Otto Loewi

“A drug is a substance which, if injected into a rabbit, produces a paper.”


 

Otto Loewi was a German-born pharmacologist and psychobiologist who discovered the role of acetylcholine as the body’s neurotransmitter. He was awarded the Nobel Prize in Physiology or Medicine in 1936 for his discovery. Although his statement was simplistic and exaggerated, the essence of the message was correct and indicative of recent decades. However, in addition to the ethical complications, it has become apparent in the last 100 years that animal experiments are not sufficiently and comprehensively suited to be a model for the human organism.

Combining next-generation bioinformatics with high-performance computing techniques and deep learning enables a deeper understanding of biological processes and contributes to future drug and protein research pipelines.

Catapulting knowledge of protein dynamics and interactions to the next level is, therefore, the greatest challenge and rewarding motivation. The methods and data obtained enable new approaches, e.g. for understanding signal transduction, membrane transport, electron transfer systems, cell metabolism, apoptosis or muscle contractions in healthy and diseased states. Further applications are not limited to the human organism and allow the study of bacteria, archaea, plants or even synthetic biomolecular interactions within and between species that help to understand allergies, develop new antibiotics, design the next series of synthetic organisms or finally even replace animal experiments by running virtual clinical trials.

 

 

Eleven highlighted, peer-reviewed research papers


 

 

Most recent paper 2021, about disrupting ribosome production, a renewed potential for cancer therapy. My role was the analysis of the diazaborine binding site using various cavity analysis tools.

M. Prattes, I. Grishkovskaya, V.V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach & H. Bergler
Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine.
Nature Communications 12, 3483 (2021)

nature.com/articles/s41467-021-23854-x   

 

Very recent paper 2021, about structural biology of SARS-CoV-2 variants. I designed, supervised and evaluated the experiments; wrote, submitted and revised the manuscript as corresponding author.

Singh, A., Steinkellner, G., Köchl, K., Gruber, K. & Gruber, C. C.*
Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2.
Sci Rep 11, 4320 (2021).

nature.com/articles/s41598-021-83761-5  

 

My milestone on a genome wide level in 2021. My contribution to this consortial work was to establish the dynamic structural viral proteome and to identify potential binding sites in 17 target proteins.

Gorgulla, C. et al.
A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening.
iScience 24, 102021 (2021).

cell.com/iscience/fulltext/S2589-0042(20)31218-9 

 

The proof-of-principle of the Catalophore technology and basis of the foundation of the company Innophore. I planned, executed and analysed the bioinformatics data mining experiments (*equal contribution).

Steinkellner, G.* & Gruber C.C.* et al.
Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations.
Nature communications 5, 1–9 (2014)

nature.com/articles/ncomms5150 

 

As senior scientist, I used molecular dynamics for various protein and protein-interface systems. In these exemplary publications and contributed the bioinformatics simulations, refinements and analysis.

Rengachari, S. et al.
The structure of monoacylglycerol lipase from Bacillus sp. H257 reveals unexpected conservation of the cap architecture between bacterial and human enzymes.
Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids 1821, 1012–1021 (2012). (Gruber, C. C., 4th author)

pubmed.ncbi.nlm.nih.gov/22561231/

Ferrario, V. et al.
Elucidating the structural and conformational factors responsible for the activity and substrate specificity of alkanesulfonate monooxygenase.
Journal of Biomolecular Structure and Dynamics 30, 74–88 (2012). (Gruber, C. C. , 4th author)

pubmed.ncbi.nlm.nih.gov/22571434/ 

 

In my Postdoc period I focused on molecular dynamics simulation of protein-protein and protein-membrane systems using massive large-scale computing facilities.

Gruber, C. C. & Pleiss, J.

Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities.

Journal of computational chemistry 32, 600–606 (2011).

onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21645

Gruber, C. C. & Pleiss, J.

Lipase B from Candida antarctica binds to hydrophobic substrate–water interfaces via hydrophobic anchors surrounding the active site entrance.

Journal of Molecular Catalysis B: Enzymatic 84, 48–54 (2012)

sciencedirect.com/science/article/abs/pii/S1381117712001348 

 

In early works originating from my master and PhD thesis I developed computational predictive and analytical methods to predict biological systems, specifically, for biocatalytic, enzymatic networks.

Gruber, C. C. et al.

An algorithm for the deconvolution of mass spectrosopic patterns in isotope labeling studies. Evaluation for the hydrogen− deuterium exchange reaction in ketones.

The Journal of organic chemistry 72, 5778–5783 (2007)

pubs.acs.org/doi/10.1021/jo070831o

Voss, C. V. & Gruber, C. C. et al.

Orchestration of concurrent oxidation and reduction cycles for stereoinversion and deracemisation of sec-alcohols.

Journal of the American Chemical Society 130, 13969–13972 (2008)

pubs.acs.org/doi/10.1021/ja804816a

Gruber, C. C. et al.

Emulation of racemase activity by employing a pair of stereocomplementary biocatalysts.

Chemistry–A European Journal 13, 8271–8276 (2007)

chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.200700528

 

Click here for a full list of publications in Google scholar 

 

 

Four highlighted active patents  


 

 

 

Determining novel enzymatic functionalities using three-dimensional point clouds representing physico chemical properties of protein cavities

Issued Nov 3, 2020 Patent issuer and number us US20150302142A1

patents.google.com/patent/US20150302142A1/en

 

Determining novel enzymatic functionalities using three-dimensional point clouds representing physico chemical properties of protein cavities

Issued May 27, 2020 Patent issuer and number eu EP2923291A1

patents.google.com/patent/EP2923291A1/en 

 

Process for the enzymatic deracemization of secondary alcohols

Issued Feb 22, 2012 Patent issuer and number eu EP2257635B1

patents.google.com/patent/EP2257635B1/en

 

Process for the racemization of optically active secondary alcohols with the use of two alcohol dehydrogenases

Issued Apr 2006 Patent issuer and number us US7795004B

patents.google.com/patent/US7795004B2/en 

 

 

 

Funding was kindly provided by the following
agencies, institutions and companies