Manfred Auer
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View article: Democratized Discovery of Microsclerodermin F as an Immunophilin Ligand
Democratized Discovery of Microsclerodermin F as an Immunophilin Ligand Open
While immunophilins are well-recognized therapeutic targets, several members of this family of peptidyl-proline isomerases (PPIases) have yet to be subjected to ligand discovery efforts. In this study, we demonstrate a cost-effective means…
View article: Cellular Activity of CQWW Nullomer-Derived Peptides
Cellular Activity of CQWW Nullomer-Derived Peptides Open
Analysis of observed protein sequences across all species within the UniProtKB/Swiss-Prot data set reveals CQWW as the shortest absent stretch of amino acids. While DNA can be found encoding the CQWW sequence, it has never been observed to…
View article: Repositioning Brusatol as a Transmission Blocker of Malaria Parasites
Repositioning Brusatol as a Transmission Blocker of Malaria Parasites Open
Currently, primaquine is the only malaria transmission-blocking drug recommended by the WHO. Recent efforts have highlighted the importance of discovering new agents that regulate malarial transmission, with particular interest in agents t…
View article: A Novel Confocal Scanning Protein–Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin
A Novel Confocal Scanning Protein–Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin Open
Protein-protein interactions (PPIs) are some of the most challenging target classes in drug discovery. Highly sensitive detection techniques are required for the identification of chemical modulators of PPIs. Here, we introduce PPI confoca…
View article: Revealing the Indispensable Role of the RFamide Functionality using a Novel Acid Labile Benzofuranone based Amine (ALBA) Linker
Revealing the Indispensable Role of the RFamide Functionality using a Novel Acid Labile Benzofuranone based Amine (ALBA) Linker Open
The RFamide family of peptides represents an important class of GPCR ligand neuropeptides covering a wide range of biological functions. While many analogues of the highly conserved C‐terminal RFamide motif within this peptide class have b…
View article: Optimum ligand affinity for competition-based primary screens.
Optimum ligand affinity for competition-based primary screens. Open
Background and Purpose A simplistic assumption in setting up a competition assay is that a low affinity labelled ligand can be more easily displaced from a target protein than a high affinity ligand, which in turn produces a sensitive assa…
View article: Reduction in Nuclear Size by DHRS7 in Prostate Cancer Cells and by Estradiol Propionate in DHRS7-Depleted Cells
Reduction in Nuclear Size by DHRS7 in Prostate Cancer Cells and by Estradiol Propionate in DHRS7-Depleted Cells Open
Increased nuclear size correlates with lower survival rates and higher grades for prostate cancer. The short-chain dehydrogenase/reductase (SDR) family member DHRS7 was suggested as a biomarker for use in prostate cancer grading because it…
View article: OpenFEPOPS: A Python implementation of the FEPOPSmolecular similarity technique
OpenFEPOPS: A Python implementation of the FEPOPSmolecular similarity technique Open
Summary OpenFEPOPS is an open-source Python implementation of the FEature POint PharmacophoreS (FEPOPS) molecular similarity technique (Jenkins et al., 2004; Jenkins, 2013; Nettles et al., 2007) enabling descriptor generation, comparison, …
View article: Estradiol propionate reduction of nuclear size in prostate cancer lines lacking DHRS7 suggests DHRS7 absence as a biomarker for the effectiveness of estrogen therapy
Estradiol propionate reduction of nuclear size in prostate cancer lines lacking DHRS7 suggests DHRS7 absence as a biomarker for the effectiveness of estrogen therapy Open
Increased nuclear size correlates with lower survival rates for prostate cancer and is a hallmark of late-stage androgen-insensitive tumors. The short-chain dehydrogenase/reductase (SDR) family member DHRS7 was suggested as a marker for pr…
View article: Nanoscaled Discovery of a Shunt Rifamycin from <i>Salinispora arenicola</i> Using a Three-Color GFP-Tagged <i>Staphylococcus aureus</i> Macrophage Infection Assay
Nanoscaled Discovery of a Shunt Rifamycin from <i>Salinispora arenicola</i> Using a Three-Color GFP-Tagged <i>Staphylococcus aureus</i> Macrophage Infection Assay Open
Antimicrobial resistance has emerged as a global public health threat, and development of novel therapeutics for treating infections caused by multi-drug resistant bacteria is urgent. Staphylococcus aureus is a major human and animal patho…
View article: CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens
CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens Open
A simplistic assumption in setting up a competition assay is that a low affinity labeled ligand can be more easily displaced from a target protein than a high affinity ligand, which in turn produces a more sensitive assay. An often-cited p…
View article: Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion
Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion Open
Background: Lower survival rates for many cancer types correlate with changes in nuclear size/scaling in a tumor-type/tissue-specific manner. Hypothesizing that such changes might confer an advantage to tumor cells, we aimed at the identif…
View article: Fluorescence microscopy-based quantitation of GLUT4 translocation
Fluorescence microscopy-based quantitation of GLUT4 translocation Open
Postprandial insulin-stimulated glucose uptake into target tissue is crucial for the maintenance of normal blood glucose homeostasis. This step is rate-limited by the number of facilitative glucose transporters type 4 (GLUT4) present in th…
View article: MRlogP: Transfer Learning Enables Accurate logP Prediction Using Small Experimental Training Datasets
MRlogP: Transfer Learning Enables Accurate logP Prediction Using Small Experimental Training Datasets Open
Small molecule lipophilicity is often included in generalized rules for medicinal chemistry. These rules aim to reduce time, effort, costs, and attrition rates in drug discovery, allowing the rejection or prioritization of compounds withou…
View article: SimilarityLab: Molecular Similarity for SAR Exploration and Target Prediction on the Web
SimilarityLab: Molecular Similarity for SAR Exploration and Target Prediction on the Web Open
Exploration of chemical space around hit, experimental, and known active compounds is an important step in the early stages of drug discovery. In academia, where access to chemical synthesis efforts is restricted in comparison to the pharm…
View article: RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels
RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels Open
RNA–protein interactions are central to all gene expression processes and contribute to a variety of human diseases. Therapeutic approaches targeting RNA–protein interactions have shown promising effects on some diseases that are previousl…
View article: PyBindingCurve, Simulation, and Curve Fitting to Complex Binding Systems at Equilibrium
PyBindingCurve, Simulation, and Curve Fitting to Complex Binding Systems at Equilibrium Open
Understanding multicomponent binding interactions in protein-ligand, protein-protein, and competition systems is essential for fundamental biology and drug discovery. Hand-deriving equations quickly become unfeasible when the number of com…
View article: RNA pull-down-Confocal Nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-Synuclein levels
RNA pull-down-Confocal Nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-Synuclein levels Open
RNA-protein interactions are central to all gene expression processes and contribute to variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously …
View article: A two-step resin based approach to reveal survivin-selective fluorescent probes
A two-step resin based approach to reveal survivin-selective fluorescent probes Open
A dual-resin system was developed that united confocal-fluorescent imaging for hit identification and microscale NMR for hit isolation and structure elucidation. Using this approach, we identified two natural products that bound to the inh…
View article: 2-D structure of the Neurospora crassa plasma membrane ATPase as determined by electron cryomicroscopy.
2-D structure of the Neurospora crassa plasma membrane ATPase as determined by electron cryomicroscopy. Open
Large, well-ordered 2-D crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase grow rapidly on the surface of a polyethylene glycol-containing mixture similar to that originally developed for growing …
View article: PyBindingCurve, simulation and curve fitting to complex binding systems at equilibrium
PyBindingCurve, simulation and curve fitting to complex binding systems at equilibrium Open
Understanding multicomponent binding interactions in protein-ligand, protein-protein and competition systems is essential for fundamental biology and drug discovery. Hand deriving equations quickly becomes unfeasible when the number of com…
View article: Quantitative Microdialysis: Experimental Protocol and Software for Small Molecule Protein Affinity Determination and for Exclusion of Compounds with Poor Physicochemical Properties
Quantitative Microdialysis: Experimental Protocol and Software for Small Molecule Protein Affinity Determination and for Exclusion of Compounds with Poor Physicochemical Properties Open
Quantitative microdialysis is a traditional biophysical affinity determination technique. In the development of the detailed experimental protocol presented, we used commercially available equipment, rapid equilibrium dialysis (RED) device…
View article: Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D
Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D Open
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common …
View article: Chemical-Genetic Interrogation of Nuclear Size Control Reveals Cancer-Specific Effects on Cell Migration and Invasion
Chemical-Genetic Interrogation of Nuclear Size Control Reveals Cancer-Specific Effects on Cell Migration and Invasion Open
Lower survival rates for many cancer types correlate with increases or decreases in nuclear size/scaling in a tumor-type/tissue-specific manner. Postulating that nuclear size changes confer a fitness advantage on tumor cells, we screened f…
View article: Asparagine Deprivation Causes a Reversible Inhibition of Human Cytomegalovirus Acute Virus Replication
Asparagine Deprivation Causes a Reversible Inhibition of Human Cytomegalovirus Acute Virus Replication Open
HCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, lat…
View article: Asparagine deprivation causes a reversible inhibition of Human Cytomegalovirus acute virus replication
Asparagine deprivation causes a reversible inhibition of Human Cytomegalovirus acute virus replication Open
As obligate intracellular pathogens, viruses rely on the host cell machinery to replicate efficiently, with the host metabolism extensively manipulated for this purpose. High throughput siRNA screens provide a systematic approach for the i…
View article: α-Synuclein–Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation
α-Synuclein–Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation Open
α-Synuclein fibrils are considered a hallmark of Parkinson's disease and other synucleinopathies. However, small oligomers that formed during the early stages of α-synuclein aggregation are thought to be the main toxic species causing dise…
View article: Identification of novel host factors influencing human cytomegalovirus replication using a two-step siRNA screen
Identification of novel host factors influencing human cytomegalovirus replication using a two-step siRNA screen Open
As an obligate intracellular parasite, human cytomegalovirus (HCMV) completely relies on host machinery to replicate. Understanding which host factors are required for virus replication contributes to our understanding of virus biology and…
View article: Oligopeptide Signaling through TbGPR89 Drives Trypanosome Quorum Sensing
Oligopeptide Signaling through TbGPR89 Drives Trypanosome Quorum Sensing Open
Trypanosome parasites control their virulence and spread by using quorum sensing (QS) to generate transmissible "stumpy forms" in their host bloodstream. However, the QS signal "stumpy induction factor" (SIF) and its reception mechanism ar…