Emre APAYDIN

R&D Bioanalytical Analyst & Computational Bioengineer

Bahcesehir, TR.

About

Hybrid R&D Bioanalytical Analyst and Computational Bioengineer with dual expertise in in silico Molecular Dynamics (MD) simulations and in vitro analytical method development, specializing in Protein Engineering, Monoclonal Antibody (mAb) Design, and Structural Biology. Proven ability to orchestrate Lot Release testing and physicochemical characterization (HPLC/UPLC, CE-SDS) while advancing academic research in allosteric interactions and computer-aided drug design (CADD). Dedicated to accelerating therapeutic innovation by bridging computational prediction with wet-lab validation, driving high-impact results in pharmaceutical R&D.

Work

Abdi İbrahim Pharmaceuticals (AbdiBio)

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AbdiBio R&D Bioanalytical Development Analyst

Istanbul, Istanbul, Türkiye

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Summary

As AbdiBio R&D Bioanalytical Development Analyst, Emre orchestrates analytical method development and physicochemical characterization for biologics, ensuring regulatory compliance and data integrity for monoclonal antibodies.

Highlights

Led comprehensive analytical method development and qualification protocols for biologics within the Lot Release Assay team, ensuring robust and compliant testing procedures.

Executed high-precision structural and functional analysis of monoclonal antibodies (mAbs) across Drug Substance (DS), Drug Product (DP), In-Process Controls (IPC), and stability samples, delivering critical data for product quality.

Orchestrated end-to-end analysis using advanced chromatography (SE-HPLC, HIC-UPLC, ProA-HPLC) and electrophoresis (Non-Reduced CE-SDS) techniques, precisely quantifying protein aggregation, hydrophobicity, titer, and purity.

Managed full documentation lifecycles via Qmex, authoring Laboratory Procedures, Method Development, and Qualification Reports, ensuring stringent GMP/GLP regulatory compliance.

Spearheaded CAPA, Deviation Management, and Document Revision processes, maintaining high standards of quality assurance and data integrity across all analytical workflows, from sample preparation to final reporting.

Education

Marmara University

Istanbul, Istanbul, Türkiye
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Master of Science Bioengineering Grade: 3.63/4.00

Courses

Protein-Protein Interactions (FRET, Pull-down assay)

Molecular Biology Techniques (PCR, Gene Cloning, CRISPR-Cas9)

System Biology

Drug Delivery Systems

Istanbul University

Istanbul, Istanbul, Türkiye
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Associate Degree Computer Programming Grade: 3.00/4.00

Courses

Databases

Python

Open-Source Operating Systems

Marmara University

Istanbul, Istanbul, Türkiye
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Bachelor of Science Bioengineering Grade: 83.9/100 (Honor Student)

Courses

Bioprocess Design

Analytical Techniques (HPLC, SDS-PAGE, NMR, GC-MS, PCR)

Statistical Analysis (RSM, ANOVA, Taguchi, DOE) using Minitab 18

Publications

Spectroscopic and Docking Investigation of Pepsin Interaction With PET Micro- and Nanoplastics.

ChemistrySelect (Q3 Journal, Impact Factor: 2.0)

Investigated the interaction of pepsin with PET micro- and nanoplastics through spectroscopic and docking methods.

Understanding the PET micro/nanoplastics as an environmental stressor on pancreatin enzyme: leaching and binding characterization by multi-spectroscopic and molecular docking examination, and the resulting impact on Escherichia coli

Nanotoxicology (Q2 Journal, Impact Factor: 3.4)

Characterized the impact of PET micro/nanoplastics on pancreatin enzyme and Escherichia coli via multi-spectroscopic and molecular docking.

Elucidating the leaching effect of micro/nanoplastics on the binding, structural, and oxidative characteristics of bovine serum albumin, and impact on cytotoxicity and oxidative stress in the human lung cancer cell line, A549

Environmental Science: Nano (Q1 Journal, Impact Factor: 5.8)

Elucidated the effects of micro/nanoplastics on bovine serum albumin and A549 lung cancer cells, analyzing binding, structural, cytotoxicity, and oxidative stress.

Characterization and Redocking Studies of D-Class Beta-Lactamases in ESKAPE Pathogens

Trakya University (14th Chemical Physics Congress)

Presented research on the characterization and redocking studies of D-Class Beta-Lactamases.

Languages

Turkish (Native)

English (Advanced)

Certificates

Python and TensorFlow Training

BTK Akademi

Skills

Bioanalytical Techniques

SEC-HPLC, HIC-UPLC, ProA-HPLC, Non-Reduced CE-SDS, UV Spectrophotometry, qPCR, PCR, DNA Isolation, Analytical Method Development, Method Validation, Physicochemical Characterization, Lot Release Assay, Biologics Analysis.

Computational Biology & Cheminformatics

Molecular Dynamics (MD), Molecular Modeling, Drug Docking, Virtual Screening, Protein Engineering, Structural Biology, GROMACS, OpenMM, NAMD, AutoDock-GPU, AutoDock Vina, AlphaFold, Boltz, MODELLER, Maestro, PyMOL, VMD, CharmmGUI, OpenBabel, Meeko, Prody, MDAnalysis, CADD.

Programming & Scripting

Python (TensorFlow, RDKit, NumPy, Pandas, Scikit-learn, MDTraj), R Programming, Bash/Shell Scripting, MATLAB.

Quality Assurance & Data Analysis

GMP/GLP, Qmex (CAPA, Change Control), Minitab 18 (DOE, ANOVA, Taguchi, RSM, Full Factorial DOE), Data Integrity, Regulatory Compliance, Statistical Analysis.

Software & Operating Systems

GitHub, Microsoft Office, Adobe Acrobat, Figma, GNU/Linux (Ubuntu, CentOS), Windows.

Projects

Identification of D-Class Beta-Lactamase Inhibitors (TÜBİTAK 1001 Master's Scholar)

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Summary

Investigating inhibitors against D-Class Beta-Lactamases in ESKAPE pathogens through comprehensive molecular dynamics simulations.

Computational Biology and Bioinformatics Research (TÜBİTAK 1001 Scholar)

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Summary

Conducted advanced molecular modeling, docking, and MD simulations to explore protein interactions and drug repurposing, integrating computational insights with wet-lab validation.

OXA Enzyme Inhibitor Candidates (TÜBİTAK 2209-A Project Manager & Thesis)

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Summary

Managed a TÜBİTAK-supported project focused on identifying OXA enzyme inhibitor candidates through virtual screening and validation, culminating in a graduation thesis.

Characterization of Known OXA Enzymes (TÜBİTAK 2247-C STAR Scholar)

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Summary

Researched and characterized OXA enzymes, leveraging structural and phylogenetic analyses to identify known structures and mechanisms.

Bioethanol Production Facility Design Project

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Summary

Designed a comprehensive bioethanol production facility, detailing raw material procurement, process optimization, and economic feasibility.

Inhibition Dynamics of Type 4 Pili Protein Complex (TÜBİTAK 1001 Scholar)

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Summary

Modeled target proteins and performed virtual screenings to analyze ligand-protein interactions and inhibition dynamics.

Nanotechnology & Biomaterials Research Intern

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Summary

Researched and developed PLA-loaded GeIMA microneedles via DLP 3D Printing and Electrospinning, focusing on optimization and characterization.

Diagnostic Applications Intern

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Summary

Gained hands-on experience in molecular diagnostics, performing key laboratory procedures for COVID-19 testing and DNA analysis.

Call Agent (Part Time)

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Summary

Provided technical support for hardware/software inquiries while developing expertise in data privacy and security protocols.