Psilocybin (4-phosphoryloxy-N,N-dimethyltryptamine, 1) is the main indolethyl-amine natural product of psychotropic (so-called "magic") mushrooms. The majority of 1-producing species belongs to the eponymous genus Psilocybe, for which the biosynthetic events, beginning from l-tryptophan (2), and the involved enzymes have thoroughly been characterized. Some Inocybe (fiber cap) species, among them Inocybe corydalina, produce 1 as well. In product formation assays, we characterized four recombinantly produced biosynthesis enzymes of this species in vitro: IpsD, a pyridoxal-5'-phosphate-dependent l-tryptophan decarboxylase, the kinase IpsK, and two near-identical methyltransferases, IpsM1 and IpsM2. The fifth enzyme, the insoluble monooxygenase IpsH, was analyzed in silico. Surprisingly, none of the reactions intrinsic to the 1 pathway in Psilocybe species takes place in I. corydalina. Contrasting the situation in Psilocybe, the Inocybe pathway is branched and leads to baeocystin (4-phosphoryloxy-N-methyltryptamine, 3) as a second end product. Our results demonstrate that mushrooms recruited distantly or entirely unrelated enzymes to evolve the metabolic capacity for 1 biosynthesis twice independently.

The Psilocybe cubensis SAM-dependent methyltransferase, PsiM, catalyzes the last step in the biosynthesis of psilocybin. Likely evolved from monomethylating RNA methyltransferases, PsiM acquired a key amino acid exchange in the secondary sphere of the active site, M247 N, which is responsible for its capacity to dimethylate. Two variants, PsiMN247M and PsiMN247A, were generated to further examine the role of Asn247 for mono- and dimethylation in PsiM. Herein, we present the kinetic profiles of both variants and crystal structures at resolutions between 0.9 and 1.0 Å. Each variant was crystallized as a ternary complex with the non-methylated acceptor substrate, norbaeocystin and S-adenosyl-l-homocysteine, and in a second complex with the cofactor analog, sinefungin, and the monomethylated substrate, baeocystin. Consistent with the inability of the variants to catalyze a second methyl transfer, these structures reveal catalytically non-productive conformations and a high level of disorder of the methylamine group of baeocystin. Additionally, both variants exhibit destabilization in the β5-β7 sheets and a conserved β-turn of the core Rossmann fold, causing 20-fold reduced substrate binding and 2-fold lower catalytic efficiency even with norbaeocystin. Our structural and kinetic analyses of the variants suggest that Asn247 is essential to allow enough space in the active site for multiple methylations while also participating in a network of hydrogen bonds that stabilizes secondary structure elements in the immediate vicinity of the active site for optimal methylation of norbaeocystin.

AbstractPsilocybin, the natural hallucinogen produced by Psilocybe (“magic”) mushrooms, holds great promise for the treatment of depression and several other mental health conditions. The final step in the psilocybin biosynthetic pathway, dimethylation of the tryptophan-derived intermediate norbaeocystin, is catalysed by PsiM. Here we present atomic resolution (0.9 Å) crystal structures of PsiM trapped at various stages of its reaction cycle, providing detailed insight into the SAM-dependent methylation mechanism. Structural and phylogenetic analyses suggest that PsiM derives from epitranscriptomic N6-methyladenosine writers of the METTL16 family, which is further supported by the observation that bound substrates physicochemically mimic RNA. Inherent limitations of the ancestral monomethyltransferase scaffold hamper the efficiency of psilocybin assembly and leave PsiM incapable of catalysing trimethylation to aeruginascin. The results of our study will support bioengineering efforts aiming to create novel variants of psilocybin with improved therapeutic properties.

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia in 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring the ability to efficiently spread among humans and become pandemic. Its high mortality rate of up to 35% and the absence of effective targeted therapies call for the development of antiviral drugs for this pathogen. Since the beginning of the SARS-CoV-2 pandemic, extensive research has focused on identifying protease inhibitors for the treatment of SARS-CoV-2. Our intention was therefore to assess whether these protease inhibitors are viable options for combating MERS-CoV. To that end, we used previously established protease assays to quantify inhibition of SARS-CoV-2, MERS-CoV and other main proteases. Nirmatrelvir inhibited several of these proteases, whereas ensitrelvir was less broadly active. To simulate nirmatrelvir's clinical use against MERS-CoV and subsequent resistance development, we applied a safe, surrogate virus-based system. Using the surrogate virus, we previously selected hallmark mutations of SARS-CoV-2-Mpro, such as T21I, M49L, S144A, E166A/K/V and L167F. In the current study, we selected a pool of MERS-CoV-Mpro mutants, characterized the resistance and modelled the steric effect of catalytic site mutants S142G, S142R, S147Y and A171S.

Psilocybin, the natural hallucinogen from Psilocybe (magic) mushrooms, is a highly promising drug candidate for the treatment of depression and several other mental health conditions. Biosynthesis of psilocybin from the amino acid l-tryptophan involves four strictly sequential modifications. The third of these, ATP-dependent phosphorylation of the intermediate 4-hydroxytryptamine, is catalysed by PsiK. Here we present a crystallographic analysis and a structure-based mutagenesis study of this kinase, providing insight into its mode of substrate recognition. The results of our work will support future bioengineering efforts aimed at generating variants of psilocybin with enhanced therapeutic properties.

Background:Calcific aortic valve disease (CAVD) is characterized by a phenotypic switch of valvular interstitial cells to bone-forming cells. Toll-like receptors (TLRs) are evolutionarily conserved pattern recognition receptors at the interface between innate immunity and tissue repair. Type I interferons (IFNs) are not only crucial for an adequate antiviral response but also implicated in bone formation. We hypothesized that the accumulation of endogenous TLR3 ligands in the valvular leaflets may promote the generation of osteoblast-like cells through enhanced type I IFN signaling. Methods:Human valvular interstitial cells isolated from aortic valves were challenged with mechanical strain or synthetic TLR3 agonists and analyzed for bone formation, gene expression profiles, and IFN signaling pathways. Different inhibitors were used to delineate the engaged signaling pathways. Moreover, we screened a variety of potential lipids and proteoglycans known to accumulate in CAVD lesions as potential TLR3 ligands. Ligand-receptor interactions were characterized by in silico modeling and verified through immunoprecipitation experiments. Biglycan (Bgn), Tlr3, and IFN-alpha/beta receptor alpha chain (Ifnar1)-deficient mice and a specific zebrafish model were used to study the implication of the biglycan (BGN)-TLR3-IFN axis in both CAVD and bone formation in vivo. Two large-scale cohorts (GERA [Genetic Epidemiology Research on Adult Health and Aging], n=55 192 with 3469 aortic stenosis cases; UK Biobank, n=257 231 with 2213 aortic stenosis cases) were examined for genetic variation at genes implicated in BGN-TLR3-IFN signaling associating with CAVD in humans. Results:Here, we identify TLR3 as a central molecular regulator of calcification in valvular interstitial cells and unravel BGN as a new endogenous agonist of TLR3. Posttranslational BGN maturation by xylosyltransferase 1 (XYLT1) is required for TLR3 activation. Moreover, BGN induces the transdifferentiation of valvular interstitial cells into bone-forming osteoblasts through the TLR3-dependent induction of type I IFNs. It is intriguing that Bgn(-/-), Tlr3(-/-), and Ifnar1(-/-) mice are protected against CAVD and display impaired bone formation. Meta-analysis of 2 large-scale cohorts with >300 000 individuals reveals that genetic variation at loci relevant to the XYLT1-BGN-TLR3-interferon-alpha/beta receptor alpha chain (IFNAR) 1 pathway is associated with CAVD in humans. Conclusions:This study identifies the BGN-TLR3-IFNAR1 axis as an evolutionarily conserved pathway governing calcification of the aortic valve and reveals a potential therapeutic target to prevent CAVD.

Protease inhibitors are among the most powerful antiviral drugs. Nirmatrelvir is the first protease inhibitor specifically developed against the SARS-CoV-2 protease 3CLpro that has been licensed for clinical use. To identify mutations that confer resistance to this protease inhibitor, we engineered a chimeric vesicular stomatitis virus (VSV) that expressed a polyprotein composed of the VSV glycoprotein (G), the SARS-CoV-2 3CLpro, and the VSV polymerase (L). Viral replication was thus dependent on the autocatalytic processing of this precursor protein by 3CLpro and release of the functional viral proteins G and L, and replication of this chimeric VSV was effectively inhibited by nirmatrelvir. Using this system, we applied nirmatrelvir to select for resistance mutations. Resistance was confirmed by retesting nirmatrelvir against the selected mutations in additional VSV-based systems, in an independently developed cellular system, in a biochemical assay, and in a recombinant SARS-CoV-2 system. We demonstrate that some mutants are cross-resistant to ensitrelvir and GC376, whereas others are less resistant to these compounds. Furthermore, we found that most of these resistance mutations already existed in SARS-CoV-2 sequences that have been deposited in the NCBI and GISAID databases, indicating that these mutations were present in circulating SARS-CoV-2 strains.

The l-tryptophan decarboxylase PsiD catalyzes the initial step of the metabolic cascade to psilocybin, the major indoleethylamine natural product of the "magic" mushrooms and a candidate drug against major depressive disorder. Unlike numerous pyridoxal phosphate (PLP)-dependent decarboxylases for natural product biosyntheses, PsiD is PLP-independent and resembles type II phosphatidylserine decarboxylases. Here, we report on the in vitro biochemical characterization of Psilocybe cubensis PsiD along with in silico modeling of the PsiD structure. A non-canonical serine protease triad for autocatalytic cleavage of the pro-protein was predicted and experimentally verified by site-directed mutagenesis.

Protease inhibitors are among the most powerful antiviral drugs. However, for SARS-CoV-2 only a small number of protease inhibitors have been identified thus far and there is still a great need for assays that efficiently report protease activity and inhibition in living cells. Here, we engineer a safe VSV-based system to report both gain- and loss-of-function of coronavirus main protease (Mpro/3CLpro/Nsp5) activity in living cells. We use SARS-CoV-2 3CLpro in this system to confirm susceptibility to known inhibitors (boceprevir, GC376, PF-00835231, and PF-07321332/nirmatrelvir) and reevaluate other reported inhibitors (baicalein, ebselen, carmofur, ethacridine, ivermectin, masitinib, darunavir, and atazanavir). Moreover, we show that the system can be adapted to report both the function and the chemical inhibition of proteases from different coronavirus species as well as from distantly related viruses. Together with the fact that live cell assays also reflect compound permeability and toxicity, we anticipate that this system will be useful for both identification and optimization of additional coronavirus protease inhibitors.

Accurate experimentally determined structure models of biological macromolecules are used by a large and diverse community of researchers. It is an established practice to base the assessment of the structure model quality on both, expectations of correct stereochemistry and, most importantly, on examination of the model's fit to the primary experimental evidence. In the case of X-ray crystallography, the primary evidence is provided by the electron density map. The worldwide Protein Data Bank (wwPDB1) is a global repository of macromolecular models and the accompanying experimental data that allow to examine agreement between the electron density and structural model using programs such as Coot,2 Chimera,3 Pymol,4 or Molstack.5 Throughout its 50-year history, the PDB has accumulated over 180,000 macromolecular structures, and gained the reputation of the gold standard in structural biology and of the most reliable data resource in biomedical research in general.6 Recently, the PDB has seen an influx of many depositions from large-scale crystallographic fragment screening projects using a complex computational procedure called Pan-Dataset Density Analysis (PanDDA7). Based on a sophisticated multi-data-set analysis of reference models and potential ligand-complex crystals,7 such group depositions serve the purpose of identifying very low-occupancy small molecule ligands in macromolecular complexes. In brief, the idea of PanDDA consists of partial background solvent inclusion and subtraction of a virtual “multi-crystal ground state,” to produce so-called “event map,” revealing the supposed ligands in each of a multitude of different ligand data sets. As a result, the PDB accumulates large numbers of “group depositions” of many putative ligand complexes of the same protein target that presently do not conform to the primary objective of the PDB as a repository of high-quality structure models and data. In particular, the maps that can be retrieved for such deposits have dubious agreement with the models (Figure 1). While suited for fragment screening and lead discovery,8 the group deposition models dumped en masse into the PDB do not conform to the quality standards9, 10 expected of PDB entries. In particular, PanDDA deposits confuse most biomedical researchers as their data structure is different than that of other PDB deposits and the quality of the structure models, despite occasional high nominal resolution, is often questionable. The presence of group deposits that do not conform to PDB standards of data retrieval and model quality, but nevertheless are presented on a par with conventional entries, degrades the PDB integrity. For standard entries, the PDB-provided map coefficients or density maps are calculated from the supplied experimental and model data, allowing validation of the model against experiment. This procedure is not possible for PanDDA entries, as the “event maps”7 have a completely different nature and purpose. Consequently, group deposition entries are difficult or even impossible to individually validate and assess. They can mislead PDB users when selected as models to underpin further studies and may also mislead systems like AlphaFold211 during selection of optimal templates for structure prediction. Presence of nonconforming entries is particularly problematic for automated data-mining projects, including applications of Artificial Intelligence, as the presence of such data adds unexpected levels of noise during the learning and testing stages. The gold standard of structural biology, that is, the agreement of a structure model with underlying electron density, fails for group deposition models that severely disagree with the user-accessible electron density maps (Figure 1). If group deposition entries violating accepted quality metrics9, 10 become primary references for their protein families due to their reported very high resolution, the effect could be disastrous (Figure 1b). The presence of such deposits will affect the reliability of the PDB and its reputation as the most reliable repository in life sciences. While even the community of structural biologists may already have problems with understanding the limitations of group deposits, biomedical researchers, and bioinformaticians generally assume that the same quality standards and data structure are consistently applied to all models in the PDB. Nonstructural research communities rarely verify the model by comparison with the electron density, and thus rely entirely on structural biology standard metrics, such as reported resolution, and expect that PDB structure deposits represent uniformly valid and verified models. We postulate that PDB group depositions from large-scale ligand screening projects that do not present fully refined macromolecular models should be, as a minimum, very clearly marked as members of this special category. Ideally, however, such models should be relocated from the PDB into a separate database dedicated to group depositions. The inventors of the PanDDA7 ligand-screening methodology have already developed database capabilities ideally suited to storing and handling fragment screening data.12 They could, therefore, collaborate with the PDB to establish such a database, equipped with tools needed for proper examination and evaluation of fragment-screening entries. Clear annotation and separation of nonstandard entries will minimize contamination of the PDB by suboptimal structures; and importantly, structure-informed biomedical research will remain based on validated and verified experimental evidence. Mariusz Jaskolski, Alexander Wlodawer, Zbigniew Dauter, Wladek Minor, Bernhard Rupp: Conceptualization (equal); formal analysis (equal); writing – original draft (equal); writing – review and editing (equal).

The autosomal dominant monogenetic disease neurofibromatosis type 1 (NF1) affects approximately one in 3,000 individuals and is caused by mutations in the NF1 tumour suppressor gene, leading to dysfunction in the protein neurofibromin (Nf1) 1,2 . As a GTPase-activating protein, a key function of Nf1 is repression of the Ras oncogene signalling cascade. We determined the human Nf1 dimer structure at an overall resolution of 3.3 Å. The cryo-electron microscopy structure reveals domain organization and structural details of the Nf1 exon 23a splicing 3 isoform 2 in a closed, self-inhibited, Zn-stabilized state and an open state. In the closed conformation, HEAT/ARM core domains shield the GTPase-activating protein-related domain (GRD) so that Ras binding is sterically inhibited. In a distinctly different, open conformation of one protomer, a large-scale movement of the GRD occurs, which is necessary to access Ras, whereas Sec14-PH reorients to allow interaction with the cellular membrane 4 . Zn incubation of Nf1 leads to reduced Ras-GAP activity with both protomers in the self-inhibited, closed conformation stabilized by a Zn binding site between the N-HEAT/ARM domain and the GRD–Sec14-PH linker. The transition between closed, self-inhibited states of Nf1 and open states provides guidance for targeted studies deciphering the complex molecular mechanism behind the widespread neurofibromatosis syndrome and Nf1 dysfunction in carcinogenesis.

Although the dynamical refinement improves the fit significantly compared to the kinematical refinement, its current implementation still does not describe the electron diffraction data fully.To further improve the fit, it is necessary to properly account for further effects like crystal imperfections, effects of inelastic scattering and also the bonding effects in the electrostatic potential.

The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an effort to analyze and, if necessary, remediate these structures as deposited in the Protein Data Bank (PDB), this work presents a detailed analysis of 81 crystal structures of the main protease 3CLpro, an important target for the design of drugs against COVID-19. The structures of the unliganded enzyme and its complexes with a number of inhibitors were determined by multiple research groups using different experimental approaches and conditions; the resulting structures span 13 different polymorphs representing seven space groups. The structures of the enzyme itself, all determined by molecular replacement, are highly similar, with the exception of one polymorph with a different inter-domain orientation. However, a number of complexes with bound inhibitors were found to pose significant problems. Some of these could be traced to faulty definitions of geometrical restraints for ligands and to the general problem of a lack of such information in the PDB depositions. Several problems with ligand definition in the PDB itself were also noted. In several cases extensive corrections to the models were necessary to adhere to the evidence of the electron-density maps. Taken together, this analysis of a large number of structures of a single, medically important protein, all determined within less than a year using modern experimental tools, should be useful in future studies of other systems of high interest to the biomedical community.

Structural information, mainly derived by X-ray crystallography and Cryo-Electron Microscopy, is the quintessential prerequisite for structural-guided drug discovery.However, accurate structural information is only one piece of information necessary to understand the big picture of medical disorders.To provide a rapid response to emerging biomedical challenges and threats like COVID-19, we need to analyze medical data in the context of other in-vitro and in-vivo experimental results.Recent advancements in biochemical, spectroscopical, and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management framework like Advanced Information System proposed in 2017.The progress on AIS is too slow, but creating such a system is a Grand Challenge for biomedical sciences.By definition, a Grand Challenge is a challenging and extremely difficult long-term project that is not always appreciated by those looking for immediate returns.

Many macromolecular X-ray and cryo-EM structure models deposited in the PDB contain biologically relevant small molecule ligands with unsaturated fatty acid acyl chains, whose cis-trans stereochemistry is incorrect. The molecules are either not properly defined in their stereochemical restraint files, or the proper stereochemistry is neglected during model building. Often, the same molecules appear in deposited models in both isomeric configurations, one of which is almost always incorrect, and the use of the same moiety (HET) identifier and restraint files in model refinement is wrong. We present case studies of frequently occurring molecules and a compilation of identified cases of C-C=C-C cis-trans geometry in the deposited structure models. Full listings of cis/trans torsion angles are provided for models with commonly occurring molecules to assist identification and correction of cis-trans errors and prevent inadvertent use of incorrect models. Caveats for users, advice for modellers and suggestions for remediation efforts with a simple but effective restraint file modification are provided.

As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.

A bright spot in the SARS‐CoV‐2 (CoV‐2) coronavirus pandemic has been the immediate mobilization of the biomedical community, working to develop treatments and vaccines for COVID‐19. Rational drug design against emerging threats depends on well‐established methodology, mainly utilizing X‐ray crystallography, to provide accurate structure models of the macromolecular drug targets and of their complexes with candidates for drug development. In the current crisis, the structural biological community has responded by presenting structure models of CoV‐2 proteins and depositing them in the Protein Data Bank (PDB), usually without time embargo and before publication. Since the structures from the first‐line research are produced in an accelerated mode, there is an elevated chance of mistakes and errors, with the ultimate risk of hindering, rather than speeding up, drug development. In the present work, we have used model‐validation metrics and examined the electron density maps for the deposited models of CoV‐2 proteins and a sample of related proteins available in the PDB as of April 1, 2020. We present these results with the aim of helping the biomedical community establish a better‐validated pool of data. The proteins are divided into groups according to their structure and function. In most cases, no major corrections were necessary. However, in several cases significant revisions in the functionally sensitive area of protein–inhibitor complexes or for bound ions justified correction, re‐refinement, and eventually reversioning in the PDB. The re‐refined coordinate files and a tool for facilitating model comparisons are available at https://covid-19.bioreproducibility.org.DatabaseValidated models of CoV‐2 proteins are available in a dedicated, publicly accessible web service https://covid-19.bioreproducibility.org

FAH domain containing protein 1 (FAHD1) is a mammalian mitochondrial protein, displaying bifunctionality as acylpyruvate hydrolase (ApH) and oxaloacetate decarboxylase (ODx) activity. We report the crystal structure of mouse FAHD1 and structural mapping of the active site of mouse FAHD1. Despite high structural similarity with human FAHD1, a rabbit monoclonal antibody (RabMab) could be produced that is able to recognize mouse FAHD1, but not the human form, whereas a polyclonal antibody recognized both proteins. Epitope mapping in combination with our deposited crystal structures revealed that the epitope overlaps with a reported SIRT3 deacetylation site in mouse FAHD1.