Finland and India joint research on nucleoside diphosphate kinases: Protein 3D structure determination and hit identification (FINNDK)

Parasitic diseases in the tropical world range from trypanosomiasis to leishmaniasis. Many of the clinical forms are fatal if untreated. With no effective vaccine available for any of these diseases, treatment is solely dependent on chemotherapy, which is always threatened due to the development of drug resistance in the parasites.
Nucleoside Diphosphate Kinases: Protein 3D Structure Determination and Hit Identification (FINNDK)
Nucleoside Diphosphate Kinases: protein 3D structure determination and hit identification

The project FINNDK is a collaboration between Pharmaceutical Science Laboratory (PSL) and Structural Bioinformatics Laboratory (SBL), Åbo Akademi University-Turku, and the Department of Molecular Medicine at Jamia Hamdard University-New Delhi.

Dr. Outi Salo-Ahen’s computer-aided-drug design group (Åbo Akademi University) and Dr. A. Selvapandiyan from the Department of Molecular Medicine, (Jamia Hamdard University), intend to investigate putative novel targets against the pathogens causing the diseases. The project aims to determine the structures of parasitic nucleoside diphosphate kinases (NDKs) by X-ray crystallography and identify NDK inhibitors by applying AI/deep learning methods along with structure-based drug design approach and molecular dynamics (MD) simulations.

Two successful research mobilities from India to Finland have been accomplished from November 2021-April 2022. Protein production, purification, and preliminary crystallization attempts have been conducted for Leishmania donovani Nucleoside Diphosphate Kinase 2 (NDK2). In addition, preliminary structure-based drug design steps have been carried out using a comparative model of NDK2. The most promising virtual hit compounds will be purchased and tested against NDK2 using an in-vitro kinase assay kit. Once the crystal structures of NDK2 and the other two kinases are solved, the experimental structures can be used for another round of virtual screening to find even better binding candidate inhibitors. The results will be published in suitable international peer-reviewed journals.

FINNDKis seed-funded as part of the India Pilot initiative from the Finnish Ministry of Education and Culture. Aalto is coordinating the India Pilot Network FICORE (Finnish Indian Consortia for Research and Education) which involves 38higher education institutions from Finland and India.

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