Biology subjects

Lange, R.

Publications and source records attributed to Lange, R..

6 recordsLinked to original sources

bioRxiv2024

Identification of nuclear pore proteins at plasmodesmata

Plasmodesmata (PD) mediate intercellular exchange of small molecules, RNAs and proteins between plant cells with an apparent exclusion limit for passive non-specific transport, and transport of specific cargo mediated by mediators. PD and nuclear pore complexes (NPC) are nanometer sized micropores with strikingly similar properties. Cargo translocation through NPC is mediated by phase separating FG-nucleoporins (FG-NUP). Here, bioinformatics, proteomics and fluorescence imaging identified FG-NUPs at PD. Transient expression of GFP fusions at low and intermediate expression levels supported dual localization of 12 NUPs to NPC and PD. Structured illumination microscopy detected the transmembrane anchor NUP CPR5 close to orifices of PD. cpr5 mutants showed reduced intercellular short-root (SHR) transport. However, transport defects cannot be excluded due to indirect effects in the mutants. Identification of FG-NUPs at PD is consistent with the recruitment of NUPs to form a PD pore gating complex consistent with phase separation domains as diffusion barriers at PD. Further analyses will be required to determine whether NUPs are bona fide PD components, or accumulate at PD in certain conditions, or may serve intermediate NPC storage.

cell biology↗

bioRxiv2024

Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of coronavirus disease (COVID-19) since its emergence in December 2019. As of January 2024, there has been over 774 million reported cases and 7 million deaths worldwide.[1] While vaccination efforts have been successful in reducing the severity of the disease and decreasing the transmission rate, the development of effective therapeutics against SARS-CoV-2 remains a critical need.[2] The main protease (Mpro) of SARS-CoV-2 is an essential enzyme required for viral replication and has been identified as a promising target for drug development. In this study, we report the identification of novel Mpro inhibitors, using a combination of deep reinforcement learning for de novo drug design with 3D pharmacophore/shape-based alignment and privileged fragment match count scoring components followed by hit expansions and molecular docking approaches. Our experimentally validated results show that 3 novel series exhibit potent inhibitory activity against SARS-CoV-2 Mpro, with IC50 values ranging from 1.3 uM to 2.3 uM and a high degree of selectivity. These findings represent promising starting points for the development of new antiviral therapies against COVID-19.

molecular biology↗

bioRxiv2024

Discovery and binding mode of a small molecule inhibitor of the apo form of human TDO2

Tryptophan-2,3-dioxygenase (TDO2) and indoleamine-2,3-dioxygenase (IDO1) catalyze the conversion of L-tryptophan to N-formyl-kynurenine and play important roles in metabolism, inflammation, and tumor immune surveillance. Their enzymatic activities depend on their heme contents, which vary dynamically according to biological conditions. Inhibitors binding to heme-containing holo-TDO2 are known, but to date no inhibitor that binds to the heme-free state (apo-TDO2) has been reported. We describe the discovery of the first apo-TDO2 targeting inhibitors, to our knowledge, together with their co-crystal structures and inhibition of cellular TDO2 activity at low nanomolar concentrations.

biochemistry↗

bioRxiv2023

Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket

To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate binding pocket. Of 631 fragments soaked, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (2 hits) or at crystal packing interfaces (3 hits). Notably, two fragments with a pose sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. Our structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography. SynopsisAn X-ray crystallographic screen on SARS-CoV-2 3CL protease resulted in 29 fragment hits, including two isatin-based reversible covalent binders, and revealed a strong influence of the crystal form used for fragment soaking on the bound conformation of three additional reference fragments.

biophysics↗

bioRxiv2021

Sequential defects in cardiac lineage commitment and maturation cause hypoplastic left heart syndrome

BackgroundComplex molecular programs in specific cell lineages govern human heart development. Hypoplastic left heart syndrome (HLHS) is the most common and severe manifestation within the spectrum of left ventricular outflow tract obstruction defects occurring in association with ventricular hypoplasia. The pathogenesis of HLHS is unknown, but hemodynamic disturbances are assumed to play a prominent role. MethodsTo identify perturbations in gene programs controlling ventricular muscle lineage development in HLHS, we performed: i) whole-exome sequencing of 87 HLHS parent-offspring trios, ii) nuclear transcriptomics of cardiomyocytes from ventricles of 4 patients with HLHS and 15 controls at different stages of heart development, iii) single cell RNA sequencing and iv) 3D modeling in iPSCs from 3 patients with HLHS and 3 controls. ResultsGene set enrichment and protein network analyses of damaging de-novo mutations and dysregulated genes from ventricles of patients with HLHS suggested alterations in specific gene programs and cellular processes critical during fetal ventricular cardiogenesis, including cell-cycle and cardiomyocyte maturation. Single-cell and 3D modeling with iPSCs demonstrated intrinsic defects in the cell-cycle/UPR/autophagy hub resulting in disrupted differentiation of early cardiac progenitor lineages leading to defective cardiomyocyte-subtype differentiation/maturation in HLHS. Additionally, premature cell-cycle exit of ventricular cardiomyocytes from HLHS patients prevented normal tissue responses to developmental signals for growth leading to multinucleation/polyploidy, accumulation of DNA damage, and exacerbated apoptosis, all potential drivers of left ventricular hypoplasia in absence of hemodynamic cues. ConclusionsOur results highlight that despite genetic heterogeneity in HLHS, many mutations converge on sequential cellular processes primarily driving cardiac myogenesis, suggesting novel therapeutic approaches.

developmental biology↗

bioRxiv2020

Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart

RationaleGenetic factors undoubtedly contribute to the development of congenital heart disease (CHD), but still remain mostly ill-defined. ObjectiveIdentification of genetic risk factors associated with CHD and functional analysis of SNP-carrying genes. Methods and ResultsGenetic association study of 1,440 Caucasian CHD patients from the German Heart Center Munich collected from March 2009 to June 2016, 2,594 patients of previous studies provided by the Newcastle University and 8,486 controls underwent meta-analysis to detect single nucleotide polymorphisms (SNPs) associated with CHD. Results4,034 Caucasian CHD patients strictly classified according to the Society of Thoracic Surgeons nomenclature and 8,486 controls were included. One SNP on chromosome 5 reached genome-wide significance across all CHD phenotypes (rs185531658,OR:2.16, p=5.28x10-9) and was also indicative for septal defects (OR:2.16, p=6.15x10-8). One region on chromosome 20 pointing to the MACROD2 locus, identified four SNPs (rs150246290,OR:3.78, p=1.27x10-10; rs149890280,OR:3.74, p=1.8x10-10; rs149467721,OR:3.53; p=1.39x10-9, rs77094733,OR:3.53, p=1.73x10-9) in patients with transposition of the great arteries (TGA). A second region was detected on chromosome 8 located at ZBTB10 (rs148563140,OR:3.42, p=3.28x10-8; rs143638934,OR:3.42, p=3.51x10-8) in the same subgroup. Three highly significant risk variants on chromosome 17 (rs76774446,OR:1.60, p=9.95x10-8; rs11874,OR:1.60, p=6.64x10-8; rs17677363,OR:1.60, p=9.81x10-8) within the GOSR2 locus were identified in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence expression of WNT3, and variant rs870142 related to septal defects is proposed to influence expression of MSX1. Cardiac differentiation of human and murine induced pluripotent stem cells and single cell RNAseq analyses of developing murine and human hearts show essential functional roles for MACROD2, GOSR2, WNT3 and MSX1 at all developmental stages. ConclusionsFor the first time genetic risk factors in CHD patients with TGA and ATAV were identified. Several candidate genes play an essential functional role in heart development at the embryonic, newborn and adult stage.

genomics↗