Kalyoncu Lab. on Antibody Engineering
OVERVIEW
Antibodies currently represent more than half of the total sales of all biopharmaceutical products and their market size has been growing steadily. Because nature uses antibodies to fight against diseases, they have many advantages for therapeutic and diagnostic uses such as being highly target-specific, low immunogenicity, longer half-life and faster clinical approval. Most of therapeutic antibodies are full-length, but smaller antibody fragments are gaining more attention over the last decade. Right now, antibody fragments represent 10% of approved antibody therapeutics on the market but this number is increasing exponentially. Kalyoncu Lab aims to design, discover, engineer and characterize antibody fragments for therapeutic and diagnostic applications.
RESEARCH INTERESTS
Our goal is to develop antibody fragments in several formats for therapeutic and diagnostic applications. Currently, our research interests are: (1) Development of antibody fragments such as Fab, scFv, VH from full-length antibodies and their test and characterization for therapeutic or diagnostic use. (2) Several protein engineering approaches such as linker design, protein fusions and conjugates to develop next-generation antibody fragments (3) Antibody discovery for novel targets by phage display and yeast surface display
Group Members
Kalyoncu Lab. on Antibody Engineering
Research Group Leader
Sibel KALYONCU
sibel.kalyoncu@ibg.edu.tr
+90 232 299 41 00
(5181)
+9
0 (232) 299 41 68
Aslı KURDEN PEKMEZCİ
Researcher
asli.kurden@ibg.edu.tr
Şuğra YÜCEER
MSc Student
sugra.yuceer@ibg.edu.tr
Smyrna ERGÖNÜL
MSc Student
smyrna.ergonul@ibg.edu.tr
Former Members
Aslı KURDEN PEKMEZCİ
Research Assistant
asli.kurden@ibg.edu.tr
Murat KARADAĞ
PhD Student
murat.karadag@ibg.edu.tr
Saniye Gül KAYA
MSc Student
saniyegul.kaya@msfr.ibg.edu.tr
Merve ARSLAN
PhD Student
merve.arslan@ibg.edu.tr
Dilara İTİK
Researcher
dilara.itik@ibg.edu.tr
Eda ESKİER
PhD Student
eda.kaleli@ibg.edu.tr
Hasan Buğra ÇOBAN
Researcher
bugra.coban@ibg.edu.tr
Ayşe ARGÜNDOĞAN
Undergraduate Student
ayse.argundogan@ibg.edu.tr
Aslı KURDEN PEKMEZCİ
Visiting Researcher
asli.kurden@ibg.edu.tr
Erhan BAL
Visiting Researcher
erhan.bal@ibg.edu.tr
Şuğra YÜCEER
MSc Student
sugra.yuceer@ibg.edu.tr
Eda ESKİER
PhD Student
eda.kaleli@ibg.edu.tr
Selected Publications
Kalyoncu S, Yilmaz S, Kuyucu AZ, Sayili D, Mert O, Soyturk H, Gullu S, Akinturk H, Citak E, Arslan M, Taskinarda MG, Tarman IO, Altun GY, Ozer C, Orkut R, Demirtas A, Tilmensagir I, Keles U, Ulker C, Aralan G, Mercan Y, Ozkan M, Caglar HO, Arik G, Ucar MC, Yildirim M, Yildirim TC, Karadag D, Bal E, Erdogan A, Senturk S, Uzar S, Enul H, Adiay C, Sarac F, Ekiz AT, Abaci I, Aksoy O, Polat HU, Tekin S, Dimitrov S, Ozkul A, Wingender G, Gursel I, Ozturk M, Inan M. Process development for an effective COVID-19 vaccine candidate harboring recombinant SARS-CoV-2 delta plus receptor binding domain produced by Pichia pastoris.. Scientific reports. 2023 March ; 13 (1) : 5224. doi:10.1038/s41598-023-32021-9. Download
Arslan M, Karadag M, Onal E, Gelinci E, Cakan-Akdogan G, Kalyoncu S. Effect of non-repetitive linker on in vitro and in vivo properties of an anti-VEGF scFv.. Scientific reports. 2022 March ; 12 (1) : 5449. doi:10.1038/s41598-022-09324-4. Download
Deniz Doğan; Merve Arslan; Tuğçe Uluçay; Sibel Kalyoncu; Stefan Dimitrov; Seyit Kale. CENP-A nucleosome is a sensitive allosteric scaffold for DNA and chromatin factors. Journal of Molecular Biology. 2021 March ; 433 (6) . doi:10.1016/j.jmb.2020.166789. Download
Saniye Gul Kaya, Seniz Inanc-Surer, Gulcin Cakan-Akdogan, Gulgun Oktay, Canan Asli Utine, Sibel Kalyoncu. Roles of matrix metalloproteinases in the cornea: A special focus on macular corneal dystrophy. Medicine in Drug Discovery. 2021 September ; 11 : 100095. doi:10.1016/j.medidd.2021.100095. Download
Arslan M, Karadag D, Kalyoncu S. Conformational changes in a Vernier zone region: Implications for antibody dual specificity.. Proteins. 2020 November ; 88 (11) : 1447-1457. doi:10.1002/prot.25964. Download
Karadag M, Arslan M, Kaleli NE, Kalyoncu S. Physicochemical determinants of antibody-protein interactions.. Advances in protein chemistry and structural biology. 2020 January ; 121 : 85-114. doi:10.1016/bs.apcsb.2019.08.011. Download
Lou W, Stimple SD, Desai AA, Makowski EK, Kalyoncu S, Mogensen JE, Spang LT, Asgreen DJ, Staby A, Duus K, Amstrup J, Zhang Y, Tessier PM. Directed evolution of conformation-specific antibodies for sensitive detection of polypeptide aggregates in therapeutic drug formulations.. Biotechnology and bioengineering. 2020 October ; 118 (2) : 797-808. doi:10.1002/bit.27610. Download
Nazlı Eda Kaleli, Murat Karadag, Sibel Kalyoncu. Phage display derived therapeutic antibodies have enriched aliphatic content: Insights for developability issues. Proteins: Structure, Function, and Bioinformatics. 2019 July ; 87 (7) : 607-618. doi:10.1002/prot.25685. Download
Merve Arslan, Dilara Karadag, Sibel Kalyoncu. Protein engineering approaches for antibody fragments: directed evolution and rational design approaches. Turkish Journal of Biology. 2019 February ; 43 (1) : 1-12. doi:10.3906/biy-1809-28. Download
Stimple SD, Kalyoncu S, Desai AA, Mogensen JE, Spang LT, Asgreen DJ, Staby A, Tessier PM. Sensitive detection of glucagon aggregation using amyloid fibril‐specific antibodies. Biotechnology and Bioengineering. 2019 April . doi:10.1002/bit.26994. Download
Naing SH, Kalyoncu S, Smalley DM, Kim H, Tao X, George JB, Jonke AP, Oliver RC, Urban VS, Torres MP, Lieberman RL. Both positional and chemical variables control in vitro proteolytic cleavage of a presenilin ortholog. Journal of Biological Chemistry. 2018 March ; 293 (13) : 4653-4663. doi:10.1074/jbc.RA117.001436. Download
Kalyoncu S, Heaner DP Jr, Kurt Z, Bethel CM, Ukachukwu CU, Chakravarthy S, Spain JC, Lieberman RL. Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution.. Nature chemical biology. 2016 December ; 12 (12) : 1031-1036. doi:10.1038/nchembio.2191. Download
Johnson JL, Entzminger KC, Hyun J, Kalyoncu S, Heaner DP Jr, Morales IA, Sheppard A, Gumbart JC, Maynard JA, Lieberman RL. Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.. Acta crystallographica. Section D, Biological crystallography. 2015 April ; 71 (Pt 4) : 896-906. doi:10.1107/S1399004715001856. Download
Naing SH, Vukoti KM, Drury JE, Johnson JL, Kalyoncu S, Hill SE, Torres MP, Lieberman RL. Catalytic Properties of Intramembrane Aspartyl Protease Substrate Hydrolysis Evaluated Using a FRET Peptide Cleavage Assay.. ACS chemical biology. 2015 September ; 10 (9) : 2166-74. doi:10.1021/acschembio.5b00305. Download
Kalyoncu S, Hyun J, Pai JC, Johnson JL, Entzminger K, Jain A, Heaner DP Jr, Morales IA, Truskett TM, Maynard JA, Lieberman RL. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments.. Proteins. 2014 September ; 82 (9) : 1884-95. doi:10.1002/prot.24542. Download
Kalyoncu S, Keskin O, Gursoy A. Interaction prediction and classification of PDZ domains.. BMC bioinformatics. 2010 June ; 11 : 357. doi:10.1186/1471-2105-11-357. Download
Total : 16
Selected Book Chapters
Antikorlar İçin Protein Mühendisliği Yaklaşımları (2021). PROTEİN: YAPISI, MÜHENDİSLİĞİ, ETKİLEŞİMLERİ, DİNAMİĞİ VE İLAÇ TASARIMINDAKİ YERİ. Ankara Nobel Tıp Yayınevi.
Kodom Optimizasyonu Ve Rekombinant Protein Üretimindeki Yeri (2021). PROTEİN: YAPISI, MÜHENDİSLİĞİ, ETKİLEŞİMLERİ, DİNAMİĞİ VE İLAÇ TASARIMINDAKİ YERİ. Ankara Nobel Tıp Yayınevi.
Physicochemical determinants of antibody-protein interactions (2020). APCSB: Protein Interactions as Targets in Drug Discovery. Elsevier.
Lessons from an α-Helical Membrane Enzyme: Expression, Purification, and Detergent Optimization for Biophysical and Structural Characterization (2016). Heterologous Expression of Membrane Proteins. Humana Press.
Total : 4
Projects
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of A Topical Therapy Approach for Macular Corneal Dystrophy, Ongoing
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development and Prodcution of Lung Cancer Monoclonal Antibodies Commonly Used in Clinical Pathology, Institution Changed
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of next-generation recombinant antibody fragments against VEGF for cancer therapy., Ongoing
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Target Specific Pan-Cancer Therapies (PAN-TER), Ongoing
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Makuler Kornea Distrofisinin In Vivo Modellemesi: Zebrabalığı Mutantlarının Crispr/Cas9 Ile Oluşturulması, Chst6?Nın Gelişimdeki Rolünün Ve Mkd Hastalık Fenotipinin Araştırılması, Ongoing
Other Private Sector - RD : Scientific and technological cooperation project for the development of new biopharmaceutical products to be used in the field of ophthalmology, Ongoing
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Recombinant Protein Based Vaccine Against SARS-CoV-2, Ongoing
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of Drugs Based on “Ghost Receptor-Antibody” Against SARS-CoV-2, Ongoing
The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Determination of bilirubin carrying capacity of recombinant human serum albumin variants and investigation of theraputic potential in an in vivo zebrafish model., Ongoing
Patents
- Efe Can, Sibel Kalyoncu Uzunlar, Şeyda Güllü, Ceren Özer Çokgezme, Gülçin Çakan Akdoğan, Mehmet Inan, Ebru Önal 2022 , STABLE AND POTENT ANTI-ANGIOGENIC SCFV FRAGMENTS AND USES AS VEGF ANTAGONIST THEREOF, PCT/TR2022/050990
Awards
- Science Academy’s Young Scientist Awards Program (BAGEP) 2023 by Science Academy, 2023
- L’Oréal & UNESCO Turkey National Women in Science Award by L'Oréal UNESCO, 2023
Contact
Kalyoncu Lab. on Antibody Engineering
Research Group Leader
Sibel KALYONCU
sibel.kalyoncu@ibg.edu.tr
+90 232 299 41 00
(5181)
+9
0 (232) 299 41 68