Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference.

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a KD <20 µM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.

Structural basis for collagen recognition by the immune receptor OSCAR.

The osteoclast-associated receptor (OSCAR) is a collagen-binding immune receptor with important roles in dendritic cell maturation and activation of inflammatory monocytes as well as in osteoclastogenesis. The crystal structure of the OSCAR ectodomain is presented, both free and in complex with a consensus triple-helical peptide (THP). The structures revealed a collagen-binding site in each immunoglobulin-like domain (D1 and D2). The THP binds near a predicted collagen-binding groove in D1, but a more extensive interaction with D2 is facilitated by the unusually wide D1-D2 interdomain angle in OSCAR. Direct binding assays, combined with site-directed mutagenesis, confirm that the primary collagen-binding site in OSCAR resides in D2, in marked contrast to the related collagen receptors, glycoprotein VI (GPVI) and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1). Monomeric OSCAR D1D2 binds to the consensus THP with a KD of 28 µM measured in solution, but shows a higher affinity (KD 1.5 µM) when binding to a solid-phase THP, most likely due to an avidity effect. These data suggest a 2-stage model for the interaction of OSCAR with a collagen fibril, with transient, low-affinity interactions initiated by the membrane-distal D1, followed by firm adhesion to the primary binding site in D2.

A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters.

With the ever-increasing instances of resistance to frontline TB drugs there is the need to develop novel strategies to fight the worldwide TB epidemic. Boosting the effect of the existing second-line antibiotic ethionamide by inhibiting the mycobacterial transcriptional repressor protein EthR is an attractive therapeutic strategy. Herein we report the use of a fragment based drug discovery approach for the structure-guided systematic merging of two fragment molecules, each binding twice to the hydrophobic cavity of EthR from M. tuberculosis. These together fill the entire binding pocket of EthR. We elaborated these fragment hits and developed small molecule inhibitors which have a 100-fold improvement of potency in vitro over the initial fragments.

Use of sertraline and agomelatine in hemodialysis patients: A case series report.

OBJECTIVE: Major depressive disorder (MDD) is one of the most common psychiatric issues in hemodialysis population. However, the research on proper diagnostic tools and its treatment is still insufficient. The study was performed to investigate the safety and effectiveness of sertraline and agomelatine in a group of hemodialysis patients. PATIENTS AND METHODS: 78 adult patients from one dialysis centre in Poland were included into the study. The Beck Depression Inventory II (BDI-II) was used to screen for depressive symptoms and was followed by the clinical interview with the psychiatrist. Nine patients diagnosed with major depressive disorder received antidepressant treatment with sertraline or agomelatine, according to the best clinical practice. The additional treatment with vortioxetine was used if the initial one was not effective. The time of observation was 24 weeks. The psychiatric follow up as well as the laboratory data were obtained during the course of observation. RESULTS: All patients receiving sertraline achieved remission of depressive symptoms. In patients receiving agomelatine no remission was observed despite dose augmentation. The side effects of antidepressants were mild and did not result in treatment discontinuation. No abnormalities in liver enzymes levels were observed. In five cases the significant decrease of haemoglobin level was noticed, with no cases of bleeding reported. CONCLUSION: In patients receiving sertraline the antidepressant effect was satisfactory. No remission of depressive symptoms was observed in patients taking agomelatine. The side effects of antidepressants were mild and transient. Further research on depression treatment in hemodialysis patients is needed, including newer medications.

Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference.

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a K D <20 µM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.

Structural Characterization of Mycobacterium abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications for Fragment-Based Drug Design.

Anti-microbial resistance is a rising global healthcare concern that needs urgent attention as growing number of infections become difficult to treat with the currently available antibiotics. This is particularly true for mycobacterial infections like tuberculosis and leprosy and those with emerging opportunistic pathogens such as Mycobacterium abscessus, where multi-drug resistance leads to increased healthcare cost and mortality. M. abscessus is a highly drug-resistant non-tuberculous mycobacterium which causes life-threatening infections in people with chronic lung conditions such as cystic fibrosis. In this study, we explore M. abscessus phosphopantetheine adenylyl transferase (PPAT), an enzyme involved in the biosynthesis of Coenzyme A, as a target for the development of new antibiotics. We provide structural insights into substrate and feedback inhibitor binding modes of M. abscessus PPAT, thereby setting the basis for further chemical exploration of the enzyme. We then utilize a multi-dimensional fragment screening approach involving biophysical and structural analysis, followed by evaluation of compounds from a previous fragment-based drug discovery campaign against M. tuberculosis PPAT ortholog. This allowed the identification of an early-stage lead molecule exhibiting low micro molar affinity against M. abscessus PPAT (Kd 3.2 ± 0.8 µM) and potential new ways to design inhibitors against this enzyme. The resulting crystal structures reveal striking conformational changes and closure of solvent channel of M. abscessus PPAT hexamer providing novel strategies of inhibition. The study thus validates the ligandability of M. abscessus PPAT as an antibiotic target and identifies crucial starting points for structure-guided drug discovery against this bacterium.

Capabilities of Modern Semiconductor Gamma Cameras in Radionuclide Diagnosis of Coronary Artery Disease.

This paper presents a review of the literature concerning the clinical application of modern semiconductor (CZT) gamma cameras in the radioinuclide diagnosis of coronary artery disease. It contains information on the diagnostic efficacy of myocardial perfusion studies performed with those cameras compared with the widely used scintillation (Anger) cameras, an overview of their effectiveness in comparison with coronary angiography (also fractional flow reserve) and currently available clinical results of a myocardial flow reserve measured with a dynamic SPECT study. Introduction of this imaging modality to the measurement of a myocardial flow reserve aims to facilitate access to this type of study compared to the less available and more expensive PET method used so far.

Perceived Stress Levels among Ukrainian Migrant and LGBT+ Minorities in Poland during the COVID-19 Pandemic.

The Coronavirus disease 2019 (COVID-19) pandemic, immigrant status and being a member of the LGBT+ community are all independent factors associated with increased stress levels. Few studies provide more complex analysis on this issue, and there has been no research on the cumulative burden of perceived stress that people belonging to both minorities experience in the current epidemiological situation. The aim of this study was to assess the ability to deal with an external situation during the third wave of the COVID-19 pandemic in Poland in the following groups with different stress levels (total sample n = 370): Polish heterosexual men (n = 202), heterosexual men from Ukraine (n = 131) and homo- and bisexual men (men who have sex with men-MSM) from Ukraine (n = 37). A Perceived Stress Scale (PSS-10) was used. The analysis of the survey did not show statistically significant differences between the three study groups in the general level of perceived stress (24.71, 24.77 and 26.49 points, respectively, p = 0.551), but it revealed numerous differences in coping with various aspects of everyday functioning between these groups. Negative assessment of one's own health proved to be the main factor negatively affecting the level of perceived stress, however specific health risks, medical history or the participants' previous experience have not been taken into account in the study. Our research shows differences in the needs, resources and methods of coping with stress between men who are Polish citizens and migrants from Ukraine, both heterosexual and belonging to the MSM group. Proper identification and addressing of these needs, taking into account different availability of health services, could be the responsibility of NGOs or insurance providers. This should result in the reduction of mental health burdens and the risk of developing serious mental disorders, and consequently in better functioning of persons belonging to minorities and in a reduced burden on the health care system.

Inter- and Intraobserver Repeatability of Myocardial Flow Reserve Values Determined with SPECT Study Using a Discovery NM530c Camera and Corridor 4DM Software.

BACKGROUND: Myocardial blood flow (MBF) and flow reserve (MFR) examination, especially useful in the diagnosis of multivessel coronary artery disease (CAD), can be assessed with a cadmium-zinc-telluride (CZT) SPECT gamma camera, as an alternative to the expensive and less available PET. However, study processing is not free from subjective factors. Therefore, this paper aims to evaluate intra- and interobserver repeatability of MBF and MFR values obtained by the same operator and two independent operators. METHODS: This study included 57 adult patients. MBF and MFR were assessed using a Discovery NM530c camera in a two-day, rest/dipyridamople protocol, using 99mTc-MIBI. Data were processed using Corridor4DM software, twice by one operator and once by another operator. RESULTS: The repeatability of the assessed values was quite good in the whole myocardium, LAD and LCX vascular territories, but was poor in the RCA territory. CONCLUSIONS: The poor repeatability of MBF and MFR in RCA vascular territory can be explained by poor automatic orientation of the heart axis during post-processing and a so-called "cardiac creep" phenomenon. Better automatic heart orientation and introduction of automatic motion correction is likely to drastically improve this repeatability. In the present state of the software, PET is better for patients requiring assessment of MFR in the RCA territory.

Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site.

Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.

Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate.

Trehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential in Mycobacterium tuberculosis, with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Here, we report the first mycobacterial OtsA structures from Mycobacterium thermoresistibile in both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of substrate preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme, and map a new allosteric site.IMPORTANCE Mycobacterial infections are a significant source of mortality worldwide, causing millions of deaths annually. Trehalose is a multipurpose disaccharide that plays a fundamental structural role in these organisms as a component of mycolic acids, a molecular hallmark of the cell envelope of mycobacteria. Here, we describe the first mycobacterial OtsA structures. We show mechanisms of substrate preference and show that OtsA is regulated allosterically by 2-oxoglutarate and 2-phosphoglycerate at an interfacial site. These results identify a new allosteric site and provide insight on the regulation of trehalose synthesis through the OtsAB pathway in mycobacteria.

Assessment of the relation between pelvicalyceal dilatation in ultrasound and features of obstructive uropathy in dynamic renal scintigraphy.

BACKGROUND: Ultrasound is the first-line imaging in the diagnostics of the urinary system. It provides valuable morphological information, but its usefulness in assessment of the function of renal parenchyma is limited. Dynamic renal scintigraphy provides much more accurate information about parenchymal function of kidneys and urinary outflow. The aim of the study was to establish morphological ultrasound criteria for high likelihood of obstructive uropathy. MATERIAL AND METHODS: 59 patients (38 women, 21 men, between 18 and 82 years old, average age 50) with the pelvis dilatation > 10 mm in one or both kidneys newly diagnosed in ultrasound, without earlier history of kidney and urinary tract diseases or renal surgery. A total of 79 kidneys were included in the study. Ultrasound and dynamic renal scintigraphy were performed on the same day. In ultrasound, maximum anteroposterior diameter of the renal pelvis (mAPD) and anteroposterior pelvic diameter at hilum (hAPD) were obtained. The ratio of total pelvicalyceal area to the whole kidney area (%PCS) was also calculated. Uropathy was determined by the positive diuretic test in renal scintigraphy performed using 111 MBq of 99mTc-EC. RESULTS: In dynamic renal scintigraphy, features of uropathy were found in 18 out of 79 kidneys (23%). Optimal thresholds for detection of obstructive uropathy for measured ultrasound parameters were determined based on the ROC curves: mAPD ≥ 23 mm (sensitivity 94%, specificity 76%, accuracy 80%, AUROC 0.91) hAPD ≥ 20 mm (sensitivity 78%, specificity 87%, accuracy 85%, AUROC 0.82) PCA/WKA ≥ 22% (sensitivity 83%, specificity 74%, accuracy 76%, AUROC 0.85). CONCLUSIONS: Determined thresholds of parameters measuring pelvicalyceal dilatation in ultrasound, including the easiest one to obtain in routine diagnostics - mADP, provide satisfactory effectiveness in isolating kidneys with high likelihood of obstructive uropathy. Their application can optimize the selection of patients for further kidney diagnostic imaging (dynamic renal scintigrapy or urography).

Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew.

Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.

Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach.

Mycobacterium phenotypic hits are a good reservoir for new chemotypes for the treatment of tuberculosis. However, the absence of defined molecular targets and modes of action could lead to failure in drug development. Therefore, a combination of ligand-based and structure-based chemogenomic approaches followed by biophysical and biochemical validation have been used to identify targets for Mycobacterium tuberculosis phenotypic hits. Our approach identified EthR and InhA as targets for several hits, with some showing dual activity against these proteins. From the 35 predicted EthR inhibitors, eight exhibited an IC50 below 50 µM against M. tuberculosis EthR and three were confirmed to be also simultaneously active against InhA. Further hit validation was performed using X-ray crystallography yielding eight new crystal structures of EthR inhibitors. Although the EthR inhibitors attain their activity against M. tuberculosis by hitting yet undefined targets, these results provide new lead compounds that could be further developed to be used to potentiate the effect of EthA activated pro-drugs, such as ethionamide, thus enhancing their bactericidal effect.

Structural insights into the EthR-DNA interaction using native mass spectrometry.

EthR is a transcriptional repressor that increases Mycobacterium tuberculosis resistance to ethionamide. In this study, the EthR-DNA interaction has been investigated by native electrospray-ionization mass spectrometry for the first time. The results show that up to six subunits of EthR are able to bind to its operator.

Fragment-Sized EthR Inhibitors Exhibit Exceptionally Strong Ethionamide Boosting Effect in Whole-Cell Mycobacterium tuberculosis Assays.

Small-molecule inhibitors of the mycobacterial transcriptional repressor EthR have previously been shown to act as boosters of the second-line antituberculosis drug ethionamide. Fragment-based drug discovery approaches have been used in the past to make highly potent EthR inhibitors with ethionamide boosting activity both in vitro and ex vivo. Herein, we report the development of fragment-sized EthR ligands with nanomolar minimum effective concentration values for boosting the ethionamide activity in Mycobacterium tuberculosis whole-cell assays.

Structure of Mycobacterium thermoresistibile GlgE defines novel conformational states that contribute to the catalytic mechanism.

GlgE, an enzyme of the pathway that converts trehalose to α-glucans, is essential for Mycobacterium tuberculosis. Inhibition of GlgE, which transfers maltose from a maltose-1-phosphate donor to α-glucan/maltooligosaccharide chain acceptor, leads to a toxic accumulation of maltose-1-phosphate that culminates in cellular death. Here we describe the first high-resolution mycobacterial GlgE structure from Mycobacterium thermoresistibile at 1.96 Å. We show that the structure resembles that of M. tuberculosis and Streptomyces coelicolor GlgEs, reported before, with each protomer in the homodimer comprising five domains. However, in M. thermoresistibile GlgE we observe several conformational states of the S domain and provide evidence that its high flexibility is important for enzyme activity. The structures here reported shed further light on the interactions between the N-terminal domains and the catalytic domains of opposing chains and how they contribute to the catalytic reaction. Importantly this work identifies a useful surrogate system to aid the development of GlgE inhibitors against opportunistic and pathogenic mycobacteria.

Achieving high signal-to-noise in cell regulatory systems: Spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors.

How is information communicated both within and between cells of living systems with high signal to noise? We discuss transmembrane signaling models involving two receptor tyrosine kinases: the fibroblast growth factor receptor (FGFR) and the MET receptor. We suggest that simple dimerization models might occur opportunistically giving rise to noise but cooperative clustering of the receptor tyrosine kinases observed in these systems is likely to be important for signal transduction. We propose that this may be a more general prerequisite for high signal to noise in transmembrane receptor signaling.

Crystal structure of Escherichia coli enterobactin-specific isochorismate synthase (EntC) bound to its reaction product isochorismate: implications for the enzyme mechanism and differential activity of chorismate-utilizing enzymes.

EntC, one of two isochorismate synthases in Escherichia coli, is specific to the biosynthesis of the siderophore enterobactin. Here, we report the crystal structure of EntC in complex with isochorismate and Mg(2+)at 2.3 A resolution, the first structure of a chorismate-utilizing enzyme with a non-aromatic reaction product. EntC exhibits a complex alpha+beta fold like the other chorismate-utilizing enzymes, such as salicylate synthase and anthranilate synthase. Comparison of active site structures allowed the identification of several residues, not discussed previously, that might be important for the isochorismate activity of the EntC. Although EntC, MenF and Irp9 all convert chorismate to isochorismate, only Irp9 subsequently exhibits isochorismate pyruvate lyase activity resulting in the formation of salicylate and pyruvate as the reaction products. With a view to understanding the roles of these amino acid residues in the conversion of chorismate to isochorismate and to obtaining clues about the pyruvate lyase activity of Irp9, several mutants of EntC were generated in which the selected residues in EntC were substituted for those of Irp9: these included A303T, L304A, F327Y, I346L and F359Q mutations. Biochemical analysis of these mutants indicated that the side chain of A303 in EntC may be crucial in the orientation of the carbonyl to allow formation of a hydrogen bond with isochorismate. Some mutations, such as L304A and F359Q, give rise to a loss of catalytic activity, whereas others, such as F327Y and I346L, show that subtle changes in the otherwise closely similar active sites influence activity. We did not find a combination of these residues that conferred pyruvate lyase activity.

N-triazinylammonium tetrafluoroborates. A new generation of efficient coupling reagents useful for peptide synthesis.

A new generation of triazine-based coupling reagents (TBCRs), designed according to the concept of "superactive esters", was obtained by treatment of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) chloride with lithium or silver tetrafluoroborate. The structure of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium tetrafluoroborate was confirmed by X-ray diffraction. Activation of carboxylic acids by using this reagent proceeds via triazine "superactive ester". The coupling reagent was successfully used for the synthesis of Z-, Boc-, and Fmoc-protected dipeptides derived from natural and unnatural sterically hindered amino acids and for fragment condensation, in 80-100% yield and with high enantiomeric purity. The manual SPPS of the ACP(65-74) peptide fragment (H-Val-Gln-Ala-Ala-Ile-Asp-Tyr-Ile-Asn-Gly-OH) proceeded significantly faster than with TBTU or HATU, as well as the automated SPPS of the same fragment gave a purer product than by using TBTU or PyBOP. The reagent was also demonstrated to be efficient in on-resin head-to-tail cyclization of constrained cyclopeptides, in SPPS synthesis of Aib peptides, and in the synthesis of esters from appropriate acids, alcohols, and phenols. The high efficiency and versatility of this new generation of TBCRs confirm, for the first time, the usefulness of the concept of "superactive esters" in rational design of the structure of coupling reagents.