scholarly journals Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Shuyi Ma ◽  
Suraj Jaipalli ◽  
Jonah Larkins-Ford ◽  
Jenny Lohmiller ◽  
Bree B. Aldridge ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Computational Model ◽  
Drug Combinations ◽  
Broth Culture ◽  
Multiple Drug ◽  
Content Type ◽  
Drug Synergy ◽  
Drug Regimens

ABSTRACT The rapid spread of multidrug-resistant strains has created a pressing need for new drug regimens to treat tuberculosis (TB), which kills 1.8 million people each year. Identifying new regimens has been challenging due to the slow growth of the pathogen Mycobacterium tuberculosis (MTB), coupled with the large number of possible drug combinations. Here we present a computational model (INDIGO-MTB) that identified synergistic regimens featuring existing and emerging anti-TB drugs after screening in silico more than 1 million potential drug combinations using MTB drug transcriptomic profiles. INDIGO-MTB further predicted the gene Rv1353c as a key transcriptional regulator of multiple drug interactions, and we confirmed experimentally that Rv1353c upregulation reduces the antagonism of the bedaquiline-streptomycin combination. A retrospective analysis of 57 clinical trials of TB regimens using INDIGO-MTB revealed that synergistic combinations were significantly more efficacious than antagonistic combinations (P value = 1 × 10−4) based on the percentage of patients with negative sputum cultures after 8 weeks of treatment. Our study establishes a framework for rapid assessment of TB drug combinations and is also applicable to other bacterial pathogens. IMPORTANCE Multidrug combination therapy is an important strategy for treating tuberculosis, the world’s deadliest bacterial infection. Long treatment durations and growing rates of drug resistance have created an urgent need for new approaches to prioritize effective drug regimens. Hence, we developed a computational model called INDIGO-MTB that identifies synergistic drug regimens from an immense set of possible drug combinations using the pathogen response transcriptome elicited by individual drugs. Although the underlying input data for INDIGO-MTB was generated under in vitro broth culture conditions, the predictions from INDIGO-MTB correlated significantly with in vivo drug regimen efficacy from clinical trials. INDIGO-MTB also identified the transcription factor Rv1353c as a regulator of multiple drug interaction outcomes, which could be targeted for rationally enhancing drug synergy.

scholarly journals Transcriptomic signatures predict regulators of drug synergy and clinical regimen efficacy against Tuberculosis

2019 ◽  
Author(s):  
Shuyi Ma ◽  
Suraj Jaipalli ◽  
Jonah Larkins-Ford ◽  
Jenny Lohmiller ◽  
Bree B. Aldridge ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Computational Model ◽  
Drug Combinations ◽  
Broth Culture ◽  
Multiple Drug ◽  
P Value ◽  
Drug Synergy ◽  
Drug Regimens

ABSTRACTThe rapid spread of multi-drug resistant strains has created a pressing need for new drug regimens to treat tuberculosis (TB), which kills 1.8 million people each year. Identifying new regimens has been challenging due to the slow growth of the pathogen M. tuberculosis (MTB), coupled with large number of possible drug combinations. Here we present a computational model (INDIGO-MTB) that identified synergistic regimens featuring existing and emerging anti-TB drugs after screening in silico over 1 million potential drug combinations using MTB drug transcriptomic profiles. INDIGO-MTB further predicted the gene Rv1353c as a key transcriptional regulator of multiple drug interactions, and we confirmed experimentally that Rv1353c up-regulation reduces the antagonism of the bedaquiline-streptomycin combination. Retrospective analysis of 57 clinical trials of TB regimens using INDIGO-MTB revealed that synergistic combinations were significantly more efficacious than antagonistic combinations (p-value = 1 × 10−4) based on the percentage of patients with negative sputum cultures after 8 weeks of treatment. Our study establishes a framework for rapid assessment of TB drug combinations and is also applicable to other bacterial pathogens.IMPORTANCEMulti-drug combination therapy is an important strategy for treating tuberculosis, the world’s deadliest bacterial infection. Long treatment durations and growing rates of drug resistance have created an urgent need for new approaches to prioritize effective drug regimens. Hence, we developed a computational model called INDIGO-MTB, which identifies synergistic drug regimens from an immense set of possible drug combinations using pathogen response transcriptome elicited by individual drugs. Although the underlying input data for INDIGO-MTB was generated under in vitro broth culture conditions, the predictions from INDIGO-MTB correlated significantly with in vivo drug regimen efficacy from clinical trials. INDIGO-MTB also identified the transcription factor Rv1353c as a regulator of multiple drug interaction outcomes, which could be targeted for rationally enhancing drug synergy.

scholarly journals Importance of Confirming Data on theIn VivoEfficacy of Novel Antibacterial Drug Regimens against Various Strains of Mycobacterium tuberculosis

2011 ◽  
Vol 56 (2) ◽  
pp. 731-738 ◽  
Author(s):  
Mary A. De Groote ◽  
Veronica Gruppo ◽  
Lisa K. Woolhiser ◽  
Ian M. Orme ◽  
Janet C. Gilliland ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Animal Studies ◽  
Strain Difference ◽  
Drug Combinations ◽  
Antibacterial Drug ◽  
Preclinical Testing ◽  
Content Type ◽  
Drug Regimens

ABSTRACTIn preclinical testing of antituberculosis drugs, laboratory-adapted strains ofMycobacterium tuberculosisare usually used both forin vitroandin vivostudies. However, it is unknown whether the heterogeneity ofM. tuberculosisstocks used by various laboratories can result in different outcomes in tests of antituberculosis drug regimens in animal infection models. In head-to-head studies, we investigated whether bactericidal efficacy results in BALB/c mice infected by inhalation with the laboratory-adapted strains H37Rv and Erdman differ from each other and from those obtained with clinical tuberculosis strains. Treatment of mice consisted of dual and triple drug combinations of isoniazid (H), rifampin (R), and pyrazinamide (Z). The results showed that not all strains gave the samein vivoefficacy results for the drug combinations tested. Moreover, the ranking of HRZ and RZ efficacy results was not the same for the two H37Rv strains evaluated. The magnitude of this strain difference also varied between experiments, emphasizing the risk of drawing firm conclusions for human trials based on single animal studies. The results also confirmed that the antagonism seen within the standard HRZ regimen by some investigators appears to be anM. tuberculosisstrain-specific phenomenon. In conclusion, the specific identity ofM. tuberculosisstrain used was found to be an important variable that can change the apparent outcome ofin vivoefficacy studies in mice. We highly recommend confirmation of efficacy results in late preclinical testing against a differentM. tuberculosisstrain than the one used in the initial mouse efficacy study, thereby increasing confidence to advance potent drug regimens to clinical trials.

scholarly journals DTF: Deep Tensor Factorization for predicting anticancer drug synergy

2020 ◽  
Vol 36 (16) ◽  
pp. 4483-4489
Author(s):  
Zexuan Sun ◽  
Shujun Huang ◽  
Peiran Jiang ◽  
Pingzhao Hu
Keyword(s):  
Logistic Regression ◽  
Performance Metrics ◽  
Factorization Method ◽  
Drug Combinations ◽  
Supplementary Information ◽  
Tensor Factorization ◽  
Drug Synergy ◽  
Synergistic Drug Combinations

Abstract Motivation Combination therapies have been widely used to treat cancers. However, it is cost and time consuming to experimentally screen synergistic drug pairs due to the enormous number of possible drug combinations. Thus, computational methods have become an important way to predict and prioritize synergistic drug pairs. Results We proposed a Deep Tensor Factorization (DTF) model, which integrated a tensor factorization method and a deep neural network (DNN), to predict drug synergy. The former extracts latent features from drug synergy information while the latter constructs a binary classifier to predict the drug synergy status. Compared to the tensor-based method, the DTF model performed better in predicting drug synergy. The area under precision-recall curve (PR AUC) was 0.58 for DTF and 0.24 for the tensor method. We also compared the DTF model with DeepSynergy and logistic regression models, and found that the DTF outperformed the logistic regression model and achieved similar performance as DeepSynergy using several performance metrics for classification task. Applying the DTF model to predict missing entries in our drug–cell-line tensor, we identified novel synergistic drug combinations for 10 cell lines from the 5 cancer types. A literature survey showed that some of these predicted drug synergies have been identified in vivo or in vitro. Thus, the DTF model could be a valuable in silico tool for prioritizing novel synergistic drug combinations. Availability and implementation Source code and data are available at https://github.com/ZexuanSun/DTF-Drug-Synergy. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Impact of Exposure of Methicillin-Resistant Staphylococcus aureus to Polyhexanide In Vitro and In Vivo

2017 ◽  
Vol 61 (10) ◽  
Author(s):  
A. Renzoni ◽  
E. Von Dach ◽  
C. Landelle ◽  
S. M. Diene ◽  
C. Manzano ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Bacterial Resistance ◽  
Broth Culture ◽  
Cross Resistance ◽  
Methicillin Resistant ◽  
Content Type ◽  
Genomic Changes ◽  
Low Concentrations

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) resistant to decolonization agents such as mupirocin and chlorhexidine increases the need for development of alternative decolonization molecules. The absence of reported severe adverse reactions and bacterial resistance to polyhexanide makes it an excellent choice as a topical antiseptic. In the present study, we evaluated the in vitro and in vivo capacity to generate strains with reduced polyhexanide susceptibility and cross-resistance with chlorhexidine and/or antibiotics currently used in clinic. Here we report the in vitro emergence of reduced susceptibility to polyhexanide by prolonged stepwise exposure to low concentrations in broth culture. Reduced susceptibility to polyhexanide was associated with genomic changes in the mprF and purR genes and with concomitant decreased susceptibility to daptomycin and other cell wall-active antibiotics. However, the in vitro emergence of reduced susceptibility to polyhexanide did not result in cross-resistance to chlorhexidine. During in vivo polyhexanide clinical decolonization treatment, neither reduced polyhexanide susceptibility nor chlorhexidine cross-resistance was observed. Together, these observations suggest that polyhexanide could be used safely for decolonization of carriers of chlorhexidine-resistant S. aureus strains; they also highlight the need for careful use of polyhexanide at low antiseptic concentrations.

scholarly journals Antimalarial Activity of Small-Molecule Benzothiazole Hydrazones

2016 ◽  
Vol 60 (7) ◽  
pp. 4217-4228 ◽  
Author(s):  
Souvik Sarkar ◽  
Asim A. Siddiqui ◽  
Shubhra J. Saha ◽  
Rudranil De ◽  
Somnath Mazumder ◽  
...  
Keyword(s):  
Murine Model ◽  
Resistant Strain ◽  
Therapeutic Potential ◽  
Antimalarial Activity ◽  
Hematological Parameters ◽  
Plasmodium Yoelii ◽  
Multiple Drug ◽  
Content Type

ABSTRACTWe synthesized a new series of conjugated hydrazones that were found to be active against malaria parasitein vitro, as well asin vivoin a murine model. These hydrazones concentration-dependently chelated free iron and offered antimalarial activity. Upon screening of the synthesized hydrazones, compound 5f was found to be the most active iron chelator, as well as antiplasmodial. Compound 5f also interacted with free heme (KD[equilibrium dissociation constant] = 1.17 ± 0.8 μM), an iron-containing tetrapyrrole released after hemoglobin digestion by the parasite, and inhibited heme polymerization by parasite lysate. Structure-activity relationship studies indicated that a nitrogen- and sulfur-substituted five-membered aromatic ring present within the benzothiazole hydrazones might be responsible for their antimalarial activity. The dose-dependent antimalarial and heme polymerization inhibitory activities of the lead compound 5f were further validated by following [3H]hypoxanthine incorporation and hemozoin formation in parasite, respectively. It is worth mentioning that compound 5f exhibited antiplasmodial activityin vitroagainst a chloroquine/pyrimethamine-resistant strain ofPlasmodium falciparum(K1). We also evaluatedin vivoantimalarial activity of compound 5f in a murine model where a lethal multiple-drug-resistant strain ofPlasmodium yoeliiwas used to infect Swiss albino mice. Compound 5f significantly suppressed the growth of parasite, and the infected mice experienced longer life spans upon treatment with this compound. Duringin vitroandin vivotoxicity assays, compound 5f showed minimal alteration in biochemical and hematological parameters compared to control. In conclusion, we identified a new class of hydrazone with therapeutic potential against malaria.

scholarly journals Synergistic Effect of Antituberculosis Drugs and AzolesIn Vitroagainst Histoplasma capsulatum var. capsulatum

2011 ◽  
Vol 55 (9) ◽  
pp. 4482-4484 ◽  
Author(s):  
Rossana de Aguiar Cordeiro ◽  
Francisca Jakelyne de Farias Marques ◽  
Raimunda Sâmia Nogueira Brilhante ◽  
Kylvia Rocha de Castro e Silva ◽  
Charles Ielpo Mourão ◽  
...  
Keyword(s):  
Synergistic Effect ◽  
Histoplasma Capsulatum ◽  
Drug Combinations ◽  
Antituberculosis Drug ◽  
Growth Forms ◽  
Antituberculosis Drugs ◽  
Content Type ◽  
Synergistic Interactions

ABSTRACTThis study evaluatedin vitrointeractions of antituberculosis drugs and triazoles againstHistoplasma capsulatum. Nine drug combinations, each including an antituberculosis drug (isoniazid, pyrazinamide, or ethambutol) plus a triazole (itraconazole, fluconazole, or voriconazole), were tested against both growth forms ofH. capsulatum. Stronger synergistic interactions were seen in isoniazid or pyrazinamide plus triazoles for the mold form and ethambutol plus voriconazole for the yeast-like form. Further studies should evaluate these combinationsin vivo.

scholarly journals The Cyclic Peptide Ecumicin Targeting ClpC1 Is Active against Mycobacterium tuberculosis In Vivo

2014 ◽  
Vol 59 (2) ◽  
pp. 880-889 ◽  
Author(s):  
Wei Gao ◽  
Jin-Yong Kim ◽  
Jeffrey R. Anderson ◽  
Tatos Akopian ◽  
Seungpyo Hong ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
High Throughput Screening ◽  
Cyclic Peptide ◽  
Genome Mining ◽  
Subcutaneous Administration ◽  
Multiple Drug ◽  
Drug Resistant ◽  
Content Type

ABSTRACTDrug-resistant tuberculosis (TB) has lent urgency to finding new drug leads with novel modes of action. A high-throughput screening campaign of >65,000 actinomycete extracts for inhibition ofMycobacterium tuberculosisviability identified ecumicin, a macrocyclic tridecapeptide that exerts potent, selective bactericidal activity againstM. tuberculosisin vitro, including nonreplicating cells. Ecumicin retains activity against isolated multiple-drug-resistant (MDR) and extensively drug-resistant (XDR) strains ofM. tuberculosis. The subcutaneous administration to mice of ecumicin in a micellar formulation at 20 mg/kg body weight resulted in plasma and lung exposures exceeding the MIC. Complete inhibition ofM. tuberculosisgrowth in the lungs of mice was achieved following 12 doses at 20 or 32 mg/kg. Genome mining of lab-generated, spontaneous ecumicin-resistantM. tuberculosisstrains identified the ClpC1 ATPase complex as the putative target, and this was confirmed by a drug affinity response test. ClpC1 functions in protein breakdown with the ClpP1P2 protease complex. Ecumicin markedly enhanced the ATPase activity of wild-type (WT) ClpC1 but prevented activation of proteolysis by ClpC1. Less stimulation was observed with ClpC1 from ecumicin-resistant mutants. Thus, ClpC1 is a valid drug target againstM. tuberculosis, and ecumicin may serve as a lead compound for anti-TB drug development.

scholarly journals The Efflux Pump Inhibitor Timcodar Improves the Potency of Antimycobacterial Agents

2014 ◽  
Vol 59 (3) ◽  
pp. 1534-1541 ◽  
Author(s):  
Trudy H. Grossman ◽  
Carolyn M. Shoen ◽  
Steven M. Jones ◽  
Peter L. Jones ◽  
Michael H. Cynamon ◽  
...  
Keyword(s):  
Mouse Model ◽  
Efflux Pump ◽  
Fold Increase ◽  
Broth Culture ◽  
Efflux Pump Inhibitor ◽  
Content Type ◽  
Combination Studies ◽  
Drug Dependent

ABSTRACTPrevious studies indicated that inhibition of efflux pumps augments tuberculosis therapy. In this study, we used timcodar (formerly VX-853) to determine if this efflux pump inhibitor could increase the potency of antituberculosis (anti-TB) drugs againstMycobacterium tuberculosisinin vitroandin vivocombination studies. When used alone, timcodar weakly inhibitedM. tuberculosisgrowth in broth culture (MIC, 19 μg/ml); however, it demonstrated synergism in drug combination studies with rifampin, bedaquiline, and clofazimine but not with other anti-TB agents. WhenM. tuberculosiswas cultured in host macrophage cells, timcodar had about a 10-fold increase (50% inhibitory concentration, 1.9 μg/ml) in the growth inhibition ofM. tuberculosisand demonstrated synergy with rifampin, moxifloxacin, and bedaquiline. In a mouse model of tuberculosis lung infection, timcodar potentiated the efficacies of rifampin and isoniazid, conferring 1.0 and 0.4 log10reductions in bacterial burden in lung, respectively, compared to the efficacy of each drug alone. Furthermore, timcodar reduced the likelihood of a relapse infection when evaluated in a mouse model of long-term, chronic infection with treatment with a combination of rifampin, isoniazid, and timcodar. Although timcodar had no effect on the pharmacokinetics of rifampin in plasma and lung, it did increase the plasma exposure of bedaquiline. These data suggest that the antimycobacterial drug-potentiating activity of timcodar is complex and drug dependent and involves both bacterial and host-targeted mechanisms. Further study of the improvement of the potency of antimycobacterial drugs and drug candidates when used in combination with timcodar is warranted.

scholarly journals An In Vitro Enrichment Strategy for Formulating Synergistic Synbiotics

2019 ◽  
Vol 85 (16) ◽  
Author(s):  
Car Reen Kok ◽  
David Fabian Gomez Quintero ◽  
Clement Niyirora ◽  
Devin Rose ◽  
Amanda Li ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Synergistic Effects ◽  
Bifidobacterium Longum ◽  
High Rate ◽  
Host Responses ◽  
Ecological Niches ◽  
Bacterial Populations ◽  
Content Type

ABSTRACT Research on the role of diet on gut and systemic health has led to considerable interest toward identifying novel therapeutic modulators of the gut microbiome, including the use of prebiotics and probiotics. However, various host responses have often been reported among many clinical trials. This is in part due to competitive exclusion as a result of the absence of ecological niches as well as host-mediated constraints via colonization resistance. In this research, we developed a novel in vitro enrichment (IVE) method for isolating autochthonous strains that can function as synergistic synbiotics and overcome these constraints. The method relied on stepwise in vitro fecal fermentations to enrich for and isolate Bifidobacterium strains that ferment the prebiotic xylooligosaccharide (XOS). We subsequently isolated Bifidobacterium longum subsp. longum CR15 and then tested its establishment in 20 unique fecal samples with or without XOS. The strain was established in up to 18 samples but only in the presence of XOS. Our findings revealed that the IVE method is suitable for isolating potential synergistic probiotic strains that possess the genetic and biochemical ability to ferment specific prebiotic substrates. The IVE method can be used as an initial high-throughput screen for probiotic selection and isolation prior to further characterization and in vivo tests. IMPORTANCE This study describes an in vitro enrichment method to formulate synergistic synbiotics that have potential for establishing autochthonous strains across multiple individuals. The rationale for this approach—that the chance of survival of a bacterial strain is improved by providing it with its required resources—is based on classic ecological theory. From these experiments, a human-derived strain, Bifidobacterium longum subsp. longum CR15, was identified as a xylooligosaccharide (XOS) fermenter in fecal environments and displayed synergistic effects in vitro. The high rate of strain establishment observed in this study provides a basis for using synergistic synbiotics to overcome the responder/nonresponder phenomenon that occurs frequently in clinical trials with probiotic and prebiotic interventions. In addition, this approach can be applied in other protocols that require enrichment of specific bacterial populations prior to strain isolation.

scholarly journals TheREnantiomer of the Antitubercular Drug PA-824 as a Potential Oral Treatment for Visceral Leishmaniasis

2013 ◽  
Vol 57 (10) ◽  
pp. 4699-4706 ◽  
Author(s):  
Stephen Patterson ◽  
Susan Wyllie ◽  
Laste Stojanovski ◽  
Meghan R. Perry ◽  
Frederick R. C. Simeons ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Visceral Leishmaniasis ◽  
Phase Ii ◽  
Leishmania Donovani ◽  
Oral Treatment ◽  
Parasite Burden ◽  
Content Type ◽  
Phase Ii Clinical Trials

ABSTRACTThe novel nitroimidazopyran agent (S)-PA-824 has potent antibacterial activity againstMycobacterium tuberculosisin vitroandin vivoand is currently in phase II clinical trials for tuberculosis (TB). In contrast toM. tuberculosis, where (R)-PA-824 is inactive, we report here that both enantiomers of PA-824 show potent parasiticidal activity againstLeishmania donovani, the causative agent of visceral leishmaniasis (VL). In leishmania-infected macrophages, (R)-PA-824 is 6-fold more active than (S)-PA-824. Both des-nitro analogues are inactive, underlining the importance of the nitro group in the mechanism of action. Although thein vitroandin vivopharmacological profiles of the two enantiomers are similar, (R)-PA-824 is more efficacious in the murine model of VL, with >99% suppression of parasite burden when administered orally at 100 mg kg of body weight−1, twice daily for 5 days. InM. tuberculosis, (S)-PA-824 is a prodrug that is activated by a deazaflavin-dependent nitroreductase (Ddn), an enzyme which is absent inLeishmaniaspp. Unlike the case with nifurtimox and fexinidazole, transgenic parasites overexpressing the leishmania nitroreductase are not hypersensitive to either (R)-PA-824 or (S)-PA-824, indicating that this enzyme is not the primary target of these compounds. Drug combination studiesin vitroindicate that fexinidazole and (R)-PA-824 are additive whereas (S)-PA-824 and (R)-PA-824 show mild antagonistic behavior. Thus, (R)-PA-824 is a promising candidate for late lead optimization for VL and may have potential for future use in combination therapy with fexinidazole, currently in phase II clinical trials against VL.

Sign in / Sign up

Export Citation Format

Share Document