Projects / Programmes
Design of novel Mur ligase inhibitors and dynamical model of the E. coli MurD enzyme
| Code |
Science |
Field |
Subfield |
| 1.09.00 |
Natural sciences and mathematics |
Pharmacy |
|
| Code |
Science |
Field |
| B740 |
Biomedical sciences |
Pharmacological sciences, pharmacognosy, pharmacy, toxicology |
| Code |
Science |
Field |
| 3.01 |
Medical and Health Sciences |
Basic medicine |
Antibiotics antibacterial active agents, bacterial peptidoglican, bacterial Mur ligases, enzyme inhibitors, structure-based drug design, ligand-based drug design, virtual screening, molecular simulations, molecular dynamics, in vitro testing, structural studies
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
25493 |
PhD Andrej Perdih |
Pharmacy |
Head |
2011 - 2013 |
267 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0104 |
National Institute of Chemistry |
Ljubljana |
5051592000 |
21,007 |
Abstract
The discovery of antibacterial agents, which provided an efficient instrument to tackle bacterial infections, stands on the podium of history as one of the scientific triumphs However, the evolutionary pressure and inappropriate and sometimes excessive use of antibiotics assisted in a rapid development of bacterial resistance. In the last 20 years numerous pathogenic bacterial species were identified that displayed resistance to most of the identified antibiotics.
Peptidoglycan is a crucial component of the bacterial cell wall enabling its integrity as well as survival in various osmotic environments. Among prospective antibacterial targets the enzymes involved into bacterial peptidoglycan biosynthesis represent an attractive collection of potential targets. Synthesis of the peptide moiety of the bacterial peptidoglycan occurs inside the prokaryotic cell by successive addition of the incoming amino acids to the initial UDP-precursor (UDP-MurNAc) catalyzed by the family of Mur ligases (MurC, MurD, MurE in MurF). The Mur ligase family is a collection of structurally and functionally similar enzymes.
In the scope of the postdoctoral project the focus will be on the bacterial Mur ligases, which have been a subject of our previous research activities. Our current dynamical MurD model will be further developed, thus providing more in-depth information for the successful antibacterial drug discovery efforts. The energy demands connected with the flexibility, especially the opening and closing motion of the MurD enzyme, will be investigated.This will help to identify intermediate structures easily available to the enzyme and offer a direct quantitative evaluation of the protein structures for the novel structure-based virtual screening campaigns. Obtained results complementing our previous dynamical model results will also be correlated with the available experimental data.
Derived dynamical model data together with the available experimental data will be utilized in the design of novel superior Mur ligase inhibitors. This innovative approach to drug design where fundamental computational molecular modeling approaches are coupled with classical virtual screening techniques represents a novelty in the field. In addition to the molecular design based on a dynamical protein structure target, classical virtual screening based on static protein models will be also performed. For this part of the research different virtual screening techniques will be used ranging from three dimensional ligand-based and structure-based pharmacophores, shape-based screening approaches and molecular docking calculations. The designed compounds will be experimentally assayed in tests of enzyme inhibition (collaboration with the research group at the Faculty of Pharmacy). This will enable direct validation of the design hypothesis based on the dynamical model data and subsequent results-driven optimization of screening conditions resulting in optimal compounds with potent inhibition of these bacterial enzymes. In collaboration with the researchers from Grenoble (France) protein crystallography experiments aimed to determine the x-ray structure of the inhibitor-enzyme complex will be initiated.
Results obtained in the scope of the postdoctoral project will significantly complement the present knowledge and understanding of the Mur ligase family at the molecular level. Application of the dynamical modeling results will enable the identification of novel superior inhibitors of Mur ligases and give additional conformation to the utility of novel approaches in drug design. Novel bio-active compounds will, moreover, importantly contribute to the antibacterial research efforts to combat resistant bacterial infections.
Significance for science
Main scientific relevance of the performed research in the scope of the postdoctoral project Z1-4111 was the discovery of novel inhibitors of the bacterial Mur ligases which are suitable for subsequent development leading towards novel antibacterial drugs and further development of the existing dynamical model of the MurD ligase. In the first stage of our research we have further developed the dynamical model of the MurD enzyme. The energy demands connected with the motion of the MurD enzyme C-terminal domain were investigated using a recently developed off-path simulation (OPS) method and binding free energies of the newly identified inhibitors were calculated using Linear Interaction Energy (LIE) method to provide critical insights into the driving forces responsible for successful molecular recognition. The published research article about the application of the OPS method represents one of the first reported applications of the OPS method in the literature. By using various methods of computer-aided molecular design and theoretical computational chemistry we successfully identified and characterized several chemical classes of Mur ligase inhibitors. The most important research breakthroughs obtained during the duration of the research project were successfully identified and experimentally characterized multiple inhibitors of the whole Mur ligase family (MurC-MurF) and the discovery of the first know ATP-competitive inhibitor of the MurD ligase. Important methodological scientific advance of the Z1-4111 project is also reflected in a developed complex mechanistic-based approach to drug design in which we coupled classical structure-based approaches with dynamical methods of molecular modeling such as molecular dynamics simulation studies and virtual screening experiments using multiple protein structures. This integrated design approach is still in its infancy, partially due to longer timescales necessary to complete the studies, partially due to its relative recent presence in the field. Our results confirmed its promising utility for a better understanding of the investigated protein targets as well as identification of novel promising compounds. Performed research studies yielded novel data important for better understanding of the bacterial Mur ligases. This gained knowledge can be quickly utilized in further development of the discovered compounds by the pharmaceutical industry which can ultimately produce novel antibacterial drugs as effective therapeutics for bacterial infections. The most important research results obtained during the duration of the postdoctoral project were published in nine original scientific articles and three review articles in highly ranked international scientific journals. In addition, several articles also describing the outcomes of this project are at the time of submission of this final report in reviewing process.
Significance for the country
Postdoctoral program Z1-4111 addressed the important problem of bacterial resistance and thus generated and provided new potential solutions in the research field of antibacterials. On one hand it increased the atomistic understanding of the family of the bacterial Mur ligases as well as it enabled the identification of novel Mur ligase inhibitors. The whole society must have a constant awareness that research and identification of novel antibacterial agents is an essential activity to preserve the achieved quality of life and effective functioning of the health care services. Slovenian pharmaceutical industry represents an important and successful field of the Slovenian economy which throughout its existence supported and financed research activities in the field of pharmaceutical. Thus, it is of fundamental importance for the Slovenian researchers, which are active in the academic field, to contribute as many new applicable ideas and concepts in the scope of their expertise as possible. In the past, the antibacterial research was also successfully performed in the Slovenian industry setting which is reflected by many filled patent applications and granted patents. Research results of this postdoctoral project Z1-4111 such as novel integrated platforms for computer-aided drug design and inclusion of the targets dynamical aspect in the design experiments can form the basis for the initiation of subsequent fruitful collaborations with the pharmaceutical and biotechnological industry and also commercialization of the gained knowledge. This is in accordance with the currently adapted state guidelines for further development of the Slovenian economy. In addition, the financing of the postdoctoral project enabled the project leader to conduct his research activities at two highly established research institutions FU Berlin, Germany and University of Michigan, Ann Arbor, USA, strengthening the collaboration between Slovenian and established academic research institutions abroad. New gained “know-how” which resulted as a consequence of the application of theoretical computational approaches coupled with performed experiments (done in collaboration with other research groups) on the investigated biological systems of Mur ligases represents an important step forward in the development of the Slovenian medicinal chemistry field and drug design approaches performed at the Slovenian research facilities. The sole possibility that this highly specialized knowledge could have emerged proves that Slovenian society supports the knowledge-based society paradigm as well as encourages innovative scientific research. An indirect impact of this project on the Slovenian society was also displayed in its higher scientific reputation as a consequence of several novel publications appearing in highly respected scientific journals, active participation of the project leader at the international scientific conferences and meetings and several invited talks concerning this topic. Finally, postdoctoral project Z1-4111 has also, hopefully, illustrated the importance of the interdisciplinary approach, when tackling biomedical scientific challenges, via tight collaboration of the researchers from different research groups and backgrounds all aiming to achieve a common goal – in our case - improved health status in the society. This collaboration emits a strong message that the whole research society must support the collaborative synergetic approach, which often goes beyond national borders as well as the expertise of a certain research field.
Most important scientific results
Annual report
2011,
2012,
final report,
complete report on dLib.si
Most important socioeconomically and culturally relevant results
Annual report
2011,
2012,
final report,
complete report on dLib.si
