2013 Abstract The symptoms of C. difficile infection are primarily caused by two toxins, toxin A and toxin B. Some strains produce a third known toxin, C. difficile transferase (CDT) toxin; however, its role in virulence remains unclear. I aimed to develop synthetic antibodies using phage display technology to block toxin entry by binding to the receptor-binding domain (RBD) of the toxins. I first described the generation of anti-toxin A and anti-toxin B Fabs. I presented Fab A3, which bound to the full-length toxin, but did not functionally inhibit toxin entry. In chapter 2, I described the generation of novel anti-CDTb antibodies. I further demonstrated that five of the anti-CDTb antibodies could functionally inhibit CDTb binding in an ELISA-based assay and on cultured cells. These antibodies can be used as tools to understand the toxins’ role in human disease and potentially be used as therapeutics. ii Acknowledgments I am very thankful for having the chance to work with many great scientists in Dr. Jason Moffat’s and Dr. Sachdev Sidhu’s labs. These people made the lab a very motivating, supportive, and intellectually stimulating environment, where I was able to learn and expand my critical thinking skills. -
Affimer Proteins Inhibit Immune Complex Binding to Fcγriiia with High Specificity Through Competitive and Allosteric Modes of Action
Affimer proteins inhibit immune complex binding to FcγRIIIa with high specificity through competitive and allosteric modes of action James I. Robinsona,b, Euan W. Baxtera,b,1, Robin L. Owenc,1, Maren Thomsend,1, Darren C. Tomlinsond,e,1, Mark P. Waterhousea,b,1, Stephanie J. Wina,b, Joanne E. Nettleshipf,g, Christian Tiedee, Richard J. Fosterd,h, Raymond J. Owensf,g, Colin W. G. Fishwickd,h, Sarah A. Harrisd,i, Adrian Goldmane,j, Michael J. McPhersond,e,2, and Ann W. Morgana,b,2 aLeeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds LS9 7TF, United Kingdom; bNational Institute of Health Research-Leeds Biomedical Research Centre, Chapel Allerton Hospital, Leeds LS7 4SA, United Kingdom; cDiamond Light Source, Didcot OX11 0DE, United Kingdom; dAstbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; eBioScreening Technology Group, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; fOxford Protein Production Facility-United Kingdom Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, United Kingdom; gDivision of Structural Biology, Wellcome Trust Centre for Genomic Medicine, Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, United Kingdom; hSchool of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; iSchool of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom; and jFaculty of Biological and Environmental Sciences, University of Helsinki, FIN-0014 Helsinki, Finland Edited by Lawrence Steinman, Stanford University School of Medicine, Stanford, CA, and approved November 17, 2017 (received for review May 15, 2017) Protein–protein interactions are essential for the control of cellular domains and chains, poor stability, high production costs, and functions and are critical for regulation of the immune system. -
Wo 2008/048970 A2
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date (10) International Publication Number 24 April 2008 (24.04.2008) PCT WO 2008/048970 A2 (51) International Patent Classification: (72) Inventors; and A61K 39/395 (2006 01) (75) Inventors/Applicants (for US only): JOHNSTON, Stephen, Albert [US/US], 8606 S Dorsey Lane, Tempe, (21) International Application Number: AZ 85284 (US) WOODBURY, Neal [US/US], 1001 S PCT/US2007/081536 McAllister Avenue, Tempe, AZ 85287 (US) CHAPUT, John, C. [US/US], 3069 E Dry Creed Road, Phoenix, AZ (22) International Filing Date: 16 October 2007 (16 10 2007) 85048 (US) DIEHNELT, Chris, W. [US/US], 20941 N Leona Boulevard, Maπ copa, AZ 85239 (US) YAN, Hao (25) Filing Language: English [CN/US], 1300 N Brentwood Place, Chandler, AZ 85224 (26) Publication Language: English (US) (74) Agent: LIEBESCHUETZ, Joe, Townsend and Townsend (30) Priority Data: and Crew LLP , 8th floor, Two Embarcadero Center, San 60/852,040 16 October 2006 (16 10 2006) US Francisco, CA 941 11-3834 (US) 60/975,442 26 September 2007 (26 09 2007) US (81) Designated States (unless otherwise indicated, for every (71) Applicant (for all designated States except US): THE kind of national protection available): AE, AG, AL, AM, ARIZONA BOARD OF REGENTS, A BODY COR¬ AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, PORATE OF THE STATE OF ARIZONA acting for CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, and on behalf -
Affimer Technology Nov 2017
Non-confidential Technical Introduction to the Affimer® Technology for Therapeutics and Reagents Dr. Alastair Smith Chief Executive, Avacta Group plc Introduction Avacta Group plc AIM: AVCT • 80 staff over two sites: • 1300 m2 of bespoke laboratory, production and logistics space in Wetherby. • 790 m2 of bespoke laboratory space in Cambridge. • Balance sheet to support existing plans. Wetherby • Experienced management team with interests aligned to shareholders. • Strongly supportive shareholder base. Cambridge London Shareholders >5% . IP Group plc 24.8% Lombard Odier 11.4% Aviva 9.6% Baillie Gifford 7.2% Ruffer LLP 7.1% Fidelity 5.9% J O Hambro 5.7% © Avacta Group plc 2 Leadership Team Dr Alastair Smith, CEO Dr Matt Johnson, CTO Mr Tony Gardiner, CFO • Over 10 years experience as a public • Genetics & Microbiology Molecular • Joined Avacta from AHR, an company CEO Biology international architecture practice • Was a leading UK biophysicist - founded • 8 years at Abcam becoming global • Chief Financial Officer of AIM listed Avacta in 2006 Head of R&D Fusion IP plc 2007 – 2011 which was acquired by IP Group plc in 2014 • World class scientific and technical • Joined Avacta in 2014 knowledge with a highly commercial • Joined Avacta in 2016 mindset Dr Philippe Cotrel, CCO Dr Amrik Basran, CSO • Over 20 years’ commercial experience in senior • Over 10 years’ experience of both the biotech and positions in Amersham Pharmacia Biotech, Oxford pharma industries Glycosciences, Affymetrix and Abcam • Director of Protein Biosciences at Domantis, Head of • Commercial Director of Abcam since 2008 – grew Topical Delivery (Biopharm) at GSK revenue from £36.7m to £144m over a 7-year period • Joined Avacta in 2013 • Joined Avacta in 2016 © Avacta Group plc 3 Affimer Technology Affimer®: A proprietary protein scaffold with key technical benefits What is an Affimer? Binding Surface • Based on a naturally occurring proteins (cystatins) and engineered to stably display two loops which create a binding surface. -
Computational Design of Peptide Ligands Based on Antibody-Antigen Interface Properties
Computational design of peptide ligands based on antibody-antigen interface properties By Benjamin Thomas VIART Thesis Advisor Prof. Dra. Liza Figueiredo Felicori Vilela Thesis Co-advisor Dr. Franck Molina Universidade Federal de Minas Gerais Instituto de Ciências Biológicas Programa de Pós-Graduação em Bioinformática Avenida Presidente Antônio Carlos, 6627 Pampulha 31270-901 Belo Horizonte - MG To my parents, ii Acknowledgments • Firstly, I would like to express my sincere gratitude to my advisor Dr. Prof. Liza Figueiredo Felicori Vilela for the continuous support of my Ph.D study, for her patience, motivation and knowledge. Her advices and guidance helped me better understand the scientific gait, the rules of research, the importance of the details. I would like to thank her as well for making feel welcome in Brazil, helping me with the transition to this new culture that is now part of me as the French culture is part of her. • Secondly, I would like to deeply thank my co-advisor Dr Franck Molina, without whom I would never have done this PhD. I am forever grateful to him for believing in me and helping me achieve this goal. • From the department, I would like to thanks Prof. Jader, Prof. Vasco, Prof. Miguel, Prof. Lucas, Prof. Gloria as well as Sheila. • This thesis is dedicated to my parents, Frédéric and Françoise Viart, who helped me throughout my life to become a good person. I thank them for their unconditional love and support. • I would like to thank all my family, especially my sisters, Sophie and Lisa, for their smiles and grimaces; my grand-parents, Bob, Nanou and Mémé for their support and love and also my uncle, Bruno, for all his help when I was in first year of medical school. -
Nanobodies and Recombinant Binders in Cell Biology
JCB: Review Nanobodies and recombinant binders in cell biology Jonas Helma,1 M. Cristina Cardoso,2 Serge Muyldermans,3 and Heinrich Leonhardt1 1Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany 2Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany 3Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium Antibodies are key reagents to investigate cellular pro- exclusive to small and stable binding molecules and cannot cesses. The development of recombinant antibodies and be performed easily with full-length antibodies, as a result of crucial inter- and intramolecular disulphide bridges that do not binders derived from natural protein scaffolds has ex- form in the cytoplasm. Thus, researchers have found a plethora panded traditional applications, such as immunofluores- of new applications in which binders have been combined with cence, binding arrays, and immunoprecipitation. In enzymatic or structural functionalities in living systems. addition, their small size and high stability in ectopic en- The development of in vitro screening techniques has been a decisive step for the rise and generation of recombinant vironments have enabled their use in all areas of cell re- binding reagents. These methods include classic phage display Downloaded from search, including structural biology, advanced microscopy, but also bacterial and yeast display as well as ribosomal and and intracellular expression. Understanding these novel mRNA display. With such in vitro display techniques at hand, directed evolution strategies and genetic manipulation of binder reagents as genetic modules that can be integrated into sequences allow targeted engineering of key features, such as cellular pathways opens up a broad experimental spec- specificity, valence, affinity, and stability, enable derivatization trum to monitor and manipulate cellular processes. -
EURL ECVAM Recommendation on Non-Animal-Derived Antibodies
EURL ECVAM Recommendation on Non-Animal-Derived Antibodies EUR 30185 EN Joint Research Centre This publication is a Science for Policy report by the Joint Research Centre (JRC), the European Commission’s science and knowledge service. It aims to provide evidence-based scientific support to the European policymaking process. The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication. For information on the methodology and quality underlying the data used in this publication for which the source is neither Eurostat nor other Commission services, users should contact the referenced source. EURL ECVAM Recommendations The aim of a EURL ECVAM Recommendation is to provide the views of the EU Reference Laboratory for alternatives to animal testing (EURL ECVAM) on the scientific validity of alternative test methods, to advise on possible applications and implications, and to suggest follow-up activities to promote alternative methods and address knowledge gaps. During the development of its Recommendation, EURL ECVAM typically mandates the EURL ECVAM Scientific Advisory Committee (ESAC) to carry out an independent scientific peer review which is communicated as an ESAC Opinion and Working Group report. In addition, EURL ECVAM consults with other Commission services, EURL ECVAM’s advisory body for Preliminary Assessment of Regulatory Relevance (PARERE), the EURL ECVAM Stakeholder Forum (ESTAF) and with partner organisations of the International Collaboration on Alternative Test Methods (ICATM). Contact information European Commission, Joint Research Centre (JRC), Chemical Safety and Alternative Methods Unit (F3) Address: via E. -
Monobodies and Other Synthetic Binding Proteins for Expanding Protein Science
Reviews Protein Science DOI 10.1002/pro.3148 Monobodies and Other Synthetic Binding Proteins for Expanding Protein Science Fern Sha,1,4 Gabriel Salzman,1 Ankit Gupta1,2 and Shohei Koide1,2,3* 1Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA 2Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA 3Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY 10016, USA 4Present address, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20148, USA *Correspondence to: Shohei Koide, Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA. E-mail: [email protected] Abstract Synthetic binding proteins are constructed using non-antibody molecular scaffolds. Over the last two decades, in-depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, -
Introduction and Key Feature Comparison
Affimer® non-Antibody Binders for Affinity Applications: Introduction and Key Feature Comparison Affimer® non-Antibody Binders for Affinity Applications: Introduction and Key Feature Comparison 1 Contents Abstract Introduction Affinity-based applications in the detection, analysis and manipulation of protein targets In vitro applications Diagnostic applications Therapeutic applications Antibodies and their limitations as affinity binders Production considerations: ease, speed, cost and process control Size and structural complexity Stability under assay conditions Immobilisation onto solid support Success rate Limitations of antibodies as biosensors – stability, size and orientation Limitations of antibodies as therapeutics – immunogenicity, toxicity and 3D structure recognition Antibody engineering: future directions Alternatives to antibodies Engineered antibody fragments Aptamers Aptamer engineering – future enhancements Non-antibody protein scaffolds Affimer binders: what’s different? Affimer binders can be generated to almost any protein target, and show high discriminatory powers In practice: Development of novel Affimer diagnostic reagents for Zika virus outbreak management In practice: Affimer binders can be targeted to extracellular effector domains and allosteric regions of receptor proteins In practice: The ability of Affimer proteins to form multimers and fusion proteins allows fine tuning of therapeutic activity and stability in vivo Conclusion References Affimer® non-Antibody Binders for Affinity Applications: Introduction -
The Two Tortoitu Muutuu Tononi Mitin
THETWO TORTOITUUS MUUTUU20180022800A1 TONONI MITIN ( 19) United States (12 ) Patent Application Publication (10 ) Pub. No. : US 2018/ 0022800 A1 West et al. (43 ) Pub . Date : Jan . 25 , 2018 (54 ) BIOMARKER Publication Classification ( 51) Int. Ci. ( 71) Applicant: ISIS INNOVATION LIMITED , CO7K 16 /24 ( 2006 . 01 ) Oxford (GB ) A61K 31 / 56 ( 2006 .01 ) A61K 38 / 17 ( 2006 .01 ) GOIN 33868 (2006 . 01 ) (72 ) Inventors : Nathaniel Richard West, Oxford (GB ) ; A61K 38 /20 ( 2006 .01 ) Benjamin Michael Joseph Owens, (52 ) U . S . CI. Oxford (GB ) ; Ahmed Nabil Hegazy , CPC . .. CO7K 16 / 248 ( 2013 .01 ) ; GOIN 33 /6869 Oxford (GB ) ; Fiona Margaret Powrie , ( 2013 .01 ) ; A61K 38 / 204 ( 2013 . 01 ) ; A61K Oxford (GB ) 38 / 1793 ( 2013 .01 ) ; CO7K 16 / 241 ( 2013 .01 ) ; A61K 31 /56 ( 2013 .01 ) ; GOIN 2800 / 52 (2013 .01 ) ; GOIN 2800 /065 (2013 .01 ) ; COZK ( 21) Appl . No. : 15 /547 , 154 2317 / 76 ( 2013 . 01 ) ; GOIN 2333 / 5412 ( 2013. 01 ) ; CO7K 2317 / 24 (2013 .01 ) ; A61K ( 22 ) PCT Filed : Jan . 28 , 2016 2039 / 505 ( 2013 .01 ) ( 86 ) PCT No .: PCT /GB2016 /050185 (57 ) ABSTRACT The invention relates to methods of treating chronic intes $ 371 (c ) ( 1 ) , tinal inflammation and /or inflammatory bowel disease by ( 2 ) Date : Jul . 28 , 2017 administering an antagonist of oncostatin - M (OSM ) and / or OSM receptor - B (OSMR ) . The invention also relates to ( 30 ) Foreign Application Priority Data methods for diagnosing or prognosing chronic intestinal inflammation and /or inflammatory bowel disease in an indi Jan . 29 , 2015 (GB ) .. .. .. .. .. .. .. .. 1501480 .6 vidual and for predicting whether or not an individual will Jan . 29 , 2015 (GB )) .. .. .. .. .. .. .. .. .. .. .. .. .. 1501511 . 8 respond to an anti - TNFa therapy .