{ "meta": { "api_type": "NWO Projects API", "version": "1.0.2", "licence": { "name": "CC0 1.0 Universal", "url": "https://creativecommons.org/publicdomain/zero/1.0", "description": "To the extent possible under law, all copyright and related or neighbouring rights have been waived worldwide to the data made available through this API." }, "documentation": "https://doi.org/10.5281/zenodo.14918287", "release_date": "2025-08-20T00:00:00", "funder": "https://doi.org/10.13039/501100003246", "ror_id": "https://ror.org/04jsz6e67", "date": "2026-11-05T00:00:00", "count": 1, "per_page": 100, "pages": 1, "page": 1 }, "projects": [ { "project_id": "MP-104-2005", "title": "Hybrid Quantum Mechanics-Molecular Mechanics study of the Bleomycin Acitvity", "funding_scheme_id": 2264, "funding_scheme": "Rekentijd nationale computersystemen Rekentijd nationale computersystemen 2005 EW", "department": "Exacte en Natuurwetenschappen", "sub_department": "Exacte Wetenschappen", "start_date": "2006-02-15T00:00:00", "end_date": "2007-09-03T00:00:00", "reporting_year": 2005, "summary_nl": "The project involves the application of state-of-the-art molecular modeling techniques for the study of chemical reactions in biomolecules. We are especially interested in the characterization of oxidation reactions in the non-heme iron enzyme bleomycin (BLM) and its ability to cleave DNA. [1] To tackle this problem we will make use of a recently developed hybrid Quantum Mechanics - Molecular Mechanics (QM/MM) approach. This QM/MM approach combining Car Parrinello molecular dynamics and force field is a rapidly evolving technique and it has been successfully applied to simulate several enzymatic systems and can be also very useful in farmacochemistry in testing the new drugs \"in silico\". [2] The main goal of our project is to use the QM/MM approach to simulate various reaction mechanisms that are possibly involved in the reaction between activated BLM and DNA. The system is partitioned in one QM part where the reaction takes place, described within the Density Functional Theory (DFT), and one part including a DNA portion in solution, described with a classical force-field. By using such an extensive and ralistic model we expect to clarify issues on the reaction mechanicsm that cannot be easily addressed within simplified models.\n\n\n\n", "summary_en": "The project involves the application of state-of-the-art molecular modeling techniques for the study of chemical reactions in biomolecules. We are especially interested in the characterization of oxidation reactions in the non-heme iron enzyme bleomycin (BLM) and its ability to cleave DNA. [1] To tackle this problem we will make use of a recently developed hybrid Quantum Mechanics - Molecular Mechanics (QM/MM) approach. This QM/MM approach combining Car Parrinello molecular dynamics and force field is a rapidly evolving technique and it has been successfully applied to simulate several enzymatic systems and can be also very useful in farmacochemistry in testing the new drugs \"in silico\". [2] The main goal of our project is to use the QM/MM approach to simulate various reaction mechanisms that are possibly involved in the reaction between activated BLM and DNA. The system is partitioned in one QM part where the reaction takes place, described within the Density Functional Theory (DFT), and one part including a DNA portion in solution, described with a classical force-field. By using such an extensive and ralistic model we expect to clarify issues on the reaction mechanicsm that cannot be easily addressed within simplified models.\n\n\n\n", "project_members": [ { "role": "Project leader", "member_id": 104490, "last_name": "Buda", "degree_pre_nominal": "dr.", "initials": "F.", "first_name": "Francesco", "organisation": "Universiteit Leiden||Faculteit der Wiskunde en Natuurwetenschappen||Leiden Institute of Chemistry (LIC)", "organisation_id": 73960, "ror": "https://ror.org/027bh9e22", "active": false }, { "role": "Main Applicant", "member_id": 104490, "last_name": "Buda", "degree_pre_nominal": "dr.", "initials": "F.", "first_name": "Francesco", "organisation": "Universiteit Leiden||Faculteit der Wiskunde en Natuurwetenschappen||Leiden Institute of Chemistry (LIC)||Biofysische organische chemie", "organisation_id": 80475, "ror": "https://ror.org/027bh9e22", "active": true } ], "products": [ { "title": "The anticancer drug bleomycin investigated by density functional theory", "year": 2006, "type": "Wetenschappelijk artikel", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Auteur", "index_number": 1 }, { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Auteur", "index_number": 2 } ] }, { "title": "The mechanism of bleomycin action: firstprinciples molecular dynamics investigation", "year": 2007, "type": "Wetenschappelijk artikel", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Auteur", "index_number": 1 }, { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Auteur", "index_number": 2 } ] }, { "title": "The mechanism of the bleomycin suicide: a Car-Parrinello molecular\ndynamics study", "year": 2006, "type": "Wetenschappelijk artikel", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Auteur", "index_number": 1 }, { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Auteur", "index_number": 4 }, { "last_name": "Roethlisberger", "initials": "U.", "first_name": "Ursula", "role": "Auteur", "index_number": 3 }, { "last_name": "Gossens", "initials": "C.", "role": "Auteur", "index_number": 2 } ] }, { "title": "Ab-initio Molecular Dynamics Simulations - from Solid State Physics to Chemistry and Biology", "year": 2005, "type": "Overige Output", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Maker", "index_number": 1 }, { "last_name": "Buda", "initials": "F.", "first_name": "Francesco", "role": "Maker", "index_number": 2 } ] }, { "title": "Conference 'Multi-scale modelling: Electrons, Molecules and\n(Bio)Materials", "year": 2006, "type": "Overige Output", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Maker", "index_number": 1 } ] }, { "title": "Multi-scale modelling: Electrons, Molecules and (Bio)Materials", "year": 2006, "type": "Overige Output", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Maker", "index_number": 1 } ] }, { "title": "The Mechanism of the Bleomycin Activity, Lorentz Workshop on Progress in ab initio modeling of biomolecules", "year": 2006, "type": "Overige Output", "authors": [ { "last_name": "Karawajczyk", "initials": "A.", "first_name": "Anna", "role": "Maker", "index_number": 1 } ] } ] } ] }