Berglund, N. A. | Search bioRxiv

bioRxiv2025

Unlocking Scalable Ligand Residence Time Predictions with Koffee Unbinding Kinetics Simulations

A great number of drug discovery programs fail due to poor in vivo efficacy and ADMET liabilities. On- and off-target ligand residence times can act as important drivers of these problems. While modern experimental techniques have made measuring compound kinetics data more routine, there is a lack of accurate, high-throughput simulation techniques to guide compound prioritization by residence time. In this work, we introduce Koffee Unbinding Kinetics as a solution to the hitherto unanswered problem of scalable ligand-protein residence time prediction. By bypassing conventional approaches based on molecular dynamics simulations, Koffee Unbinding Kinetics performs physics-based residence time screening at the atomistic level in {approx} 1 GPU minute per complex using inexpensive hardware, a speed-up of at least 3 - 5 orders of magnitude compared to current state-of-the-art simulation approaches. Koffee Unbinding Kinetics can enhance compound selection to mitigate costly future program failures by adding fast, predictive residence time simulations to early-stage computational drug discovery pipelines. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/686759v3_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@120d5dcorg.highwire.dtl.DTLVardef@b86b67org.highwire.dtl.DTLVardef@193554forg.highwire.dtl.DTLVardef@1c5c6c1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2017

Structural basis for endotoxin neutralization and anti-inflammatory activity of thrombin-derived C-terminal peptides

Thrombin-derived C-terminal peptides (TCP) of about 2 kDa are present in wounds, where they exert anti-endotoxic functions. In an effort to elucidate the structural and molecular aspects of these functions, we here employ a combination of nuclear magnetic resonance spectroscopy (NMR), ellipsometry, fluorescence spectroscopy, circular dichroism (CD) measurements, and in silico multiscale modeling to define interactions and the bound conformation of a TCP generated by neutrophil elastase, HVF18 (HVFRLKKWIQKVIDQFGE) in complex with bacterial lipopolysaccharide (LPS). In contrast to the disordered state of HVF18 in aqueous solution, its binding to LPS leads to a structural transition, wherein the N- terminus of the peptide forms a unique {beta}-turn whilst the C-terminus becomes helical. In silico modelling and simulations demonstrated that HVF18, as well as related peptides, target the LPS-binding site of CD14, and this interaction was experimentally supported using microscale thermophoresis. Collectively, the results demonstrate the role of structural transitions in LPS complex formation as well as in CD 14 interaction, and provide a molecular explanation for the previously observed therapeutic effects of TCPs in experimental models of bacterial sepsis and endotoxin shock.\n\nSignificanceThrombin-derived C-terminal peptides (TCPs) of various sizes are present in human wounds, where they bind bacteria as well as \"free\" lipopolysaccharide (LPS), and thereby reduce inflammation. In this work, employing a combination of cellular, biophysical and structural studies, combined with in silico multiscale modeling, we present the molecular structure of a TCP in association with LPS, and define a previously undisclosed interaction between TCPs and CD14. Further, we show that TCPs exhibit relatively weak but specific affinities, all in the M range, to both LPS and CD14. These novel structural insights into the function of this class of host-defense molecules will facilitate rational design of novel \"dual function\" anti-infectives, which target both bacteria and inflammatory signaling.

biophysics↗