Chaithanya Kotyada
Bengaluru
Summary
Results-driven scientist with 10+ years of experience in protein engineering and structural biology, specializing in working cross-functional and cross-country teams within global R&D environments. Proven track record of training and mentoring design teams, coordinating innovation pipelines, and acting as the site-specific SPOC for intellectual property and trade secret management. Skilled in antibody and immunogen design, enzyme engineering, cancer biology, drug design and fostering international collaboration across scientific and business units.
Overview
13
13
years of professional experience
7
7
years of post-secondary education
Work History
Senior Scientist-II
ThermoFisher Scientific
05.2024 - Current
- Lead and coordinate immunogen design workflow and team deliverables
- Act as SPOC for antibody/antigen design and project coordination
- Serve as site-specific IP coordinator, facilitating international IP meetings
- Design novel antibodies, conjugation handles, enzyme mutants, and purification workflows
- Conduct molecular modeling and dynamics simulations on antibody-related targets
Scientist-II
ThermoFisher Scientific
11.2021 - 04.2024
- Designed protein antigens, humanized antibodies and camelized nanobodies
- Designed bi/tri-specific antibodies, novel scFv's, enzyme stable mutants, and universal hinge's
- Utilized AKTA systems and gravity column chromatography for protein purification
- Performed Fab domain fluorescent conjugations
Research Associate
Jubilant Biosys
04.2021 - 10.2021
- Drug Discovery
- Conducted drug binding assays and thermal shift assays
- Crystallized EGFR-drug complexes and solved their structures via X-ray diffraction
Senior Research Fellow
Mazumdar Shaw Center
11.2019 - 04.2021
- Cancer Biomarker discovery
- Discovered cancer biomarkers and novel protein variants in tissue samples
- Performed RNA extraction, qPCR, and molecular modeling
Junior Research Fellow
IISc Bangalore
01.2016 - 01.2018
- Studied Mycobacterium Tuberculosis toxin-antitoxin modules
- Conducted molecular dynamics simulations and X-ray crystallography
- Purified proteins from E.coli expression systems and co-authored publications
Junior Research Fellow
NCBS
01.2015 - 12.2015
- Investigated lipid transfer proteins and their structures
- Carried out protein-lipid binding studies using ITC and SPR
- Performed crystallization and protein purification
Junior Research Fellow
IISER Bhopal
09.2012 - 10.2014
- Studied Ras superfamily oncology mutations
- Used MANT fluorescence, radioactive GTP assays, and anisotropy studies
- Co-authored international publications
Education
PhD Discontinued - Structural Biology
University of Auckland & University of Leicester
Auckland, New Zealand 04.2018 - 07.2019
Other Degree - Biotechnology
Illinois Institute of Technology
Chicago, US 08.2011 - 06.2012
Post Graduate Diploma - Biotechniques
IBAB
Bengaluru, India 08.2010 - 06.2011
B.Tech. - Biotechnology
GITAM University
Visakhapatnam, India 01.2006 - 01.2010
Skills
Protein Design and Engineering
Project Management
Technical Skill Training
undefinedPatents
- Provisional patent filed for novel conjugation handle (Helical Domain), 2024
- Fab domains using the patented helical domain to launch from ThermoFisher, 2025
Exams Cleared
- GATE, 2009, 2010, AIR 608
- GRE Subject, 2010, For IIT Chicago admission
- JGEEBILS, 2011, 2014
- IELTS, 2017
- TOEFL, 2017, 107
Presentations And Workshops
- ThermoFisher I-STAG Symposium, 2023, Humanization of mouse CD28
- NuBS, IISc, 2016, Type-III toxin-antitoxin modules
- Annual Biology Meet, IISER Bhopal, 2014, Rab21 study
- Workshop on NextGen Proteomics, 2014, Bengaluru
- VIT Poster Presentation, Green molecule water purification
Technical Skills
Python programming, Linux (Ubuntu) environment, BLAST tools, sequence alignment tools, PubMed, RCSB/PDB, Virtual screening: AutoDock Vina, AutoDock Tools, Immunogen design: IEDB, Antigen Profiler, Antibody CDR analysis: IMGT, Paratome, IgBlast, Molecular dynamics simulations: GROMACS, Structure and dynamics visualization: VMD, UCSF Chimera, PyMOL, Molecular modeling tools: SwissModel, Modeller, Phyre2, AlphaFold, I-TASSER, Additional tools: PRODRG, Caver Analyst, COZOID, Conventional cloning, site-directed mutagenesis, Competent cell preparation, transformations (DH5α, BL21 DE3/pLysE), Plasmid DNA extraction, RNA isolation, cDNA synthesis, Agarose gel electrophoresis, PCR, RT-PCR, Gravity flow, peristaltic pump, GE AKTA (Pure) systems, Affinity columns: His-tag, GST-tag, Size exclusion chromatography, SDS-PAGE analysis, Construct design, crystal drop setup (hanging drop, sitting drop, oil immersion), Crystal screens and additive screens, Protein-ligand co-crystal optimization, Crystal mounting, X-ray diffraction (in-house diffractometer), Structure solution and refinement (CCP4, COOT), ligand fitting (AFITT), Thermal shift assays (SYPRO Orange), Tryptophan fluorescence and anisotropy-based binding (e.g., VPS35, Rab GTPases), Isothermal calorimetry (ITC) for protein-lipid binding (PITPα, PI/PA/PC), Surface plasmon resonance (SPR) for protein-protein and protein-lipid interactions, MANT fluorescence-based GTP hydrolysis assays (Rab GTPases), Tryptophan fluorescence-based GTP/GDP loading and hydrolysis assays, GTPγ32 radiolabeled assays using scintillation counter, Procedures include HPLC purifications, NAP5/PD10 columns, and temperature-dependent hydrolysis measurements
Publications
- Atypical Switch-I Arginine plays a catalytic role in GTP hydrolysis of Rab21 from Entamoeba histolytica, Kotyada C, et al., Biochem.Biophys. Res. Commun., 11/30/18, 506, 3, 660-667
- Mechanistic Insights into the Differential Catalysis by Rheb and its Mutants: Y35A and Y35A-D65A, Kotyada C, et al., ACS Omega, 2017, 2, 10, 6691-6702
- SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation, Sarikhani M, Mishra S, Maity S, Kotyada C, et al., Elife, 03/05/18, 10.7554/eLife.32952
- SIRT2 regulates oxidative stress-induced cell death through deacetylation of c-Jun NH2-terminal kinase, Sarikhani M, Mishra S, Desingu PA, Kotyada C, et al., Cell Death Differ., 02/15/18, 10.1038/s41418-018-0069-8
- 2.09 Å resolution structure of E. coli HigBA toxin-antitoxin complex reveals an ordered DNA binding domain and intrinsic dynamics in HigA antitoxin, Jadhav PV, Sinha VK, Chugh S, Kotyada C, et al., BiochemJ, 10/30/20, 477, 20, 4001-4019, 10.1042/BCJ20200363
- Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications, Hari PS, Balakrishnan L, Kotyada C, et al., Mol Cell Proteomics, 04/01/22, 21, 4, 100220
- Molecular insights into the open-closed-phosphorylation states of PITPα protein, Kotyada C, Biorxiv, https://doi.org/10.1101/152587
Activities
- Coordinator, BIOMICAL, 2010, GITAM University
- NCC Cadet, Indian Navy
Timeline
Senior Scientist-II
ThermoFisher Scientific
05.2024 - Current
Scientist-II
ThermoFisher Scientific
11.2021 - 04.2024
Research Associate
Jubilant Biosys
04.2021 - 10.2021
Senior Research Fellow
Mazumdar Shaw Center
11.2019 - 04.2021
PhD Discontinued - Structural Biology
University of Auckland & University of Leicester
04.2018 - 07.2019
Junior Research Fellow
IISc Bangalore
01.2016 - 01.2018
Junior Research Fellow
NCBS
01.2015 - 12.2015
Junior Research Fellow
IISER Bhopal
09.2012 - 10.2014
Other Degree - Biotechnology
Illinois Institute of Technology
08.2011 - 06.2012
Post Graduate Diploma - Biotechniques
IBAB
08.2010 - 06.2011
B.Tech. - Biotechnology
GITAM University
01.2006 - 01.2010
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