Biology subjects

Kirchmeyer, M.

Publications and source records attributed to Kirchmeyer, M..

4 recordsLinked to original sources

bioRxiv2025

Lab-in-the-loop therapeutic antibody design with deep learning

Therapeutic antibody design is a complex multi-property optimization problem with substantial promise for improvement with the application of machine-learning methods. Towards realizing that promise, we introduce "Lab-in-the-loop," a new approach that orchestrates state-of-the-art repertoire mining methods, generative machine learning models, multi-task property predictors, active learning ranking and selection, and in vitro experimentation in a semi-autonomous, iterative optimization loop. By automating the design of antibody variants, property prediction, ranking and selection of designs to assay in the lab, and ingestion of in vitro data, we enable an end-to-end approach to developing computationally-informed therapeutic antibody design pipelines. We apply lab-in-the-loop to eleven seed antibodies obtained via animal immunization with four clinically relevant antigen targets: EGFR, IL-6, HER2, and OSM. Over 1,800 unique antibody variants are tested throughout four rounds of iterative optimization identifying 3-100x better binding variants for all targets and 10/11 seeds, with the best binders exceeding 100 pM affinity, demonstrating a process by which end-to-end machine learning can be developed for therapeutic antibody development.

bioengineering↗

bioRxiv2024

Targeting the energy metabolism of melanoma cells: FX-11 acts as a mitochondrial uncoupler

In a compound screen on melanoma cells, which included different microenvironmental contexts aiming at better representing the environmental and growth characteristics of tumours, we identified several drugs efficiently suppressing cell viability. Here we focus on results obtained with FX-11, reported to be an inhibitor of lactate dehydrogenase (LDH). FX-11 dose-dependently inhibited growth of 624Mel and Wm3248 melanoma cells grown in a modular physiologic medium (MPM). Importantly, FX-11 was able to reduce the growth of the corresponding drug-resistant melanoma sublines equipotently. When testing the on-target activity of FX-11, the results were unexpected: in contrast to other LDH inhibitors (used as positive controls), FX-11 did not decrease the NAD+/NADH ratio, the glucose uptake, or the lactate secretion of melanoma cells. However, in seahorse assays, FX-11 increased the oxygen consumption rate as well as the extracellular acidification rate of cells, behaving like the mitochondrial uncouplers FCCP and Bam15. Treatment with FX-11, FCCP, or Bam15 induced an increase in acetyl-CoA carboxylase phosphorylation and a decrease in serine 65 phosphorylation of the eukaryotic initiation factor 4E-binding protein 1, indicative of AMPK activation by a decreased ATP/ADP ratio. Importantly, FX-11 and Bam15 drastically decreased the mitochondrial membrane potential in contrast to the LDH inhibitors LDH-IN-I and GNE-140. Taken together, we provide evidence that FX-11 effectively inhibits the growth of melanoma cells, including drug-resistant ones. FX-11 profoundly affects their energy metabolism, although it does not seem to act as other LDH inhibitors, but as a mitochondrial uncoupler.

cancer biology↗

bioRxiv2024

Metabolism-oriented compound screen in physiological culture conditions identifies a NAMPT inhibitor highly effective against drug-naive and -resistant melanoma cells

Many melanoma patients do not respond to therapy or rapidly develop resistance to MAPK pathway inhibitors and immune checkpoint blockade treatments, highlighting the urgent need for additional therapeutic strategies for these patients. To identify compounds that target drug-naive and -resistant melanoma cells (Encorafenib/Binimetinib-resistant), we performed a screen using a metabolism-oriented compound library in different cell culture media and growth conditions (2D and 3D). The efficacy of several compounds varied considerably under changing test conditions, but importantly, we also detected compounds that work across all tested conditions. In general, drug activity was reduced under hypoxia and in 3D spheroids. Thorough validation was performed for drugs showing potency in all conditions with a focus on efficacy in 3D spheroids grown in an in- house physiological culture medium. Using hydrogel matrix-embedded multi-cell type 3D models, we found that FK866, a nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, is very potently suppressing melanoma cell growth while not affecting the growth of healthy cells such as fibroblasts and endothelial cells.

cancer biology↗

bioRxiv2024

Ferroptosis susceptibility of melanoma cells: dependence on cell-type, acquired drug resistance, and medium composition

Resistance of melanoma cells to targeted therapy (BRAF and MEK inhibitors) is a major clinical problem and alternative treatments are sought. We describe the establishment of modular physiologic medium (MPM) and Mel-MPM (which contains additional supplements and sustains the 3D growth of melanoma cells, fibroblasts (NHDFs) and HMEC-1 endothelial cells) as novel resources for melanoma and combine them with a multi-cell-type matrix-embedded 3D culture model to investigate melanoma cell vulnerabilities in a more physiological setting. We made use of the modular nature of MPM to interrogate NEAA dependencies in melanoma cells and we found them to be particularly sensitive to the depletion of C/C. We additionally describe that melanoma cells are less sensitive to ferroptosis inducing compounds when cultured in MPM compared to RPMI and we could attribute this to different components of MPM and Mel-MPM (selenite, B27). Cell death induced by the glutathione peroxidase 4 inhibitor, ML162, had characteristics of ferroptosis or apoptosis depending on cell type, its drug resistance status and the culture medium. Cystine/cysteine starvation and ML162 treatment combinations increased melanoma cell death in 2D, 3D, and also in the complex matrix embedded multi-cell-type-3D system in OrganoplatesTM. This underlines the potential of combining metabolism-oriented drug treatments with amino acid starvation conditions, which is of interest in view of future therapeutic approaches to combat melanoma and other cancer types.

cancer biology↗