Projects / Programmes
Dynamic aspect of ligand-protein binding
| Code |
Science |
Field |
Subfield |
| 1.04.00 |
Natural sciences and mathematics |
Chemistry |
|
| Code |
Science |
Field |
| P003 |
Natural sciences and mathematics |
Chemistry |
| Code |
Science |
Field |
| 1.04 |
Natural Sciences |
Chemical sciences |
ligand-protein, dynamic processes, mechanism of binding, NMR spectroscopy, vibrational spectroscopy, molecular dynamics simulation
Researchers (12)
Organisations (2)
Abstract
A variety of processes essential to living organisms involve ligand-protein binding, where the ligands are switching proteins between different functional states. The atomic resolution structures of ligand-protein complexes provide the basis for the understanding of ligand-protein interactions. However, it is becoming obvious that dynamic processes are playing an important role in the mechanism of ligand-protein binding. Therefore the combined structural and dynamic characterization of ligand-protein binding is required for the thorough understanding of its mechanism and its functional role in a particular life process. Despite the recent advances in biophysical techniques and computational approaches for the investigation of biomolecular systems, the characterization of dynamic processes remains a demanding challenge due to their elusive nature.
The aim of this project is a site specific characterization of dynamic processes in ligand-protein complexes on a wide time scale at atomic level using a combined approach of nuclear magnetic resonance spectroscopy (NMR), vibrational spectroscopy and molecular dynamics (MD) simulations. The research will consist of a detailed characterization of protein dynamics in ligand-protein complexes, including the involvement of low-populated protein high energy states. Special attention will be paid on the characterization of coupled ligand-protein motions and on a yet very poorly understood relationship between ligand intrinsic flexibility and its biological potency. Our resent results have indicated that beside intrinsic protein motions, these dynamic processes can also severely effect ligand-protein interactions and can be related to ligand functional activities. The capabilities of NMR spectroscopy, to identify and investigate protein motions on a picosecond to millisecond time scale, are well-known. Based on our characterization of highly intrinsically flexible dipeptides in aqueous environments, we believe that vibrational spectroscopy will significantly contribute to the NMR studies through its ability to directly detect short-lived states, especially to the characterization of ligand intrinsic flexibilities. In order to provide a model based understanding of the correlation between individual types of motion and their effect on ligand-protein binding, we will use MD simulations and develop computational tools that will allow the comparison of computational results with the experimental data.
We will investigate ligand binding to Mur ligase D, a multi-domain enzyme protein, which reflects conformational dynamics on a wide range of scales in time and space. The results of these studies will be implemented in the design and development of more potent Mur ligase D inhibitors, which will be synthesized and biologically evaluated. Thus, the potential of our findings for target-based design and discovery of small-molecule drugs will be considered. The general applicability of this new knowledge will be inspected through its application in the investigation of ligand binding to other proteins, sterol 14α-demethylase and nerve growth factor, with up to now not yet fully understood ligand-driven activation mechanisms.
The results of the proposed studies may significantly contribute to the advance of molecular medicine and will be of high interest to many specific research fields, such as molecular recognition, molecular signalling, enzyme catalysis, protein folding, target-based design and discovery of drugs.
Significance for science
The aim of this project is a site specific characterization of dynamic processes in ligand-protein complexes on a wide range time scale at atomic level, which is required for the proper understating of ligand-protein binding mechanisms. This new knowledge will contribute also to the characterization of intrinsically disordered proteins, protein-protein binding, DNA-protein binding and other processes, which involve protein flexibility, such as protein folding and allosteric mechanisms. In general, the anticipated results will inspire future research of the poorly explored role of dynamics and molecular flexibility in biological processes.
In particular, the detailed physicochemical characterization of ligand-protein binding is related to target-based design and discovery of small molecule drugs. Despite the large efforts of private companies and academia over the past decades, the output in discovering novel therapeutic agents is rather low. It is argued that the current drug design methodologies might not be efficient enough. For example; a contribution in the renowned scientific journal Nature has revealed alarming facts about the current situation in the development of new antibacterial agents. These are: (i) only four new classes of antibiotics have been launched in the last 40 years and (ii) many large pharmaceutical companies have discarded the research and development of activities regrading antibiotics agents although the bacterial resistance has become critical all over the world (Nature, 472, 2011, 32). The anticipated results of this project aim to open a new basis for the development of more efficient methodologies for the drug design and discovery. In fact, the proper treatment of dynamic effects is currently the hot topic in the drug-design community and will enable the establishment of the so called “flexibility era” in drug discovery.
Significance for the country
Proposed project is harmonized with the national Strategic Development Innovation Partnerships (SRIP) in particular the »Health-medicine« partnership. National SRIP were established to strengthen the research-development-innovation integration of independent stakeholders (business, research organizations and other relevant development stakeholders) with the aim of systematic integration in international value chains and providing an integrated support environment in Slovenia including the development of human resources.
The results of the project will advance understanding of the molecular mechanisms underlying the biological action of muramyl ligase D (MurD), sterol 14?-demethylase (CYP51) and nerve growth factor (NGF). Detailed physicochemical characterization of ligand-MurD and ligand-Cyp51 binding can result in the design of new leads, which can have immediate effect on the development of urgently required new antibiotics and antimycotics. In the EU two million patients in hospitals catch bacterial infections every year and almost 200 thousand of them die, because the existent antibiotics do not help. The fungal resistance is also becoming critical, especially considering high mortality rates of systemic fungal infections, which threaten patients, whose immune system is compromised, including AIDS, cancer, transplant patients, and many others. The NGF is involved in maintenance and growth of different neuronal populations. Besides its role in the nervous system, NGF also takes part in the activation of immune and endocrine system and is involved in the pain pathway. Therefore, the interest in the use of NGF as a drug with neuroprotective action is high, although its active use has been so far hindered by the induction of severe nociception in clinical trials. Given the biomedical interest in the use of NGF as a drug, as well as the identification of active antagonists able to block the nociceptive activity, it remains of great interest to unravel the molecular mechanisms at the basis of the NGF signalling pathway, which involve binding of ligands.
Results of the proposed project will be valuable for pharmaceutical companies and will further extend the collaboration of National Institute of Chemistry and Faculty of Pharmacy with Slovenian pharmaceutical industry, Lek and Krka Pharmaceuticals. The members of the group have successfully performed many projects for these two companies in the past. The young researchers, who will be involved in this project, will be able to use new skills and knowledge for the establishment of spin-off companies.
Most important scientific results
Interim report,
final report
Most important socioeconomically and culturally relevant results
Interim report,
final report
