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1.
Nat Commun ; 15(1): 5239, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38937448

ABSTRACT

Tuberculosis remains a large global disease burden for which treatment regimens are protracted and monitoring of disease activity difficult. Existing detection methods rely almost exclusively on bacterial culture from sputum which limits sampling to organisms on the pulmonary surface. Advances in monitoring tuberculous lesions have utilized the common glucoside [18F]FDG, yet lack specificity to the causative pathogen Mycobacterium tuberculosis (Mtb) and so do not directly correlate with pathogen viability. Here we show that a close mimic that is also positron-emitting of the non-mammalian Mtb disaccharide trehalose - 2-[18F]fluoro-2-deoxytrehalose ([18F]FDT) - is a mechanism-based reporter of Mycobacteria-selective enzyme activity in vivo. Use of [18F]FDT in the imaging of Mtb in diverse models of disease, including non-human primates, successfully co-opts Mtb-mediated processing of trehalose to allow the specific imaging of TB-associated lesions and to monitor the effects of treatment. A pyrogen-free, direct enzyme-catalyzed process for its radiochemical synthesis allows the ready production of [18F]FDT from the most globally-abundant organic 18F-containing molecule, [18F]FDG. The full, pre-clinical validation of both production method and [18F]FDT now creates a new, bacterium-selective candidate for clinical evaluation. We anticipate that this distributable technology to generate clinical-grade [18F]FDT directly from the widely-available clinical reagent [18F]FDG, without need for either custom-made radioisotope generation or specialist chemical methods and/or facilities, could now usher in global, democratized access to a TB-specific PET tracer.


Subject(s)
Mycobacterium tuberculosis , Positron-Emission Tomography , Trehalose , Tuberculosis , Animals , Mycobacterium tuberculosis/metabolism , Positron-Emission Tomography/methods , Trehalose/metabolism , Tuberculosis/diagnostic imaging , Tuberculosis/microbiology , Tuberculosis/metabolism , Humans , Mice , Fluorine Radioisotopes , Fluorodeoxyglucose F18/metabolism , Fluorodeoxyglucose F18/chemistry , Radiopharmaceuticals/metabolism , Disease Models, Animal , Female
2.
ACS Infect Dis ; 10(5): 1679-1695, 2024 05 10.
Article in English | MEDLINE | ID: mdl-38581700

ABSTRACT

Linezolid is a drug with proven human antitubercular activity whose use is limited to highly drug-resistant patients because of its toxicity. This toxicity is related to its mechanism of action─linezolid inhibits protein synthesis in both bacteria and eukaryotic mitochondria. A highly selective and potent series of oxazolidinones, bearing a 5-aminomethyl moiety (in place of the typical 5-acetamidomethyl moiety of linezolid), was identified. Linezolid-resistant mutants were cross-resistant to these molecules but not vice versa. Resistance to the 5-aminomethyl molecules mapped to an N-acetyl transferase (Rv0133) and these mutants remained fully linezolid susceptible. Purified Rv0133 was shown to catalyze the transformation of the 5-aminomethyl oxazolidinones to their corresponding N-acetylated metabolites, and this transformation was also observed in live cells of Mycobacterium tuberculosis. Mammalian mitochondria, which lack an appropriate N-acetyltransferase to activate these prodrugs, were not susceptible to inhibition with the 5-aminomethyl analogues. Several compounds that were more potent than linezolid were taken into C3HeB/FeJ mice and were shown to be highly efficacious, and one of these (9) was additionally taken into marmosets and found to be highly active. Penetration of these 5-aminomethyl oxazolidinone prodrugs into caseum was excellent. Unfortunately, these compounds were rapidly converted into the corresponding 5-alcohols by mammalian metabolism which retained antimycobacterial activity but resulted in substantial mitotoxicity.


Subject(s)
Antitubercular Agents , Mycobacterium tuberculosis , Oxazolidinones , Prodrugs , Prodrugs/pharmacology , Prodrugs/chemistry , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Mycobacterium tuberculosis/drug effects , Oxazolidinones/pharmacology , Oxazolidinones/chemistry , Animals , Microbial Sensitivity Tests , Mice , Humans , Linezolid/pharmacology , Linezolid/chemistry , Drug Resistance, Bacterial , Mitochondria/drug effects , Mitochondria/metabolism
3.
Proc Natl Acad Sci U S A ; 121(14): e2321336121, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38530888

ABSTRACT

Host-directed therapies (HDTs) represent an emerging approach for bacterial clearance during tuberculosis (TB) infection. While most HDTs are designed and implemented for immuno-modulation, other host targets-such as nonimmune stromal components found in pulmonary granulomas-may prove equally viable. Building on our previous work characterizing and normalizing the aberrant granuloma-associated vasculature, here we demonstrate that FDA-approved therapies (bevacizumab and losartan, respectively) can be repurposed as HDTs to normalize blood vessels and extracellular matrix (ECM), improve drug delivery, and reduce bacterial loads in TB granulomas. Granulomas feature an overabundance of ECM and compressed blood vessels, both of which are effectively reduced by losartan treatment in the rabbit model of TB. Combining both HDTs promotes secretion of proinflammatory cytokines and improves anti-TB drug delivery. Finally, alone and in combination with second-line antitubercular agents (moxifloxacin or bedaquiline), these HDTs significantly reduce bacterial burden. RNA sequencing analysis of HDT-treated lung and granuloma tissues implicates up-regulated antimicrobial peptide and proinflammatory gene expression by ciliated epithelial airway cells as a putative mechanism of the observed antitubercular benefits in the absence of chemotherapy. These findings demonstrate that bevacizumab and losartan are well-tolerated stroma-targeting HDTs, normalize the granuloma microenvironment, and improve TB outcomes, providing the rationale to clinically test this combination in TB patients.


Subject(s)
Latent Tuberculosis , Mycobacterium tuberculosis , Tuberculosis , Humans , Animals , Rabbits , Bevacizumab/pharmacology , Losartan/pharmacology , Tuberculosis/microbiology , Antitubercular Agents/pharmacology , Granuloma , Latent Tuberculosis/microbiology
4.
CPT Pharmacometrics Syst Pharmacol ; 13(4): 673-685, 2024 04.
Article in English | MEDLINE | ID: mdl-38404200

ABSTRACT

Tuberculosis (TB) is a life-threatening infectious disease. The standard treatment is up to 90% effective; however, it requires the administration of four antibiotics (isoniazid, rifampicin, pyrazinamide, and ethambutol [HRZE]) over long time periods. This harsh treatment process causes adherence issues for patients because of the long treatment times and a myriad of adverse effects. Therefore, the World Health Organization has focused goals of shortening standard treatment regimens for TB in their End TB Strategy efforts, which aim to reduce TB-related deaths by 95% by 2035. For this purpose, many novel and promising combination antibiotics are being explored that have recently been discovered, such as the bedaquiline, pretomanid, and linezolid (BPaL) regimen. As a result, testing the number of possible combinations with all possible novel regimens is beyond the limit of experimental resources. In this study, we present a unique framework that uses a primate granuloma modeling approach to screen many combination regimens that are currently under clinical and experimental exploration and assesses their efficacies to inform future studies. We tested well-studied regimens such as HRZE and BPaL to evaluate the validity and accuracy of our framework. We also simulated additional promising combination regimens that have not been sufficiently studied clinically or experimentally, and we provide a pipeline for regimen ranking based on their efficacies in granulomas. Furthermore, we showed a correlation between simulation rankings and new marmoset data rankings, providing evidence for the credibility of our framework. This framework can be adapted to any TB regimen and can rank any number of single or combination regimens.


Subject(s)
Diarylquinolines , Nitroimidazoles , Tuberculosis, Multidrug-Resistant , Tuberculosis , Animals , Humans , Antitubercular Agents/therapeutic use , Linezolid/therapeutic use , Tuberculosis/drug therapy , Tuberculosis, Multidrug-Resistant/drug therapy
5.
PLoS Comput Biol ; 20(2): e1011847, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38335224

ABSTRACT

Physiological abnormalities in pulmonary granulomas-pathological hallmarks of tuberculosis (TB)-compromise the transport of oxygen, nutrients, and drugs. In prior studies, we demonstrated mathematically and experimentally that hypoxia and necrosis emerge in the granuloma microenvironment (GME) as a direct result of limited oxygen availability. Building on our initial model of avascular oxygen diffusion, here we explore additional aspects of oxygen transport, including the roles of granuloma vasculature, transcapillary transport, plasma dilution, and interstitial convection, followed by cellular metabolism. Approximate analytical solutions are provided for oxygen and glucose concentration, interstitial fluid velocity, interstitial fluid pressure, and the thickness of the convective zone. These predictions are in agreement with prior experimental results from rabbit TB granulomas and from rat carcinoma models, which share similar transport limitations. Additional drug delivery predictions for anti-TB-agents (rifampicin and clofazimine) strikingly match recent spatially-resolved experimental results from a mouse model of TB. Finally, an approach to improve molecular transport in granulomas by modulating interstitial hydraulic conductivity is tested in silico.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Animals , Mice , Rabbits , Oxygen/metabolism , Tuberculosis/drug therapy , Tuberculosis/pathology , Granuloma/pathology , Disease Models, Animal , Nutrients , Mycobacterium tuberculosis/metabolism
6.
Pharmaceuticals (Basel) ; 17(2)2024 Feb 06.
Article in English | MEDLINE | ID: mdl-38399426

ABSTRACT

Tuberculosis (TB) is notorious as the leading cause of death worldwide due to a single infectious entity and its causative agent, Mycobacterium tuberculosis (Mtb), has been able to evolve resistance to all existing drugs in the treatment arsenal complicating disease management programs. In drug discovery efforts, natural products are important starting points in generating novel scaffolds that have evolved to specifically bind to vulnerable targets not only in pathogens such as Mtb, but also in mammalian targets associated with human diseases. Structural diversity is one of the most attractive features of natural products. This review provides a summary of fused-nitrogen-containing heterocycles found in the natural products reported in the literature that are known to have antitubercular activities. The structurally targeted natural products discussed in this review could provide a revealing insight into novel chemical aspects with novel biological functions for TB drug discovery efforts.

7.
Nat Med ; 30(3): 896-904, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38365949

ABSTRACT

New tuberculosis treatments are needed to address drug resistance, lengthy treatment duration and adverse reactions of available agents. GSK3036656 (ganfeborole) is a first-in-class benzoxaborole inhibiting the Mycobacterium tuberculosis leucyl-tRNA synthetase. Here, in this phase 2a, single-center, open-label, randomized trial, we assessed early bactericidal activity (primary objective) and safety and pharmacokinetics (secondary objectives) of ganfeborole in participants with untreated, rifampicin-susceptible pulmonary tuberculosis. Overall, 75 males were treated with ganfeborole (1/5/15/30 mg) or standard of care (Rifafour e-275 or generic alternative) once daily for 14 days. We observed numerical reductions in daily sputum-derived colony-forming units from baseline in participants receiving 5, 15 and 30 mg once daily but not those receiving 1 mg ganfeborole. Adverse event rates were comparable across groups; all events were grade 1 or 2. In a participant subset, post hoc exploratory computational analysis of 18F-fluorodeoxyglucose positron emission tomography/computed tomography findings showed measurable treatment responses across several lesion types in those receiving ganfeborole 30 mg at day 14. Analysis of whole-blood transcriptional treatment response to ganfeborole 30 mg at day 14 revealed a strong association with neutrophil-dominated transcriptional modules. The demonstrated bactericidal activity and acceptable safety profile suggest that ganfeborole is a potential candidate for combination treatment of pulmonary tuberculosis.ClinicalTrials.gov identifier: NCT03557281 .


Subject(s)
Amino Acyl-tRNA Synthetases , Tuberculosis, Pulmonary , Tuberculosis , Male , Humans , Rifampin/therapeutic use , Antitubercular Agents/adverse effects , Tuberculosis/drug therapy , Tuberculosis, Pulmonary/drug therapy , Tuberculosis, Pulmonary/microbiology , Amino Acyl-tRNA Synthetases/therapeutic use
8.
ACS Med Chem Lett ; 14(9): 1275-1283, 2023 Sep 14.
Article in English | MEDLINE | ID: mdl-37736177

ABSTRACT

The continuing prevalence of drug-resistant tuberculosis threatens global TB control programs, highlighting the need to discover new drug candidates to feed the drug development pipeline. In this study, we describe a high-throughput screening hit (4-benzylpiperidin-1-yl)(1-(5-phenyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl)methanone (P1) as a potent antitubercular agent. Structure-activity guided synthesis led to the discovery of several analogs with high in vitro potency. P1 was found to have promising potency against many drug-resistant strains, as well as drug-susceptible clinical isolates. It also showed cidality against Mtb growing in host macrophages. Whole genome sequencing of genomic DNA from resistant mutants raised to P1 revealed mutations in decaprenylphosphoryl-ß-d-ribose 2'-oxidase (DprE1). This novel oxadiazole scaffold expands the set of chemical tools for targeting a well-validated pathway to treat tuberculosis.

9.
Transplant Proc ; 55(8): 1917-1920, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37625934

ABSTRACT

BACKGROUND: Myelolipomas are benign tumors usually found in adrenal glands. They can also be found extra-adrenally, either in 1 or multiple locations. Perinephric transplant myelolipoma has rarely been reported in the English literature. There's only been 1 instance of such a case reported in a kidney transplant patient, which was found on the explanted kidney. We report a case involving an asymptomatic patient with an ill-defined perinephric transplant mass. METHODS: The mass was then identified as myelolipoma on biopsy. The patient was then managed conservatively with serial imaging and laboratory testing. RESULTS: At the time of our report, the patient continues to have stable renal function and is doing well 24 months after the mass was first identified. CONCLUSIONS: We report the first case of perinephric transplant myelolipoma in a patient with ongoing stable renal allograft function. Based on our case report, we recommended that conservative management with serial imaging and routine testing be considered for patients with perinephric transplant myelolipoma.

10.
bioRxiv ; 2023 Apr 03.
Article in English | MEDLINE | ID: mdl-37333343

ABSTRACT

Tuberculosis remains a large global disease burden for which treatment regimens are protracted and monitoring of disease activity difficult. Existing detection methods rely almost exclusively on bacterial culture from sputum which limits sampling to organisms on the pulmonary surface. Advances in monitoring tuberculous lesions have utilized the common glucoside [18F]FDG, yet lack specificity to the causative pathogen Mycobacterium tuberculosis (Mtb) and so do not directly correlate with pathogen viability. Here we show that a close mimic that is also positron-emitting of the non-mammalian Mtb disaccharide trehalose - 2-[18F]fluoro-2-deoxytrehalose ([18F]FDT) - can act as a mechanism-based enzyme reporter in vivo. Use of [18F]FDT in the imaging of Mtb in diverse models of disease, including non-human primates, successfully co-opts Mtb-specific processing of trehalose to allow the specific imaging of TB-associated lesions and to monitor the effects of treatment. A pyrogen-free, direct enzyme-catalyzed process for its radiochemical synthesis allows the ready production of [18F]FDT from the most globally-abundant organic 18F-containing molecule, [18F]FDG. The full, pre-clinical validation of both production method and [18F]FDT now creates a new, bacterium-specific, clinical diagnostic candidate. We anticipate that this distributable technology to generate clinical-grade [18F]FDT directly from the widely-available clinical reagent [18F]FDG, without need for either bespoke radioisotope generation or specialist chemical methods and/or facilities, could now usher in global, democratized access to a TB-specific PET tracer.

11.
Cell Chem Biol ; 30(5): 420-435, 2023 05 18.
Article in English | MEDLINE | ID: mdl-37207631

ABSTRACT

Mycobacterium tuberculosis (Mtb), perhaps more than any other organism, is intrinsically appealing to chemical biologists. Not only does the cell envelope feature one of the most complex heteropolymers found in nature1 but many of the interactions between Mtb and its primary host (we humans) rely on lipid and not protein mediators.2,3 Many of the complex lipids, glycolipids, and carbohydrates biosynthesized by the bacterium still have unknown functions, and the complexity of the pathological processes by which tuberculosis (TB) disease progress offers many opportunities for these molecules to influence the human response. Because of the importance of TB in global public health, chemical biologists have applied a wide-ranging array of techniques to better understand the disease and improve interventions.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Humans , Tuberculosis/drug therapy , Mycobacterium tuberculosis/metabolism , Glycolipids , Cell Membrane/metabolism , Biology
12.
mBio ; 14(2): e0059823, 2023 04 25.
Article in English | MEDLINE | ID: mdl-37017524

ABSTRACT

Caseous necrosis is a hallmark of tuberculosis (TB) pathology and creates a niche for drug-tolerant persisters within the host. Cavitary TB and high bacterial burden in caseum require longer treatment duration. An in vitro model that recapitulates the major features of Mycobacterium tuberculosis (Mtb) in caseum would accelerate the identification of compounds with treatment-shortening potential. We have developed a caseum surrogate model consisting of lysed and denatured foamy macrophages. Upon inoculation of Mtb from replicating cultures, the pathogen adapts to the lipid-rich matrix and gradually adopts a nonreplicating state. We determined that the lipid composition of ex vivo caseum and the surrogate matrix are similar. We also observed that Mtb in caseum surrogate accumulates intracellular lipophilic inclusions (ILI), a distinctive characteristic of quiescent and drug-tolerant Mtb. Expression profiling of a representative gene subset revealed common signatures between the models. Comparison of Mtb drug susceptibility in caseum and caseum surrogate revealed that both populations are similarly tolerant to a panel of TB drugs. By screening drug candidates in the surrogate model, we determined that the bedaquiline analogs TBAJ876 and TBAJ587, currently in clinical development, exhibit superior bactericidal against caseum-resident Mtb, both alone and as substitutions for bedaquiline in the bedaquiline-pretomanid-linezolid regimen approved for the treatment of multidrug-resistant TB. In summary, we have developed a physiologically relevant nonreplicating persistence model that reflects the distinct metabolic and drug-tolerant state of Mtb in caseum. IMPORTANCE M. tuberculosis (Mtb) within the caseous core of necrotic granulomas and cavities is extremely drug tolerant and presents a significant hurdle to treatment success and relapse prevention. Many in vitro models of nonreplicating persistence have been developed to characterize the physiologic and metabolic adaptations of Mtb and identify compounds active against this treatment-recalcitrant population. However, there is little consensus on their relevance to in vivo infection. Using lipid-laden macrophage lysates, we have designed and validated a surrogate matrix that closely mimics caseum and in which Mtb develops a phenotype similar to that of nonreplicating bacilli in vivo. The assay is well suited to screen for bactericidal compounds against caseum-resident Mtb in a medium-throughput format, allowing for reduced reliance on resource intensive animal models that present large necrotic lesions and cavities. Importantly, this approach will aid the identification of vulnerable targets in caseum Mtb and can accelerate the development of novel TB drugs with treatment-shortening potential.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis, Multidrug-Resistant , Tuberculosis , Animals , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , Antitubercular Agents/therapeutic use , Tuberculosis/drug therapy , Tuberculosis/microbiology , Lipids
13.
J Am Chem Soc ; 145(2): 851-863, 2023 01 18.
Article in English | MEDLINE | ID: mdl-36603206

ABSTRACT

Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against Mycobacterium tuberculosis. To ensure compound supply for further development, we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by the development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing, and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. These studies open avenues for structure-based scaffold improvement toward development as an antibacterial agent.


Subject(s)
Mycobacterium tuberculosis , Myxococcales , Anti-Bacterial Agents/chemistry , Ribosomes/metabolism , Protein Biosynthesis
14.
J Hosp Med ; 18(1): 5-14, 2023 01.
Article in English | MEDLINE | ID: mdl-36326255

ABSTRACT

BACKGROUND: Handoff miscommunications are a leading source of medical errors. Harmful medical errors decreased in pediatric academic hospitals following implementation of the I-PASS handoff improvement program. However, implementation across specialties has not been assessed. OBJECTIVE: To determine if I-PASS implementation across diverse settings would be associated with improvements in patient safety and communication. DESIGN: Prospective Type 2 Hybrid effectiveness implementation study. SETTINGS AND PARTICIPANTS: Residents from diverse specialties across 32 hospitals (12 community, 20 academic). INTERVENTION: External teams provided longitudinal coaching over 18 months to facilitate implementation of an enhanced I-PASS program and monthly metric reviews. MAIN OUTCOME AND MEASURES: Systematic surveillance surveys assessed rates of resident-reported adverse events. Validated direct observation tools measured verbal and written handoff quality. RESULTS: 2735 resident physicians and 760 faculty champions from multiple specialties (16 internal medicine, 13 pediatric, 3 other) participated. 1942 error surveillance reports were collected. Major and minor handoff-related reported adverse events decreased 47% following implementation, from 1.7 to 0.9 major events/person-year (p < .05) and 17.5 to 9.3 minor events/person-year (p < .001). Implementation was associated with increased inclusion of all five key handoff data elements in verbal (20% vs. 66%, p < .001, n = 4812) and written (10% vs. 74%, p < .001, n = 1787) handoffs, as well as increased frequency of handoffs with high quality verbal (39% vs. 81% p < .001) and written (29% vs. 78%, p < .001) patient summaries, verbal (29% vs. 78%, p < .001) and written (24% vs. 73%, p < .001) contingency plans, and verbal receiver syntheses (31% vs. 83%, p < .001). Improvement was similar across provider types (adult vs. pediatric) and settings (community vs. academic).


Subject(s)
Internship and Residency , Patient Handoff , Adult , Humans , Child , Prospective Studies , Internal Medicine , Communication
15.
MedEdPORTAL ; 18: 11267, 2022.
Article in English | MEDLINE | ID: mdl-35990195

ABSTRACT

Introduction: Patient and family-centered rounds (PFCRs) are an important element of family-centered care often used in the inpatient pediatric setting. However, techniques and best practices vary, and faculty, trainees, nurses, and advanced care providers may not receive formal education in strategies that specifically enhance communication on PFCRs. Methods: Harnessing the use of structured communication, we developed the Patient and Family-Centered I-PASS Safer Communication on Rounds Every Time (SCORE) Program. The program uses a standardized framework for rounds communication via the I-PASS mnemonic, principles of health literacy, and techniques for patient/family engagement and bidirectional communication. The resident and advanced care provider training materials, a component of the larger SCORE Program, incorporate a flipped classroom approach as well as interactive exercises, simulations, and virtual learning options to optimize learning and retention via a 90-minute workshop. Results: Two hundred forty-six residents completed the training and were evaluated on their knowledge and confidence regarding key elements of the curriculum. Eighty-eight percent of residents agreed/strongly agreed that after training they could activate and engage families and all members of the interprofessional team to create a shared mental model; 90% agreed/strongly agreed that they could discuss the roles/responsibilities of various team members during PFCRs. Discussion: The Patient and Family-Centered I-PASS SCORE Program provides a structured framework for teaching advanced communication techniques that can improve provider knowledge of and confidence with engaging and communicating with patients/families and other members of the interprofessional team during PFCRs.


Subject(s)
Communication , Teaching Rounds , Child , Curriculum , Humans , Inpatients , Teaching Rounds/methods
16.
Transpl Int ; 35: 10626, 2022.
Article in English | MEDLINE | ID: mdl-35928347

ABSTRACT

Alloimmune responses in kidney transplant (KT) patients previously hospitalized with COVID-19 are understudied. We analyzed a cohort of 112 kidney transplant recipients who were hospitalized following a positive SARS-CoV-2 test result during the first 20 months of the COVID-19 pandemic. We found a cumulative incidence of 17% for the development of new donor-specific antibodies (DSA) or increased levels of pre-existing DSA in hospitalized SARS-CoV-2-infected KT patients. This risk extended 8 months post-infection. These changes in DSA status were associated with late allograft dysfunction. Risk factors for new or increased DSA responses in this KT patient cohort included the presence of circulating DSA pre-COVID-19 diagnosis and time post-transplantation. COVID-19 vaccination prior to infection and remdesivir administration during infection were each associated with decreased likelihood of developing a new or increased DSA response. These data show that new or enhanced DSA responses frequently occur among KT patients requiring admission with COVID-19 and suggest that surveillance, vaccination, and antiviral therapies may be important tools to prevent alloimmunity in these individuals.


Subject(s)
COVID-19 Drug Treatment , COVID-19 , Kidney Transplantation , Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antibodies , COVID-19/prevention & control , COVID-19 Testing , COVID-19 Vaccines/therapeutic use , Graft Rejection , HLA Antigens , Humans , Pandemics , SARS-CoV-2 , Transplant Recipients , Vaccination
17.
Biol Direct ; 17(1): 7, 2022 03 21.
Article in English | MEDLINE | ID: mdl-35313954

ABSTRACT

BACKGROUND: Bacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms of inter-microbial conflicts or communication. A vast class of such peptides are Ribosomally synthesized, Postranslationally modified Peptides (RiPPs), and a major group of RiPPs are graspetides, so named after ATP-grasp ligases that catalyze the formation of lactam and lactone linkages in these peptides. The diversity of graspetides, the multiple proteins encoded in the respective Biosynthetic Gene Clusters (BGCs) and their evolution have not been studied in full detail. In this work, we attempt a comprehensive analysis of the graspetide-encoding BGCs and report a variety of novel graspetide groups as well as ancillary proteins implicated in graspetide biosynthesis and expression. RESULTS: We compiled a comprehensive, manually curated set of graspetides that includes 174 families including 115 new families with distinct patterns of amino acids implicated in macrocyclization and further modification, roughly tripling the known graspetide diversity. We derived signature motifs for the leader regions of graspetide precursors that could be used to facilitate graspetide prediction. Graspetide biosynthetic gene clusters and specific precursors were identified in bacterial divisions not previously known to encode RiPPs, in particular, the parasitic and symbiotic bacteria of the Candidate phyla radiation. We identified Bacteroides-specific biosynthetic gene clusters (BGC) that include remarkable diversity of graspetides encoded in the same loci which predicted to be modified by the same ATP-grasp ligase. We studied in details evolution of recently characterized chryseoviridin BGCs and showed that duplication and horizonal gene exchange both contribute to the diversification of the graspetides during evolution. CONCLUSIONS: We demonstrate previously unsuspected diversity of graspetide sequences, even those associated with closely related ATP-grasp enzymes. Several previously unnoticed families of proteins associated with graspetide biosynthetic gene clusters are identified. The results of this work substantially expand the known diversity of RiPPs and can be harnessed to further advance approaches for their identification.


Subject(s)
Multigene Family , Peptides , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Bacteria/genetics , Peptides/chemistry , Phylogeny , Protein Processing, Post-Translational
19.
ACS Infect Dis ; 8(3): 612-625, 2022 03 11.
Article in English | MEDLINE | ID: mdl-35143160

ABSTRACT

Natural products provide a rich source of potential antimicrobials for treating infectious diseases for which drug resistance has emerged. Foremost among these diseases is tuberculosis. Assessment of the antimycobacterial activity of nargenicin, a natural product that targets the replicative DNA polymerase of Staphylococcus aureus, revealed that it is a bactericidal genotoxin that induces a DNA damage response in Mycobacterium tuberculosis (Mtb) and inhibits growth by blocking the replicative DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding of nargenicin to Mtb DnaE1 requires the DNA substrate such that nargenicin is wedged between the terminal base pair and the polymerase and occupies the position of both the incoming nucleotide and templating base. Comparative analysis across three bacterial species suggests that the activity of nargenicin is partly attributable to the DNA binding affinity of the replicative polymerase. This work has laid the foundation for target-led drug discovery efforts focused on Mtb DnaE1.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Anti-Bacterial Agents/pharmacology , Cryoelectron Microscopy , DNA-Directed DNA Polymerase , Humans , Mycobacterium tuberculosis/genetics , Tuberculosis/drug therapy , Tuberculosis/microbiology
20.
ACS Infect Dis ; 8(3): 557-573, 2022 03 11.
Article in English | MEDLINE | ID: mdl-35192346

ABSTRACT

Rising antimicrobial resistance challenges our ability to combat bacterial infections. The problem is acute for tuberculosis (TB), the leading cause of death from infection before COVID-19. Here, we developed a framework for multiple pharmaceutical companies to share proprietary information and compounds with multiple laboratories in the academic and government sectors for a broad examination of the ability of ß-lactams to kill Mycobacterium tuberculosis (Mtb). In the TB Drug Accelerator (TBDA), a consortium organized by the Bill & Melinda Gates Foundation, individual pharmaceutical companies collaborate with academic screening laboratories. We developed a higher order consortium within the TBDA in which four pharmaceutical companies (GlaxoSmithKline, Sanofi, MSD, and Lilly) collectively collaborated with screeners at Weill Cornell Medicine, the Infectious Disease Research Institute (IDRI), and the National Institute of Allergy and Infectious Diseases (NIAID), pharmacologists at Rutgers University, and medicinal chemists at the University of North Carolina to screen ∼8900 ß-lactams, predominantly cephalosporins, and characterize active compounds. In a striking contrast to historical expectation, 18% of ß-lactams screened were active against Mtb, many without a ß-lactamase inhibitor. One potent cephaloporin was active in Mtb-infected mice. The steps outlined here can serve as a blueprint for multiparty, intra- and intersector collaboration in the development of anti-infective agents.


Subject(s)
COVID-19 , Mycobacterium tuberculosis , Animals , Drug Industry , Mice , SARS-CoV-2 , Universities , beta-Lactams/pharmacology
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