Biology subjects

Slayden, R. A.

Publications and source records attributed to Slayden, R. A..

5 recordsLinked to original sources

bioRxiv2025

Pharmacokinetics and In vivo Efficacy of Epetraborole against Burkholderia pseudomallei

Melioidosis, caused by Burkholderia pseudomallei, remains a major therapeutic challenge due to high relapse rates and intrinsic antibiotic resistance. Epetraborole (EBO), a leucyl-tRNA synthetase inhibitor, represents a novel therapeutic approach with a distinct mechanism of action compared to standard-of-care antibiotics. Preclinical studies included MIC determination, pharmacokinetic (PK) profiling, dose range and fractionation studies, and efficacy assessments in a 24-hour post-bacterial challenge model of a murine B. pseudomallei lung infection. EBO demonstrated a clear dose-dependent reduction in lung bacterial burden. Doses [≥]200 mg/kg (achieving AUC-2 [~]110 {micro}g{middle dot}h/mL) produced >1.6 log CFU decreases from the start-of-therapy baseline across all ten B. pseudomallei strains. Notably, an AUC-2 of [~]110 {micro}g{middle dot}h/mL was achieved in humans with a 2000 mg IV dose in a phase 1 clincial trial where doses up to 4000 mg per day for 14 days were well tolerated with no serious adverse events or dose-limiting adverse events. When EBO doses of 600, 300 and 100 mg/kg SC were fractionated by once, twice and three times a day against the B. pseudomallei strain NCTC7383, which represents the MIC100 strain, the efficacy indicated that the pharmacokinetics-pharmacodynamics (PK/PD) driver of epetraborole is total drug exposure (AUC) rather than peak concentration (Cmax) or time above MIC. The inhibition of leucyl-tRNA synthetase represents a unique molecular target, reducing cross-resistance potential with existing {beta}-lactam antibiotics and enabling combination therapy strategies. These findings substantiate EBO as a promising therapeutic option for clinical melioidosis to improve treatment outcomes. Notably, this study represents the first demonstration of in vivo efficacy against a panel of ten genetically and geographically diverse B. pseudomallei strains in a murine model. This unprecedented breadth of strain coverage provides strong evidence of EBOs robust and strain-independent therapeutic potential. Author SummaryMelioidosis is a life-threatening disease caused by Burkholderia pseudomallei, a bacterium found in soil and water in tropical regions. It is challenging to treat because it is often resistant to standard antibiotics, requires long courses of therapy, and can relapse even after treatment. New treatment options are urgently needed. Epetraborole is an experimental antibiotic with a novel mechanism that blocks bacterial protein synthesis. In this study, we tested how well epetraborole works in mice infected with B. pseudomallei, using ten different strains of the bacteria collected from geographically diverse regions. This is the first study to test a melioidosis treatment against such a broad panel of B. pseudomallei strains in an animal model. We found that epetraborole significantly reduced bacterial counts in the lungs of infected mice. The antibiotic remained effective even against strains with higher resistance and high bacterial loads 24 hours after infection, showing promise for severe clinical infections. Our findings suggest that epetraborole could be a valuable addition to existing melioidosis treatments, especially in regions with limited therapeutic options.

microbiology↗

bioRxiv2024

Transfer Learning Models for Bacterial Strain Dissemination Biomarkers using Weighted Non-Parallel Proximal Support Vector Machines

This paper develops optimization and Machine Learning (ML) algorithms to analyze gene expression datasets from the lungs and spleen of mice, infected intranasally, with two bacterial strains, Francisella tularensis - Schu4 and Live Vaccine Strain (LVS). We propose and utilize Weighted[l] 1-norm Generalized Eigenvalue-type Problems ([l]1-WGEPs) to determine a small set of host biomarkers that report Schu4 and LVS infection of the lungs and dissemination to the spleen. The optimal solutions of[l] 1-WGEPs determine the direction onto which the datasets are projected for dimensionality reduction, with the projection scores computed and ranked for gene selection. The top k-ranked projection scores correspond to the top k most informative biomarker features. The top k features selected from the lungs data are employed to train ML models, with uninfected controls and Schu4 or LVS samples as classes. The trained models are validated on the spleen data to incorporate transfer learning. Baseline ML algorithms such as ANN, XGBoost, AdaBoost, AdaGrad, KNN, SVM, Naive Bayes, Random Forest, Logistic Regression, and Decision Tree are compared with our Weighted[l] 1-norm Non-Parallel Proximal Support Vector Machine ([l]1-WNPSVM) that is based on two non-parallel separating hyperplanes. We report average balanced accuracy scores of the methods over multiple folds. Gene ontology is performed on the most significant genes in both tissues to reveal biomarkers of disease and examine for relevant metabolic pathways for host-directed therapeutics development and treatment performance. Author SummaryIntegrating genomic datasets from homogeneous or heterogeneous sources is an area that is currently underexplored. This work develops new methodologies to integrate transcriptomic datasets from the lungs and spleen tissues infected by Francisella tularensis -- Schu4 and Live Vaccine Strain (LVS). Our objective is to identify biologically relevant gene features indicative of respiratory infection, disease severity, and bacterial dissemination to the spleen, then utilize the selected features to predict disease status using our Weighted[l] 1-norm Non-Parallel Support Vector Machines ([l]1-WNPSVM), which is trained on the lungs data and validated on the spleen data, introducing a form of transfer learning. The[l] 1-WNPSVM outperforms traditional ML techniques, achieving a 97% balanced accuracy. It also generalizes to models of similar formulations, incorporating dimensionality reduction and gene selection into the NPSVM-type framework. Currently, a direct application of existing NPSVM-type methods to analyze gene expression datasets, where the number of genes significantly exceeds the number of samples, is computationally impractical due to their large memory requirements. This work addresses this challenge. We discovered sets of 253 genes exclusively expressed in the lungs and spleen tissues. Gene ontology is performed to reveal underlying metabolic pathways. Our analysis shows that the immune system pathway is activated in both lungs and spleen.

bioinformatics↗

bioRxiv2021

A novel glucocorticoid and androgen receptor modulator reduces viral entry and innate immune inflammatory responses in the Syrian Hamster model of SARS-CoV-2

Since its initial discovery in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID19, has spread worldwide and despite significant research efforts, treatment options remain limited. Replication of SARS-CoV-2 in lung is associated with marked infiltration of macrophages and activation of innate immune inflammatory responses triggered, in part, by heightened production of interleukin-6 (IL-6) that recruits lymphocytes to the site of infection that amplify tissue injury. Antagonists of the glucocorticoid and androgen receptors have shown promise in experimental models of COVID19 and in clinical studies, because cell surface proteins required for viral entry, angiotensin converting enzyme 2 (ACE2) and the transmembrane serine protease 2 (TMPRSS2), are transcriptionally regulated by these receptors. We therefore postulated that the glucocorticoid (GR) and androgen receptor (AR) antagonist, PT150, would reduce infectivity of SARS-CoV-2 and prevent inflammatory lung injury in the Syrian golden hamster model of COVID19. Animals were infected intranasally with 2.5 x 104 TCID50/ml equivalents of SARS-CoV-2 (strain 2019-nCoV/USA-WA1/ 2020) and PT150 was administered by oral gavage at 30 and 100 mg/Kg/day for a total of 7 days. Animals were then examined at days 3, 5 and 7 post-infection (DPI) for lung histopathology, viral load and production of proteins regulating the initiation and progression of SARS-CoV-2 infection. Results of these studies indicated that oral administration of PT150 decreased replication of SARS-CoV-2 in lung, as well as expression of ACE2 and TMPRSS2 protein. Hypercellularity and inflammatory cell infiltration driven by macrophage responses were dramatically decreased in PT150-treated animals, as was tissue damage and expression of IL-6. Molecular modeling suggested that PT150 binds to the co-activator interface of the ligand binding domain of both AR and GR and thereby acts as an allosteric modulator and transcriptional repressor of these receptors. Phylogenetic analysis of AR and GR across multiple species permissive to SARS-CoV-2 infection revealed a high degree of sequence identity maintained across species, including human, suggesting that the mechanism of action and therapeutic efficacy observed in Syrian hamsters would likely be predictive of positive outcomes in patients. PT150 is therefore a strong candidate for further clinical development for the treatment of COVID19 across variants of SARS-CoV-2.

immunology↗

bioRxiv2021

TPR1, a novel rifampin derivative demonstrates efficacy alone and in combination with doxycycline against the NIAID Category A Priority Pathogen F. tularensis

ObjectivesFrancisella tularensis is a highly virulent and contagious gram-negative intracellular bacterium that causes the disease tularemia in mammals and is classified as a Category A priority pathogen. The high infectivity, difficulty of obtaining a durable cure of disseminated disease and the emergence of drug resistance warrants investigation of new drugs that can be used alone and in combination with existing standard of care clinical drugs. MethodsWe utilized a systematic analysis of antibacterial potency, extent of dissemination by analysis of bacterial burden in a secondary vital organ, and survival rates to assess the efficacy of a novel rifampicin derivative, TPR1. The efficacy of TPR1 was evaluated alone and in combination with the standard of care drug, doxycycline, against Type A F. tularensis Schu S4 using a lethal pulmonary model of infection in mice. ResultsTPR1 has an MIC value range of 0.125-4 mg/L against reference laboratory strain SchuS4 and a panel of clinical strains. TPR1 alone reduced the bacterial burden in the lungs and spleen at 40 mg/kg and 80 mg/kg, and no antagonism was observed when co-administered with doxycycline. Dosing at 40 mg/kg doxycycline reduced the bacterial burden by 1 Log10 CFU in the lungs and 4 Log10 CFU spleen in comparison to untreated controls. Co-administration of TPR1 and doxycycline demonstrated efficacy upon treatment withdrawal after 4 days of treatment, and 100% survival. ConclusionsSignificantly, TPR1 demonstrated efficacy when delivered alone and in combination with doxycycline, which provides compelling evidence of a superior treatment strategy that would normally rely on a single chemotherapeutic for efficacy. In addition, this work substantiates the use of rifampicin derivatives as a platform for the development of novel treatments to other bacterial agents in addition to tularemia.

microbiology↗

bioRxiv2020

Profiling susceptibility of NIAID Category A and B priority and emerging pathogens to define strain panels for drug discovery and active drug classes

Drug susceptibility profiles of NIAID Category A and B priority and emerging pathogens to standard of care drugs were assessed to determine susceptibility against clinical strains in addition to reference laboratory strains to establish a comparison resource for the performance of drug candidates, to define non-redundant minimal strain panels for individual species and the group of species for use in drug screening programs, and provide pharmacophore classification. Profiling of standard of care drugs against strains of each species revealed a broad spectrum of susceptibility among strains in each species with important differences between standard laboratory reference strains and strains sof clinical origin. Unbiased hierarchical clustering analyses of strain susceptibilities within each species group and strains from all the species identified subsets of non-redundant strains that are able to classify the susceptibility range for each species and able to classify all the species. This analysis established a reduced targeted set of Category A and B priority pathogen strains for testing the potency of drug candidates against each species and pan-species. This approach also discriminated pharmacophore classification for each species. This information can be applied to directed screening efforts to guide the selection of drug classes for derivatization and repurposing, and advance drug candidates with the greatest potential for efficacy against NIAID Category A and B priority and emerging pathogens.

microbiology↗