Periodic Reporting for period 1 - CaLecLig (Calcium-dependent Lectins in Human Pathogenic Infections: From Atomistic Understanding to Ligand Design)
Reporting period: 2018-06-01 to 2020-05-31
Summary
Human health and disease are defined by balance between pathogen attack and immunologic defense. In these processes, specific binding among cells mediated by recognition of carbohydrates by protein receptors, lectins, is crucial. Molecular details can be harnessed to design glycomimetic drugs, e.g. Tamiflu. This is challenging due to the flexibility of lectin–carbohydrate complexes. We utilized molecular modeling to interpret experimental data. The three studied lectins are important for infections in cystic fibrosis patients (LecA/B) and in human immune response to infection (DC-SIGN). Their ligands are bound via calcium ions, whose theoretical description is difficult. We have developed new protocols which can potentially become a fundamental toolbox in glycomimetic drug design.
Objectives
The goal is to develop a workflow for predicting dynamics of three lectins in complex with ligands. Such protocols are transferable to other systems and thus foster rational design of new potent specific compounds with high pharmaceutical potential. The specific objectives include creating, testing and validating ligand/calcium parametrisations and developing protocols for accurate binding mode predictions.
Conclusions
We tested and developed protocols for calculations of lectin/calcium/ligand complexes which are transferable to other biomolecular complexes and thus potentially useful in developing new drugs.
Importance for European Society
The benefits of this Action for the European Research Area are not only in the high-profile scientific results obtained solely at European scientific institutions and novel computational methodologies. New interdisciplinary collaborations and scientific links across Europe were formed and together with mobility of the European researchers, knowledge and skills increased. Further, presentations of the results at international conferences enhanced the attractiveness of Europe as a scientific career location. Due to the dissemination of the results and outreach activities of the Experienced Researcher, the knowledge about this Europe-based research was made known not only to scientists in this and related fields but also to pharmaceutical industry and general public. Along all these lines, the competitiveness of European Research Area was hugely increased.
Human health and disease are defined by balance between pathogen attack and immunologic defense. In these processes, specific binding among cells mediated by recognition of carbohydrates by protein receptors, lectins, is crucial. Molecular details can be harnessed to design glycomimetic drugs, e.g. Tamiflu. This is challenging due to the flexibility of lectin–carbohydrate complexes. We utilized molecular modeling to interpret experimental data. The three studied lectins are important for infections in cystic fibrosis patients (LecA/B) and in human immune response to infection (DC-SIGN). Their ligands are bound via calcium ions, whose theoretical description is difficult. We have developed new protocols which can potentially become a fundamental toolbox in glycomimetic drug design.
Objectives
The goal is to develop a workflow for predicting dynamics of three lectins in complex with ligands. Such protocols are transferable to other systems and thus foster rational design of new potent specific compounds with high pharmaceutical potential. The specific objectives include creating, testing and validating ligand/calcium parametrisations and developing protocols for accurate binding mode predictions.
Conclusions
We tested and developed protocols for calculations of lectin/calcium/ligand complexes which are transferable to other biomolecular complexes and thus potentially useful in developing new drugs.
Importance for European Society
The benefits of this Action for the European Research Area are not only in the high-profile scientific results obtained solely at European scientific institutions and novel computational methodologies. New interdisciplinary collaborations and scientific links across Europe were formed and together with mobility of the European researchers, knowledge and skills increased. Further, presentations of the results at international conferences enhanced the attractiveness of Europe as a scientific career location. Due to the dissemination of the results and outreach activities of the Experienced Researcher, the knowledge about this Europe-based research was made known not only to scientists in this and related fields but also to pharmaceutical industry and general public. Along all these lines, the competitiveness of European Research Area was hugely increased.
Results
For the three pharmaceutically-relevant lectins studied (LecA, LecB, DC-SIGN) and their oligosaccharide and glycomimetic ligands, computational analyses were performed. These were, specifically, parametrisations of ligands, testing force fields for calcium in combination with water potentials, creating homology models of huge protein tetramers and running molecular dynamics (MD) simulations. We developed new protocols for reliable description of calcium ions in classical MD and parametrisations of large ligands.
Dissemination
The data and publications were made freely available in Mendeley Repository and BioRxiv repositories for their reproducibility and dissemination, respectively. The scientific publications were published in peer-reviewed high-impact Q1 European journals Eur. J. Med Chem (IF of 5.6) and Chem. Commun. (IF of 6.0) as Open Access (Green and Gold). New results were displayed at the CERMAV web page, with mention of Marie Skłodowska-Curie Fellowship funding. The new computational tools were described and advertised in lectures/posters. The findings were communicated to researchers and students at group lectures at host and partner institutions and to peer scientists via social media (ResearchGate, Twitter).
Publications
1. Lepsik, M.; Sommer, R.; Kuhaudomlarp, S.; Lelimousin, M.; Paci, E.; Varrot, A.; Titz, A.; Imberty, A. Eur J Med Chem. 2019, 177, 212-220.
2. Zahorska, E.; Kuhaudomlarp, S.; Minervini, S.; Yousaf, S.; Lepsik, M.; Kinsinger, T.; Hirsch, A.K.H.; Imberty, A.; Titz, A. Chem. Commun., 2020, in press, DOI: 10.1039/d0cc03490h
3. Porkolab, V.; Lepšík, M.; Ordanini, S.; Le Roy, A.; Thépaut, M.; St John, A.; Paci, E.; Ebel, C.; Bernardi, A.; Fieschi, F. Dissecting the multivalent binding modes of antagonists for a C-type Lectin Receptor, manuscript in preparation.
Conferences
1. XXIème congrès du GGMM, Nice, FR; Apr 2019
2. XVII Discussions in Structural Molecular Biology, Nove Hrady, CZ; Mar 2021: postponed due to COVID-19 pandemics
3. Biophys. J . 2019, 116, 144A-144A.
4. Canadian Glycomics Virtual Poster Session, Jun 2020
5. 63rd Annual Meeting of The Biophysical Society, Baltimore, MD, U.S.A. Mar 2019
6. On the future of glycosciences: International Workshop, Grenoble, June 2019
Seminars
1. R. Richter group, University of Leeds, U.K.; Oct 2019
2. R. Bryce group, University of Manchester, U.K.; Oct 2019
3. A.Varrot group, CERMAV; Oct 2019
4. K. Hlouchova group, BIOCEV, Prague, CZ; Aug 2019
5. P. Jungwirth group, IOCB, Prague, CZ; Apr 2019
6. E. Paci group, University of Leeds, U.K.; Jan 2019
7. J. Koca, NCBR seminar, Brno, CZ; Nov 2018
8. EPCC seminar, University of Edinburgh, U.K.; Jul 2018
Outreach
1. Fete de la Science (Science Fair), Grenoble; Oct 2018; 2019
2. Shows of virtual reality for glycosciences, CERMAV
3. Rondeau Montfleury school, 3rd grade children – talk on infection and immunity; Jan 2020
4. Social media: Twitter @Lepsik_science, @AnneImberty, @CermavDirection
5. Blog: HPC Europa 3; https://www.epcc.ed.ac.uk/blog/2018/08/07/hpc-europa
Exploitation
Intellectual property rights were not applicable.
For the three pharmaceutically-relevant lectins studied (LecA, LecB, DC-SIGN) and their oligosaccharide and glycomimetic ligands, computational analyses were performed. These were, specifically, parametrisations of ligands, testing force fields for calcium in combination with water potentials, creating homology models of huge protein tetramers and running molecular dynamics (MD) simulations. We developed new protocols for reliable description of calcium ions in classical MD and parametrisations of large ligands.
Dissemination
The data and publications were made freely available in Mendeley Repository and BioRxiv repositories for their reproducibility and dissemination, respectively. The scientific publications were published in peer-reviewed high-impact Q1 European journals Eur. J. Med Chem (IF of 5.6) and Chem. Commun. (IF of 6.0) as Open Access (Green and Gold). New results were displayed at the CERMAV web page, with mention of Marie Skłodowska-Curie Fellowship funding. The new computational tools were described and advertised in lectures/posters. The findings were communicated to researchers and students at group lectures at host and partner institutions and to peer scientists via social media (ResearchGate, Twitter).
Publications
1. Lepsik, M.; Sommer, R.; Kuhaudomlarp, S.; Lelimousin, M.; Paci, E.; Varrot, A.; Titz, A.; Imberty, A. Eur J Med Chem. 2019, 177, 212-220.
2. Zahorska, E.; Kuhaudomlarp, S.; Minervini, S.; Yousaf, S.; Lepsik, M.; Kinsinger, T.; Hirsch, A.K.H.; Imberty, A.; Titz, A. Chem. Commun., 2020, in press, DOI: 10.1039/d0cc03490h
3. Porkolab, V.; Lepšík, M.; Ordanini, S.; Le Roy, A.; Thépaut, M.; St John, A.; Paci, E.; Ebel, C.; Bernardi, A.; Fieschi, F. Dissecting the multivalent binding modes of antagonists for a C-type Lectin Receptor, manuscript in preparation.
Conferences
1. XXIème congrès du GGMM, Nice, FR; Apr 2019
2. XVII Discussions in Structural Molecular Biology, Nove Hrady, CZ; Mar 2021: postponed due to COVID-19 pandemics
3. Biophys. J . 2019, 116, 144A-144A.
4. Canadian Glycomics Virtual Poster Session, Jun 2020
5. 63rd Annual Meeting of The Biophysical Society, Baltimore, MD, U.S.A. Mar 2019
6. On the future of glycosciences: International Workshop, Grenoble, June 2019
Seminars
1. R. Richter group, University of Leeds, U.K.; Oct 2019
2. R. Bryce group, University of Manchester, U.K.; Oct 2019
3. A.Varrot group, CERMAV; Oct 2019
4. K. Hlouchova group, BIOCEV, Prague, CZ; Aug 2019
5. P. Jungwirth group, IOCB, Prague, CZ; Apr 2019
6. E. Paci group, University of Leeds, U.K.; Jan 2019
7. J. Koca, NCBR seminar, Brno, CZ; Nov 2018
8. EPCC seminar, University of Edinburgh, U.K.; Jul 2018
Outreach
1. Fete de la Science (Science Fair), Grenoble; Oct 2018; 2019
2. Shows of virtual reality for glycosciences, CERMAV
3. Rondeau Montfleury school, 3rd grade children – talk on infection and immunity; Jan 2020
4. Social media: Twitter @Lepsik_science, @AnneImberty, @CermavDirection
5. Blog: HPC Europa 3; https://www.epcc.ed.ac.uk/blog/2018/08/07/hpc-europa
Exploitation
Intellectual property rights were not applicable.
State-of-the-art and Expected Results
We have overcome the current limitations of force-field calculations for difficult cases, such as polarized calcium ions mediating lectin-carbohydrate interactions. We tested and validated Ca2+ parameters with effective electronic polarization which offer an improved atomistic description. We have developed protocols which are transferable to important protein/Ca2+/ligand complexes and thus has the potential to become a fundamental toolbox for developing new drugs.
Two European collaborations (R.Richter University of Leeds, U.K.) and B.Wiltschi (Austrian Centre of Industrial Biotechnology, Graz, Austria) were established which lead to two other joint projects being finalized.
1. Birch, H.; Lepšík, M.; Paci, E.; Richter, R.: Analysis of interactions between hyaluronan and its receptors, manuscript in preparation.
2. Tobola, F.; Lepsik, M.; Leffler, H.; Nilsson, U.,; Imberty, A.; Wiltschi, B. Influence of non-canonical amino acids on the specificity of galectin towards oligosaccharides, manuscript in preparation.
Potential Socio-Economic Impacts
This project has bearings on design of glycomimetics and potential to lead to patentable compounds to fight bacteria. Such development could lead to founding a start-up company and thus positively impact the economy status of the European society. Direct potential users of this project are computational chemists and drug designers in academia and pharmaceutical companies and broadly, patients suffering from various diseases.
We have overcome the current limitations of force-field calculations for difficult cases, such as polarized calcium ions mediating lectin-carbohydrate interactions. We tested and validated Ca2+ parameters with effective electronic polarization which offer an improved atomistic description. We have developed protocols which are transferable to important protein/Ca2+/ligand complexes and thus has the potential to become a fundamental toolbox for developing new drugs.
Two European collaborations (R.Richter University of Leeds, U.K.) and B.Wiltschi (Austrian Centre of Industrial Biotechnology, Graz, Austria) were established which lead to two other joint projects being finalized.
1. Birch, H.; Lepšík, M.; Paci, E.; Richter, R.: Analysis of interactions between hyaluronan and its receptors, manuscript in preparation.
2. Tobola, F.; Lepsik, M.; Leffler, H.; Nilsson, U.,; Imberty, A.; Wiltschi, B. Influence of non-canonical amino acids on the specificity of galectin towards oligosaccharides, manuscript in preparation.
Potential Socio-Economic Impacts
This project has bearings on design of glycomimetics and potential to lead to patentable compounds to fight bacteria. Such development could lead to founding a start-up company and thus positively impact the economy status of the European society. Direct potential users of this project are computational chemists and drug designers in academia and pharmaceutical companies and broadly, patients suffering from various diseases.