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Background One-third of cancers activate endogenous synthesis of serine/glycine, and can become addicted to this pathway to sustain proliferation and survival. Mechanisms driving this metabolic rewiring remain largely unknown. Methods NKX2–1 overexpressing and NKX2–1 knockdown/knockout T-cell leukaemia and lung cancer cell line models were established to study metabolic rewiring using ChIP-qPCR, immunoblotting, mass spectrometry, and proliferation and invasion assays. Findings and therapeutic relevance were validated in mouse models and confirmed in patient datasets. Results Exploring T-cell leukaemia, lung cancer and neuroendocrine prostate cancer patient datasets highlighted the transcription factor NKX2–1 as putative driver of serine/glycine metabolism. We demonstrate that transcription factor NKX2–1 binds and transcriptionally upregulates serine/glycine synthesis enzyme genes, enabling NKX2–1 expressing cells to proliferate and invade in serine/glycine-depleted conditions. NKX2–1 driven serine/glycine synthesis generates nucleotides and redox molecules, and is associated with an altered cellular lipidome and methylome. Accordingly, NKX2–1 tumour-bearing mice display enhanced tumour aggressiveness associated with systemic metabolic rewiring. Therapeutically, NKX2–1-expressing cancer cells are more sensitive to serine/glycine conversion inhibition by repurposed anti-depressant sertraline, and to etoposide chemotherapy. Conclusion Collectively, we identify NKX2–1 as a novel transcriptional regulator of serine/glycine synthesis addiction across cancers, revealing a therapeutic vulnerability of NKX2–1-driven cancers.

Purpose: Cell-free DNA (cfDNA) analysis in plasma is an emerging technique with numerous applications in oncology. We employed cfDNA to determine chromosomal instability (CIN), nucleosome footprints (NF) and methylation profiles in metastatic colorectal cancer (mCRC) patients and to predict outcome to bevacizumab (BVZ) combination therapy. Experimental Design: Low coverage whole-genome sequencing (LC-WGS) was performed on matched tumor and plasma samples from 74 mCRC patients participating in the CTRIAL-IE 12-16 AC-ANGIOPREDICT Phase II clinical trial (NCT01822444), prior to receiving BVZ, and analyzed for CIN (3 subclusters with low, intermediate and high CIN, respectively) and nucleosomes. For 61/74 mCRC patients, plasma samples before and after BVZ treatment were available and used for targeted methylation sequencing. A validation cohort of mCRC plasma samples (n= 24) from the University Medical Center Mannheim (UMM) was similarly profiled. Results: Based on cfDNA CIN profiles, we subtyped mCRC patients with 92.3% accuracy of sample distinction into low and high CIN clusters (cluster 1 against cluster 2 and 3), demonstrating concordance between matched plasma and tumor samples. Improved survival outcome was observed in CIN high patients. Plasma-based CIN clustering and improved survival for CIN high patients was also confirmed in the UMM cohort. NF and methylation profiles differed between CIN clusters and healthy individuals, and could reliably separate cluster 1 from cluster 2 and 3 samples (AUC=0.72 and 0.85 respectively). A large methylation score decrease after BVZ treatment was associated with improved overall survival (p = 0.013). Conclusions: cfDNA can be analyzed to predict outcome to BVZ in mCRC patients. Detection of CNAs, NFs and methylation profiles facilitated stratification of samples into CIN clusters and informed patient response to treatment. Citation Format: Ian S. Miller, Valentina Thomas, Tom Venken, Ingrid Arijs, Ana Barat, Johannes Betge, Tianzuo Zhan, Timo Gaiser, Matthias P. Ebert, Jochen Prehn, Rut Klinger, Darran P. O’Connor, Brian Brian Moulton, Verena Murphy, Ray McDermott, Brian Bird, Gregory Leonard, Liam Grogan, Anne Horgan, Nadine Schulte, Markus Moehler, Nicole Prannikar, Judith Franz-Werner, Hans-Peter Feustel, Diether Lambrechts, Annette T. Byrne. Analysis of cell free DNA to predict outcome to Bevacizumab combination therapy in metastatic colorectal cancer patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5584.

Background Overcoming therapeutic resistance is one of the major hurdles in cancer care. One mechanism contributing to therapeutic resistance is a process in which epithelial cells switch to a mesenchymal state (epithelial-to-mesenchymal transition or EMT). The precise mechanisms driving EMT-mediated therapeutic resistance have, however, not been elucidated. Results Here, we study ten cell line pairs, for which parental cell lines were made resistant to either a targeted or chemotherapy-based treatment. First, we show by miRNA-200 overexpression that treatment resistance is driven by EMT. Next, we demonstrate that DNA methylation changes occur within each cell line pair and show that exposure to 5-azacytidine or knock down of DNA methyltransferases (DNMTs), both of which globally demethylate cells, result in EMT reversal and increased therapeutic sensitivity. This suggests DNA methylation to causally underlie EMT and treatment resistance. We also observe significant overlap in methylation profiles between resistant lines, suggesting a common epigenetic mechanism to cause resistance to therapy. In line with this hypothesis, cross-resistance to other targeted and chemotherapies is observed, while importantly, this is lost upon demethylation of the cells. Finally, we clinically validate that DNA methylation changes drive EMT-mediated resistance to sorafenib in patients with advanced hepatocellular carcinoma (HCC). Specifically, we develop a capture-based protocol to interrogate DNA methylation in low amounts of circulating tumor DNA (ctDNA). By interrogating the methylation status in liquid biopsies, longitudinally collected during sorafenib treatment, we assess whether DNA methylation changes also drive EMT and therapy resistance in a clinical setting. Particularly, by monitoring methylation changes in EMT genes, we are able to predict tumor response and acquired resistance to sorafenib. Conclusions We propose methylation changes underlying EMT to constitute a common resistance mechanism to cancer therapies. This process can be reversed pharmacologically and monitored non-invasively in ctDNA to predict resistance to treatment.

DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large and have high affinity for the target, the DNA in solution may get depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration $c_2$) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration $c_1 \gg c_2$). We show that depletion can give rise to a strongly-enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations $c_2/c_1$ that are up to three orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich, and exhibits a non-monotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence., Comment: 27 pages, 4 figures

In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (

Proteinase 3 (PR3) is a neutrophil serine protease present in cytoplasmic granules but also expressed at the neutrophil surface where it mediates proinflammatory effects. Studies of the underlying molecular mechanisms have been hampered by the lack of inhibitors of the PR3 membrane anchorage. Indeed while there exist inhibitors of the catalytic activity of PR3, its membrane interfacial binding site (IBS) is distinct from its catalytic site. The IBS has been characterized both by mutagenesis experiments and molecular modeling. Through docking and molecular dynamics simulations we have designed d-peptides targeting the PR3 IBS. We used surface plasmon resonance to evaluate their effect on the binding of PR3 to phospholipid bilayers. Next, we verified their ability of binding to PR3 via fluorescence spectroscopy and isothermal titration calorimetry. The designed peptides did not affect the catalytic activity of PR3. A few peptides bound to PR3 hydrophobic pockets and inhibited PR3 binding to lipids. While the (KFF)3K d-peptide inconveniently showed a significant affinity for the lipids, another d-peptide (SAKEAFFKLLAS) did not and it inhibited the PR3-membrane binding site with IC50 of about 40μM. Our work puts forward d-peptides as promising inhibitors of peripheral protein-membrane interactions, which remain high-hanging fruits in drug design.

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.

The response regulator PhoP is part of the PhoP/PhoQ two-component system, which is responsible for regulating the expression of multiple genes involved in controlling virulence, biofilm formation, and resistance to antimicrobial peptides. Therefore, modulating the transcriptional function of the PhoP protein is a promising strategy for developing new antimicrobial agents. There is evidence suggesting that phosphorylation-mediated dimerization in the regulatory domain of PhoP is essential for its transcriptional function. Disruption or stabilization of protein-protein interactions at the dimerization interface may inhibit or enhance the expression of PhoP-dependent genes. In this study, we performed molecular dynamics simulations on the active and inactive dimers and monomers of the PhoP regulatory domains, followed by pocket-detecting screenings and a quantitative hot-spot analysis in order to assess the druggability of the protein. Consistent with prior hypothesis, the calculation of the binding free energy shows that phosphorylation enhances dimerization of PhoP. Furthermore, we have identified two different putative binding sites at the dimerization active site (the α4-β5-α5 face) with energetic "hot-spot" areas, which could be used to search for modulators of protein-protein interactions. This study delivers insight into the dynamics and druggability of the dimerization interface of the PhoP regulatory domain, and may serve as a basis for the rational identification of new antimicrobial drugs.

The human phospholipid scramblase 1 (SCR) distributes lipids non-selectively between the cellular membrane leaflets. SCR has long been thought to be mostly localized in the cytoplasm (amino acids 1–287) and anchored to the membrane via the insertion of a 19 amino acid long transmembrane C-terminal helix (CTH, 288–306), which further extends to the exoplasmic side with a 12 amino acid long tail (307–318). Little is known about the structure of this protein, but recent experimental data on two CTH peptides (288–306 and 288–318) show that they insert through phospholipid bilayers and that the presence of cholesterol improves their affinity for lipid vesicles. Yet the sequence of the CTH (288KMKAVMIGACFLIDFMFFE306) contains an aspartic acid (D301), which is not exactly a prototypical amino acid for single-pass transmembrane helices. In this study, we investigate how the polar aspartate residue is accommodated in lipid bilayers containing POPC with and without cholesterol, using all-atom molecular dynamics simulations. We identify two cholesterol-binding sites: (i) A291, F298 and L299 and (ii) L299, F302 and E306 and suggest that cholesterol plays a role in stabilizing the helix in a transmembrane position. We suggest that the presence of the aspartate could be functionally relevant for the scramblase protein activity.

In contrast to lipid-specific flippases and floppases, scramblase proteins distribute lipids non-selectively between the lipid bilayer leaflets by a passive and much slower process, thereby destroying the intrinsic bilayer asymmetry. Unfortunately, the lack of structural data on scramblase proteins renders the analysis of its structure-activity relationship challenging. Experimental evidence indicates that the C-terminal segment of the human phospholipid scramblase 1 (SCR) is a transmembrane helix. Surprisingly, this 19 amino acids-long segment (CTH, 288-309) contains an aspartate (D301), a residue rarely found in single-pass transmembrane segments. In order to investigate if and how this untypical sequence is stabilized in a phospholipid bilayers, we performed molecular dynamics simulations of the CTH and on a longer construct that includes 12 additional amino acids of the SCR C-terminal end. Simulations with the IMM1 implicit membrane model yield a favorable binding energy for the transmembrane configuration, which is only about a half or a third of the energy obtained for prototypical helical membrane-binding domains. Multiple self-assembly coarse-grained simulations with POPC lipids result in a significant population (32%) of transmembrane configurations. Simulations with atomistic POPC phospholipid bilayers show that D301 of the shortest peptide induces local water defects, but less so for the longest peptide and even less in POPC:cholesterol (7:3) bilayers. The C-terminal amino acids of the CTH engage in specific polar interactions with the cholesterol hydroxyl group as well as D301, which hence contributes to the stabilization of the peptide within the membrane. Our simulations support the idea of the CTH being a transmembrane segment and we speculate that the aspartic acid D301 could have a functional role in the SCR scrambling activity.

The HIV Rev protein mediates the nuclear export of viral mRNA, and is thereby essential for the production of late viral proteins in the replication cycle. Rev forms a large organized multimeric protein-protein complex for proper functioning. Recently, the three-dimensional structures of a Rev dimer and tetramer have been resolved and provide the basis for a thorough structural analysis of the binding interaction. Here, molecular dynamics (MD) and binding free energy calculations were performed to elucidate the forces thriving dimerization and higher order multimerization of the Rev protein. It is found that despite the structural differences between each crystal structure, both display a similar behavior according to our calculations. Our analysis based on a molecular mechanics-generalized Born surface area (MM/GBSA) and a configurational entropy approach demonstrates that the higher order multimerization site is much weaker than the dimerization site. In addition, a quantitative hot spot analysis combined with a mutational analysis reveals the most contributing amino acid residues for protein interactions in agreement with experimental results. Additional residues were found in each interface, which are important for the protein interaction. The investigation of the thermodynamics of the Rev multimerization interactions performed here could be a further step in the development of novel antiretrovirals using structure based drug design. Moreover, the variability of the angle between each Rev monomer as measured during the MD simulations suggests a role of the Rev protein in allowing flexibility of the arginine rich domain (ARM) to accommodate RNA binding.

VIRus Inhibitory Peptide (VIRIP), a 20 amino acid peptide, binds to the fusion peptide (FP) of human immunodeficiency virus type 1 (HIV-1) gp41 and blocks viral entry. VIRIP derivatives with improved antiviral activity have been developed, and one of those derivatives has recently proven effective and safe in a phase 1/2 clinical trial. Here, molecular dynamics were executed in combination with molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) free energy calculations to explore the binding interaction between VIRIP derivatives and gp41 FP. A promising correlation between antiviral activity and simulated binding free energy was established thanks to restriction of the flexibility of the peptides, inclusion of configurational entropy calculations, and the use of multiple internal dielectric constants for the MM/PBSA calculations depending on the amino acid sequence. Based on these results, a virtual screening experiment was carried out to design VIRIP analogs with further improved antiretroviral activity. A selection of peptides was tested for inhibitory activity and several VIRIP derivatives were identified with significantly enhanced activity compared to the reference peptides. The results demonstrate that computational modeling strategies using an adapted MM/PBSA methodology improve the accuracy of binding free energy calculations of peptide complexes compared to the classic MM/PBSA protocol. As such, this virtual screening approach generated HIV-1 gp41 FP inhibitors with improved antiviral activity that could be useful for future clinical applications. Proteins 2011;. © 2011 Wiley-Liss, Inc.

The von Willebrand factor (VWF) A1-glycoprotein (GP) Ibα interaction is of major importance during thrombosis mainly at sites of high shear stress. Inhibitors of this interaction prevent platelet-dependent thrombus formation in vivo, without major bleeding complications. However, the size and/or protein nature of the inhibitors currently in development limit oral bioavailability and clinical development. We therefore aimed to search for a small molecule protein-protein interaction inhibitor interfering with the VWF-GPIbα binding. After determination of putative small molecule binding pockets on the surface of VWF-A1 and GPIbα using site-finding algorithms and molecular dynamics, high throughput molecular docking was performed on both binding partners. A selection of compounds showing good in silico docking scores into the predicted pockets was retained for testing their in vitro effect on VWF-GPIbα complex formation, by which we identified a compound that surprisingly stimulated the VWF-GPIbα binding in a ristocetin cofactor ELISA and increased platelet adhesion in whole blood to collagen under arterial shear rate but in contrast inhibited ristocetin-induced platelet aggregation. The selected compound adhering to the predicted binding partner GPIbα could be confirmed by saturation transfer difference NMR spectroscopy. We thus clearly identified a small molecule that modulates VWF-GPIbα binding and that will now serve as a starting point for further studies and chemical modifications to fully characterize the interaction and to manipulate specific activity of the compound.

Although there is a common agreement that hydrophobins and CO2 are responsible for primary gushing of carbonated beverages, the bio-molecular mechanism of this phenomenon is not well understood. Here, hydrophobin HFBII has been produced, extracted, and purified. A gushing test and DLS analysis was performed and allowed the authors to design an MD simulation setup to investigate the interaction of CO2 molecules with HFBII in time. The results indicate that CO2 molecules tend to aggregate at the hydrophobic patch of HFBII twice as much as to the rest of the protein. A model is proposed that elucidates the "nanobomb" formation depicting a definite chemical and biophysical description of the primary gushing mechanism. © 2012 American Society of Brewing Chemists, Inc. ispartof: JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS vol:70 issue:4 pages:249-256 status: published

Glycoside hydrolases of families 32 (GH32) and 68 (GH68) belong to clan GH-J, containing hydrolytic enzymes (sucrose/ fructans as donor substrates) and fructosyltransferases (sucrose/fructans as donor and acceptor substrates). In GH32 members, some of the sugar substrates can also function as inhibitors, this regulatory aspect further adding to the complexity in enzyme functionalities within this family. Although 3D structural information becomes increasingly available within this clan and huge progress has been made on structure-function relationships, it is not clear why some sugars bind as inhibitors without being catalyzed. Conserved aspartate and glutamate residues are well known to act as nucleophile and acid/bases within this clan. Based on the available 3D structures of enzymes and enzyme-ligand complexes as well as docking simulations, we calculated the pKa of the acid-base before and after substrate binding. The obtained results strongly suggest that most GH-J members show an acid-base catalyst that is not sufficiently protonated before ligand entrance, while the acid-base can be fully protonated when a substrate, but not an inhibitor, enters the catalytic pocket. This provides a new mechanistic insight aiming at understanding the complex substrate and inhibitor specificities observed within the GH-J clan. Moreover, besides the effect of substrate entrance on its own, we strongly suggest that a highly conserved arginine residue (in the RDP motif) rather than the previously proposed Tyr motif (not conserved) provides the proton to increase the pKa of the acid-base catalyst. ispartof: PLoS One vol:7 issue:5 ispartof: location:United States status: published

VIRus Inhibitory Peptide (VIRIP), a 20 amino acid peptide, binds to the fusion peptide (FP) of human immunodeficiency virus type 1 (HIV-1) gp41 and blocks viral entry. VIRIP derivatives with improved antiviral activity have been developed, and one of those derivatives has recently proven effective and safe in a phase 1/2 clinical trial. Here, molecular dynamics were executed in combination with molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) free energy calculations to explore the binding interaction between VIRIP derivatives and gp41 FP. A promising correlation between antiviral activity and simulated binding free energy was established thanks to restriction of the flexibility of the peptides, inclusion of configurational entropy calculations, and the use of multiple internal dielectric constants for the MM/PBSA calculations depending on the amino acid sequence. Based on these results, a virtual screening experiment was carried out to design VIRIP analogs with further improved antiretroviral activity. A selection of peptides was tested for inhibitory activity and several VIRIP derivatives were identified with significantly enhanced activity compared to the reference peptides. The results demonstrate that computational modeling strategies using an adapted MM/PBSA methodology improve the accuracy of binding free energy calculations of peptide complexes compared to the classic MM/PBSA protocol. As such, this virtual screening approach generated HIV-1 gp41 FP inhibitors with improved antiviral activity that could be useful for future clinical applications.