Doctoral fellow – IBiTech-Biommeda research group, Faculty of Engineering and Architecture - UGent
Principal investigator: prof. An Ghysels (PhD)
Doctoral fellow – Bio2Byte, Interuniversity Institute of Bioinformatics in Brussels - Vrije Universiteit Brussel
Protein-drug interactions are crucial in precision medicine in cancer. However, a number of complex factors such as acquired drug resistance, drug efficacy, mutation in oncoproteins, drug toxicity, lower protein-drug binding affinity have attributed to the failures of various computational tools that are focused on protein-drug interactions in cancer.
The standard methods in protein-drug interactions involve rigid-body docking of protein-ligand(s) (an ion, small-molecule drugs, conserved water molecules). In addition, they do not address the dynamic and conformational behaviour of proteins and ligands which can be affected by mutations, post-translational modifications such as glycosylation further affecting their binding affinity. Therefore, for the accurate diagnosis, monitoring and treatment in cancer there is a need to develop accurate biophysical fingerprints of protein-drug interactions that correspond with sequence variants, molecular dynamics of protein-ligand, post-translational modifications as well as drug pharmacodynamics.
The main objective of the research project is the development of new methodological and computational solutions implemented as a freely available web-based atlas for prediction of response to drugs through prediction of binding sites and their ligands, and prediction of the effects of sequence variants on binding affinity and dynamics for drug molecules enabling inferences in drug pharmacodynamics and pharmacokinetics.
I earned my M.Sc. in Bioinformatics at Jamia Millia Islamia, India. During my master thesis, I worked on protein-protein interactions of two oncoproteins. I started my Ph.D. in October 2019 at Vrije Universiteit Brussel (VUB), Belgium, to develop methods for biophysical alignment of proteins. In 2020, this became a joint Ph.D. in Biomedical Engineering between Ghent University (UGent, Belgium) and VUB. The current project focuses on the development of computational tools for precision medicine in cancer. I developed a method for the alignment of two protein sequences based on the biophysical predictions including features such as backbone dynamics, sidechain dynamics, disordered regions, and early folding regions. The predictions are obtained from the tools developed by the Bio2Byte group. My latest research focuses on comparing biophysical features with flexibility calculations from MD simulations, with its application field in oncoproteins, protein glycosylation and protein-ligand binding.
Contact & links
- Lab address: Campus Ghent University Hospital (UZ Gent) – Ghent 9000, Corneel Heymanslaan 10, entrance 36, 5th floor.
- Biommeda: Precision medicine for protein binding sites
- Bhawna Dixit is interested to receive invitations for presentations or talks