Molecular Search Engines

Prof. Dr. Alexander Nesterov-Mueller [Contact]

Like the Google search engine reacts on your requests, the Molecular Search Engines will experimentally provide information about relevant molecules or molecule-based processes. Molecular Search Engines copy evolutionary principle in technological manner: they use the diversity of the combinatorial synthetic molecules and the selection of these molecules in the array format.

Our group is established through the ERC Starting Grant (COMBIPATTERNING, 2011 - 2016).

                                 

Research

Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays

Highlights:

 

  • High-throughput screening for selective RNA binders;
  • Emergence of the standard genetic code from the combinatorial fusion cascade;
  • Prediction of ancient "living" membranes.

 

See for details: https://www.mdpi.com/1422-0067/23/7/3515 ;

https://www.mdpi.com/2075-1729/11/9/975

   

Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale

Highlights:

 

  • Human peptidome library design;
  • Each antibody has a number of "non-antigenic" selective binders with sub μM affinity;
  • Simultaneous measurement of dissociation constants KD of antibodies for 6000 peptides.

 

See for details: https://www.mdpi.com/1422-0067/23/7/3515

   

Serological Number for Characterization of Circulating Antibodies

Highlights:

 

  • How to determine the number of linear and conformational monoclonal antibody epitopes in the patient's sera?
  • What causes a pre-existing antibody response after vaccination?

 

See for details: https://www.mdpi.com/1422-0067/20/3/604

Selective Peptide Binders to the Perfluorinated Sulfonic Acid Ionomer Nafion

Highlights:

 

  • Discovery of new functional molecules with a selective affinity for technical polymers

 

See for details: https://doi.org/10.1002/adfm.202214932

 

Selected Publications:

  1. Schmidt, D.; Gartner, P.; Berezkin, I.; Rudat, J.; Bilger, M.; Grünert, T.; Zimmerer, N.; Quarz, P.; Scharfer, P.; Brückel, J.; Jung, A. P.; Singh, P.; Pooja, P.; Meier, B.; Stahlberger, M.; Schabel, W.; Bräse, S.; Lanza, G.; Nesterov-Mueller, A. Selective Peptide Binders to the Perfluorinated Sulfonic Acid Ionomer Nafion. Adv Func Mater 2023, https://doi.org/10.1002/adfm.202214932

  2. Jenne, F.; Berezkin, I.; Tempel, F.; Schmidt, D.; Popov, R.; Nesterov-Mueller, A. Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays. Life 2023, 13, 796. https://doi.org/10.3390/life13030796
  3. Jenne, F.; Biniaminov, S.; Biniaminov, N.; Marquardt, P.; von Bojničić-Kninski, C.; Popov, R.; Seckinger, A.; Hose, D.; Nesterov-Mueller, A. Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale. Int. J. Mol. Sci. 2022, 23, 3515.
  4. Babii, O.; Afonin, S.; Diel, C.; Huhn, M.; Dommermuth, J.; Schober, T.; Koniev, S.; Hrebonkin, A.; Nesterov-Mueller, A.; Komarov, I.V.; Ulrich A. Diarylethene-Based Photoswitchable Inhibitors of Serine Proteases. Angew Chem Int Edit 2021, 60, 21789-21794.
  5. Nesterov-Mueller, A.; Popov, R. The Combinatorial Fusion Cascade to Generate the Standard Genetic Code. Life 2021, 11, 975. https://doi.org/10.3390/life11090975
  6. Nesterov-Müller, A.; Popov, R. Die Botschaft von LUCA — der letzte universelle gemeinsame Vorfahre. Biospektrum 2020, 26, 488–489 8 (in German).
  7. Palermo, A.; Nesterov-Mueller, A. Serological Number for Characterization of Circulating Antibodies. Int J Mol Sci 2019, 20, doi:ARTN 604
  8. Held, F.E.; Guryev, A.A.; Frohlich, T.; Hampel, F.; Kahnt, A.; Hutterer, C.; Steingruber, M.; Bahsi, H.; von Bojnicic-Kninski, C.; Mattes, D.S.; Nesterov-Mueller, A.; Marschall, M.; Tsogoeva, S.  Facile access to potent antiviral quinazoline heterocycles with fluorescence properties via merging metal-free domino reactions. Nat Commun 2017, 8, doi:ARTN 15071
  9. von Bojnicic-Kninski, C.; Popov, R.; Dorsam, E.; Loeffler, F.F.; Breitling, F.; Nesterov-Mueller, A. Combinatorial Particle Patterning. Adv Funct Mater 2017, 27, doi:ARTN 1703511
  10. Nesterov-Müller, A.: Erfolgreicher Grenzgang : Bunsen und Kirchhoff: Entdeckung der Spektralanalyse, Physik in unserer Zeit 2016, 47: 233–237, DOI: 10.1002/piuz.201601440 (in German).
  11. Popova, A.A.; Schillo, S.M.; Demir, K.; Ueda, E.; Nesterov-Mueller, A.; Levkin, P.A. Droplet-Array (DA) Sandwich Chip: A Versatile Platform for High-Throughput Cell Screening Based on Superhydrophobic-Superhydrophilic Micropatterning. Adv Mater 2015, 27, 5217-5222, doi:10.1002/adma.201502115.
  12. Maerkle, F.; Loeffler, F.F.; Schillo, S.; Foertsch, T.; Muenster, B.; Striffler, J.; Schirwitz, C.; Bischoff, F.R.; Breitling, F.; Nesterov-Mueller, A. High-Density Peptide Arrays with Combinatorial Laser Fusing. Adv Mater 2014, 26, 3730-3734, doi:10.1002/adma.201305759.