NMR methods for studying amyloids
Amyloids are fibrillar structures self-assembled from proteins that have assumed a non-native, often toxic conformation. Accumulation of amyloid aggregates is associated with approximately 30 human diseases including neurodegenerative (Alzheimer’s, Parkinson’s, Huntington’s diseases, prion encephalopathies) and systemic diseases (type II diabetes, light chain amyloidosis, senile amyloidosis).
Understanding the structural and dynamic basis of amyloid formation could lead to new strategies for the treatment of amyloid disorders, including Alzheimer’s disease. However, atomic level structural studies of amyloids and especially their interactions can be challenging due to the insolubility, large molecular size and polymorphism of the aggregated forms as well as the short lifetime of the monomers and oligomers.
Our aim is to develop new solution and solid-state NMR approaches for the structural biology of amyloids, which would allow to bridge in-depth structural and dynamics studies with high throughput, thereby enabling the investigation of a variety of factors including diverse environmental conditions and amyloid cross-interactions.
- Aleksis R., Oleskovs F., Jaudzems K., Pahnke J., Biverstål H. Structural studies of amyloid-β peptides: Unlocking the mechanism of aggregation and the associated toxicity. Biochimie (2017) 140: 176-192. DOI
- Andreas L.B., Jaudzems K., Stanek J., Lalli D., Bertarello A., Le Marchand T., Cala-De Paepe D., Kotelovica S., Akopjana I., Knott B., Wegner S., Engelke F., Lesage A., Emsley L., Tars K., Herrmann T., Pintacuda G. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR. Proc. Natl. Acad. Sci. USA (2016) 113: 9187–9192. DOI (Full text)
Structural mechanism of spider silk formation, structure-property relationships of artificial spider silks
Spider silks are protein-based fibers, which hold great potential for applications in biomedicine and nanotechnology. Recent advances in biotechnology have allowed scalable production of recombinant spider silk proteins that can be processed into fibers and other macroscopic scaffolds. However, the properties of these artificial spider silks lag behind their natural counterparts. The reasons for this are lack of understanding of the molecular mechanisms of native silk spinning and structural determinants for specific mechanical properties.
We use solution and solid-state NMR to study the mechanism of formation, solid state structure and dynamics of artificial spider silks. The goal is to understand structure-property relationships of artificial spider silks and enable rational design of fibers with custom-made properties.
- Otikovs M., Andersson M., Jia Q., Nordling K., Meng Q., Andreas L.B., Pintacuda G., Johansson J., Rising A., Jaudzems K. Degree of Biomimicry of Artificial Spider Silk Spinning Assessed by NMR Spectroscopy. Angew. Chem. Int. Ed. (2017) 56: 12571–12575. DOI
- Otikovs M., Chen G., Nordling K., Landreh M., Meng Q., Jörnvall H., Kronqvist N., Rising A., Johansson J., Jaudzems K. Diversified Structural Basis of a Conserved Molecular Mechanism for pH-Dependent Dimerization in Spider Silk N-Terminal Domains. ChemBioChem (2015) 16: 1720–1724. DOI
Small molecule drug discovery
Small molecule drug discovery at LIOS involves fragment screening by NMR within the framework of fragment-based drug discovery. For this, we have acquired a fragment library of about one thousand compounds (see the physicochemical profile of the library). The goal of these studies is to identify small molecules (fragments of drug-like molecules), which bind optimally to the target protein, and evolve them to lead compounds by growing or linking several of the fragment hits. The screening is followed by identification of the fragment binding mode on the target protein or determination of the three-dimensional structure of the small molecule – protein complex.
Small molecule drug discovery is supported by our molecular modelling platform. We use molecular docking with or without experimental NMR restraints to determine the small molecule binding mode as well as molecular dynamics simulations for detailed protein-small molecule interaction analysis. The calculations are done on our CUDA GPU-enabled cluster.
- Rasina D., Otikovs M., Leitans J., Recacha R., Borysov O.V., Kanepe-Lapsa I., Domraceva I., Pantelejevs T., Tars K., Blackman M.J., Jaudzems K., Jirgensons A. Fragment-Based Discovery of 2-Aminoquinazolin-4(3H)-ones As Novel Class Nonpeptidomimetic Inhibitors of the Plasmepsins I, II, and IV. J. Med. Chem. (2016) 59: 374–387. DOI
- Zhulenkovs D., Rudevica Z., Jaudzems K., Turks M., Leonchiks A. Discovery and structure–activity relationship studies of irreversible benzisothiazolinone-based inhibitors against Staphylococcus aureus sortase A transpeptidase. Bioorg. Med. Chem. (2014) 22: 5988–6003. DOI
Small molecule NMR
The chemical and physical properties of synthetic compounds depend on their conformation and electronic structure. We use NMR to analyze conformational equilibria and estimate conformational energy barriers, probe intra-molecular and inter-molecular hydrogen bonding as well as to determine chemical reaction mechanisms.
The experimental studies are supported by quantum chemical calculations (DFT, ab initio, semi-empirical) for prediction of molecular potential energy, bond vibrations, molecular geometry, chemical reactivity, NMR chemical shifts and other parameters.
- Lends A., Olszewska E., Belyakov S., Erchak N., Liepinsh E. NMR and Quantum-Chemical Studies of Electrostatically Stabilized 1-(N,N-Substituted-aminiomethyl)spirobi[3-oxo(2,5-dioxa-1-silacyclopentan)]ates (ES-Silanates). Heteroatom Chem. (2015) 26: 12–28. DOI
- Petrova M., Muhamadejev R., Cekavicus B., Vigante B., Plotniece A., Sobolev A., Duburs G., Liepinsh E. Experimental and theoretical studies of bromination of diethyl 2,4,6-Trimethyl-1,4-dihydropyridine-3,5-dicarboxylate. Heteroatom Chem. (2014) 25: 114-126. DOI
- Goba I., Liepinsh E. 15N NMR of 1,4-dihydropyridine derivatives. Magn. Reson. Chem. (2013) 51: 391-396. DOI
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