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27 Publications visible to you, out of a total of 27
Wird KI neue Medikamente gegen Herzkrankheiten hervorbringen?

Abstract (Expand)

Zusammenfassung Angesichts der umwälzenden Auswirkungen, die künstliche Intelligenz (KI) auf Wissenschaft, Medizin und darüber hinaus hat, betrachten wir hier das Potenzial von KI für die Entdeckung …enzial von KI für die Entdeckung neuer Medikamente gegen Herzkrankheiten. Wir definieren KI im weitesten Sinne als den Einsatz von maschinellem Lernen, einschließlich Statistik und Deep Learning, um Muster in Datensätzen zu erkennen, die für Vorhersagen genutzt werden können. Jüngste Durchbrüche in der Fähigkeit, sehr große Datenmengen zu berücksichtigen, haben einen Boom in der KI-gestützten Arzneimittelentdeckung sowohl in der Wissenschaft als auch in der Industrie ausgelöst. Viele neue Unternehmen verfügen bereits über Arzneimittel-Pipelines, die bis in die klinische Erprobung reichen, aber noch keine Medikamente gegen Herzkrankheiten enthalten. Wir beschreiben hier den Einsatz von KI für die Entdeckung von niedermolekularen Medikamenten und Biologika, einschließlich therapeutischer Peptide, sowie für die Vorhersage von Wirkungen wie Kardiotoxizität. Der konzertierte Einsatz von KI zusammen mit physikbasierten Simulationen und experimentellen Rückkopplungsschleifen wird notwendig sein, um das Potenzial der KI für die Arzneimittelentdeckung und die Entwicklung von Präzisionsarzneimitteln für Herzkrankheiten voll auszuschöpfen.

Authors: Manuel Glaser, Julia Ritterhof, Patrick Most, Rebecca C. Wade

Date Published: 20th Nov 2023

Publication Type: Journal

Computational Models of Hen Egg White Lysozyme Physisorption to Silica- and Mica-like Surfaces

Abstract (Expand)

Protein-surface adsorption phenomena play a crucial role in a variety of fields, including medicine, molecular and cell biology, biotechnology, phar- maceutical sciences, and biophysics. It is therefore … desirable to develop accu- rate models to describe them. Hen-Egg-White-Lysozyme (HEWL) adsorption to silica- and mica-like surfaces entails minimal conformational changes, rendering it an ideal system for rigid-body Brownian dynamics simulations. Experimen- tal studies revealed that the fluorescence attached to HEWL exhibits a sharp overshoot followed by a trough as a function of time. This work identifies two inconsistencies in the explanation previously used by the authors to interpret the experiment. A reorientation does not seem to be the main driving factor for the overshoot. Furthermore, I examine previously used electrostatic potential models based on the Poisson-Boltzmann equation (PBE) used by Romanowska et al. and Reinhardt et al.. It is found that even though different orientations of HEWL- FITC on the surface are possible, the required amount of adsorbed proteins and corresponding reorientation is attained only with the linearized PBE-potential. The study provides a possible explanation why reaching the critical overshoot value with non-linearized PBE-based models poses difficulties. Overcoming this problem is an indispensable step in developing Brownian-dynamics-based atomic- detail multi-molecule models for protein-surface adsorption.

Author: Jakob Nießner

Date Published: 14th Nov 2023

Publication Type: Master's Thesis

Modeling of mechanistic effects of neurotrophin modulators

Abstract (Expand)

Neurotrophins (NTs) are growth factors that are expressed in the central and peripheral nervous systems. They are implicated in different phases of the development and maintenance of the nervous system … and they can regulate neuronal survival, development, function, plasticity, as well as neuronal apoptosis. NTs can be used as therapeutics for the treatment of neurodegenerative disorders. However, their poor pharmacokinetic properties and their invasive administration to patients renders them inefficient for use as pharmaceuticals. A solution to this can be offered by small molecule NT mimetics, which can elicit NT mechanisms through binding to NT receptors, which are transmembrane (TM) glycoproteins. The mechanism of activation of NT receptors remains elusive and thus, in this thesis, I have investigated the mechanism of action of NT receptors and mimetics through molecular modeling and molecular dynamics (MD) simulations. I modeled and simulated the glycosylated state of the full extracellular (EC) domains of Tropomyosin receptor kinases A and B (TrkA, TrkB) NT receptors, which revealed that the glycans can shield the accessible surface area of the receptors and participate in the contact area between receptor and NT. Most importantly, glycosylation promoted the extended conformations of the EC domains, which might facilitate NT binding. Then, I performed coarse-grained MD simulations to study the possible arrangements of the TM helical homodimers of TrkA and TrkB receptors in micelles. The results revealed arrangements that could correspond to the active state of the receptors, while metadynamics simulations indicated a stronger binding for the TrkA helices by 10 kJ/mol compared to TrkB. Next, I modeled the full-length structures of the TrkA and TrkB receptors in their homodimeric, glycosylated state bound to their NTs. I embedded the receptors in a realistic model of a neuronal asymmetric membrane. I verified the proper behavior of the membrane and proteins with smaller systems comprising of the TM and intracellular monomers of the receptors. These test simulations revealed interactions between positively charged residues of the kinase domain of TrkA with negatively charged lipids of the inner leaflet of the membrane. These interactions were also formed in the full-length system, and they might stabilize the two kinase domains of the receptor dimer in an orientation that promotes activation, even though the kinase domains were not activated during the simulations. Also, in the full-length systems, the EC domains approached and lay down on the neuronal membrane, while interacting with membrane lipids, such as gangliosides, which are able to activate the NT receptors. Finally, I investigated the binding of small-molecule NT mimetics to the EC and TM domains of TrkA and TrkB receptors, with molecular docking and MD simulations. While plausible poses were 8 obtained, they were not able to explain the selectivity of the compounds for the receptors and the simulations showed that binding was weak. Due to the cholesterol core of the NT mimetics, I tested the ability of the compounds to enter the cell membrane with MD simulations. The compounds were able to spontaneously penetrate the membranes, indicating that their binding site could also lie in the TM region of the receptors. However, simulations with the compounds bound or close to the TM helices in the membrane environment, showed no specific binding. Further experimental exploration of the binding mechanism of these compounds is required. Overall, this thesis sheds light on the dynamic behavior of TrkA and TrkB NT receptors in membranes and the mechanistic insights provide a basis for future studies to develop NT mimetics.

Author: Christina Athanasiou

Date Published: 30th Oct 2023

Publication Type: Doctoral Thesis

Design, synthesis and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids

Abstract

Not specified

Authors: Marina Roussaki, George E. Magoulas, Theano Fotopoulou, Nuno Santarem, Emile Barrias, Ina Pöhner, Sara Luelmo, Pantelis Afroudakis, Kalliopi Georgikopoulou, Paloma Tejera Nevado, Julia Eick, Eugenia Bifeld, María J. Corral, María Dolores Jiménez-Antón, Bernhard Ellinger, Maria Kuzikov, Irini Fragiadaki, Effie Scoulica, Sheraz Gul, Joachim Clos, Kyriakos C. Prousis, Juan J. Torrado, José María Alunda, Rebecca C. Wade, Wanderley de Souza, Anabela Cordeiro da Silva, Theodora Calogeropoulou

Date Published: 1st Sep 2023

Publication Type: Journal

Optimization of a Drug: Polymer Formulation Exploiting a Computational Approach based on Molecular Dynamics Simulations

Abstract

Not specified

Author: Michel Tarnow

Date Published: 22nd Aug 2023

Publication Type: Bachelor's Thesis

Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics

Abstract

Not specified

Authors: Lucas G. Viviani, Daria B. Kokh, Rebecca C. Wade, Antonia T.-do Amaral

Date Published: 14th Aug 2023

Publication Type: Journal

PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport

Abstract (Expand)

The chloroquine resistance transporter (PfCRT) confers resistance to a wide range of quinoline and quinoline-like antimalarial drugs in Plasmodium falciparum , with local drug histories driving its …rum , with local drug histories driving its evolution and, hence, the drug transport specificities. For example, the change in prescription practice from chloroquine (CQ) to piperaquine (PPQ) in Southeast Asia has resulted in PfCRT variants that carry an additional mutation, leading to PPQ resistance and, concomitantly, to CQ re-sensitization. How this additional amino acid substitution guides such opposing changes in drug susceptibility is largely unclear. Here, we show by detailed kinetic analyses that both the CQ- and the PPQ-resistance conferring PfCRT variants can bind and transport both drugs. Surprisingly, the kinetic profiles revealed subtle yet significant differences, defining a threshold for in vivo CQ and PPQ resistance. Competition kinetics, together with docking and molecular dynamics simulations, show that the PfCRT variant from the Southeast Asian P . falciparum strain Dd2 can accept simultaneously both CQ and PPQ at distinct but allosterically interacting sites. Furthermore, combining existing mutations associated with PPQ resistance created a PfCRT isoform with unprecedented non-Michaelis-Menten kinetics and superior transport efficiency for both CQ and PPQ. Our study provides additional insights into the organization of the substrate binding cavity of PfCRT and, in addition, reveals perspectives for PfCRT variants with equal transport efficiencies for both PPQ and CQ.

Authors: Guillermo M. Gomez, Giulia D’Arrigo, Cecilia P. Sanchez, Fiona Berger, Rebecca C. Wade, Michael Lanzer

Date Published: 7th Jun 2023

Publication Type: Journal

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