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Molecular Modelling of Anti-Tumour Fluorouracil Action

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Molecular Modeling of Anti-Tumour Fluouracil Action

Tech Area / Field

  • MED-DRG/Drug Discovery/Medicine

Status
8 Project completed

Registration date
22.01.1998

Completion date
04.09.2003

Senior Project Manager
Evstyukhin K N

Leading Institute
VNIITF, Russia, Chelyabinsk reg., Snezhinsk

Collaborators

  • University Medical Center / Nebraska's Helth Science Center, USA, NE, Omaha\nNapier University, UK, Edinburgh\nWashington University, USA, MO, Saint Louis\nGerman Cancer Research Center, Germany, Heidelberg

Project summary

Creating of new effective anti-tumour drugs remains to be one of the most actual problems in modern medicine. The new approach to drugs design, based on using of powerful computers for performance of realistic biopolymers structure calculations, is being developed intensively in recent years. And now the molecular modeling plays a significant role in deeper understanding of the action mechanism of medicinal substances with anti-tumour action and in future this approach will be used for creating new more effective classes of drugs.

The purpose of the project is to engage in this work the experts in technical physics, applied mathematics and computers from the Russian Nuclear Weapon Laboratory (former "Chelyabinsk-70"). The experts in drug chemistry from the Institute of Organic Synthesis (Ural Branch of RAS) will be involved as consultants during the project activities.

The study of action mechanism of fluorouracil, the substance with anti-tumour action, widely used in medicine, will be the first aim of project. Several hypotheses concerning probable interaction processes between tumour cells and fluorouracil are discussed now and this process has not been clarified in details, yet.

The second aim of the project will be development of general methods of mathematical modeling of the anti-cancer drug interaction with the biomolecules. Verification of the computational methods will be carried out by means of comparison with modern experimental data. This aim is of general purpose and the results can be used not only for the fluouracil modeling but for the study of the anti-tumour action of another existing drugs as well as for the feasibility study of new prospective substances, affecting exactly on tumour cells.

The third aim of the project will be a critical review of some new ideas in the field of anti-tumor drugs development. It is well-recognized that the new ideas are highly required in this area and attraction of scientists from other field could provide a fresh view on the problem and lead to a non-conventional and promising approach.

The technical workplan of the project includes the following key points: ab initio calculations of hydrogen bonds and other force field parameters for modified nucleotides and other nonconventional residues. GAMESS, ab initio molecular code, will be used for this purpose. Molecular mechanics calculations of the structure of modified nucleic acids and other biomolecules of interest. AMBER, code will be used as main tools for this purpose.

Some calculations will be performed by TINKER code which provides more comprehensive models of solvent and other advances but needs an additional validation. Detailed comparison of the results of calculations with experimental NMR spectra of modified oligonucleotides, verification of the computational procedures on this basis and corrections, if necessary.

The calculations will be performed at the powerful IBM workstation provided by ISTC for the work on the project #017 which has been finished, recently. All the above-mentioned codes have been installed already at the workstation and preliminary calculations are being performed, now. We have licenses from the authors of all the above-mentioned codes for the non-commercial usage of the codes.

In prospect, the activities on molecular modeling could become commercial, and the calculations could be performed by the orders of biomedical industry or on the basis of bilateral scientific cooperation. Currently, a small group of scientists at VNIITF has been working on biomolecular simulation as volunteers and the project approval will support this activity very much and will provide an opportunity for them

Potential Role of Foreign Collaborators

All the project activities are proposed to be done in close collaboration with Medical Center of Nebraska University (USA) and German Cancer Research Center (Heidelberg) which will be the foreign collaborators on the project.

There is an increasing interest towards the biomolecular simulation as applied to the advanced anti-cancer drug development, including both general computational methods and specific prospective substances studies. Therefore, this project may be of interest for representatives of other potential collaborators from Europe, Japan an USA, and all interesting parties are invited to take part in the project activities.


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