Computational modeling of small molecule binding to glycosaminoglycans and lysosomal proteins
Specialized computational services for modeling molecular interactions between glycosaminoglycans (GAGs) and small molecules, including binding analysis with lysosomal proteins. Leverages proprietary molecular dynamics and docking protocols to provide atomistic-level insights that complement and guide experimental research in drug discovery and glycobiology.
Overview
This offering provides advanced computational modeling services focused on understanding how small molecules interact with glycosaminoglycans (GAGs) and lysosomal proteins. GAGs are complex polysaccharides capable of binding a wide variety of small molecules, some of which may serve as specific ligands for lysosomal proteins involved in rare diseases such as mucopolysaccharidoses. By applying molecular dynamics and docking techniques, this service delivers atomistic-level details of these molecular systems that are difficult to obtain through experimental methods alone, enabling researchers to prioritize candidates and rationalize experimental findings before investing in costly laboratory work.
Technical specifications
Core capabilities:
- Molecular docking to localize potential binding sites on lysosomal proteins
- Clustering of binding poses to identify representative configurations for further analysis
- Molecular dynamics (MD) simulations of GAG-small molecule systems using multiple copies of the ligand for thorough sampling
- Free binding energy analysis to quantify interaction strength and specificity
- Umbrella Sampling with Potential of Mean Force (PMF) calculations for high-accuracy binding thermodynamics
Key advantages:
- Proprietary, lab-developed computational protocols specifically designed and validated for GAG-containing systems
- Demonstrated track record with over 20 different small molecule-GAG interactions described in peer-reviewed publications
- Complementary to experimental techniques, reducing time and cost of laboratory investigations
- Applicable to both polysaccharide-protein and polysaccharide-small molecule interactions
Technology readiness level
The computational protocols have been validated through multiple published studies describing GAG interactions with more than 20 different small molecules. The research group has established unique expertise and original methodologies specifically tailored for GAG-containing molecular systems, with demonstrated ability to explain and rationalize experimental data. The approach is ready for immediate application to new molecular systems of interest.
About Medical University of Gdansk
The Medical University of Gdańsk is a large public medical research university with more than 1,000 academic employees and over 300 doctoral students, combining education, research, and clinical activity in a translational setting. Its University Clinical Centre and associated medicine facilities connect academic research with patient care, clinical validation, and hospital-based expertise. A university-wide Clinical Research Support Centre assists with study design, conduct, and implementation, alongside shared biobanking, bioanalysis, imaging, animal research, and early-phase clinical research infrastructure. Research is supported by Poland’s National Science Centre, National Centre for Research and Development, Medical Research Agency, and international programmes. The Technology Transfer Office supports IP, licensing, commissioned R&D, and spin-off formation.
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