Cytochrome bd oxidase: an emerging anti-tubercular drug target.

Cytochrome bd (cyt-bd) oxidase, one of the two terminal oxidases in the Mycobacterium tuberculosis (Mtb) oxidative phosphorylation pathway, plays an indispensable role in maintaining the functionality of the metabolic pathway under stressful conditions. However, the absence of this oxidase in eukaryotic cells allows researchers to select it as a potential drug target for the synthesis of anti-tubercular (anti-TB) molecules. Cyt-bd inhibitors have often been combined with cytochrome bcc/aa3 super-complex inhibitors in anti-TB drug regimens to achieve a desired bactericidal response. The functional redundancy between both the terminal oxidases is responsible for this. The cryo-EM structure of cyt-bd oxidase from Mtb (PDB ID: 7NKZ) further accelerated the research to identify its inhibitor. Herein, we have summarized the reported anti-TB cyt-bd inhibitors, insight into the rationale behind targeting cyt-bd oxidase, and an outline of the architecture of Mtb cyt-bd oxidase.

Cell Type-Specific Extracellular Vesicles and Their Impact on Health and Disease.

Extracellular vesicles (EVs), a diverse group of cell-derived exocytosed particles, are pivotal in mediating intercellular communication due to their ability to selectively transfer biomolecules to specific cell types. EVs, composed of proteins, nucleic acids, and lipids, are taken up by cells to affect a variety of signaling cascades. Research in the field has primarily focused on stem cell-derived EVs, with a particular focus on mesenchymal stem cells, for their potential therapeutic benefits. Recently, tissue-specific EVs or cell type-specific extracellular vesicles (CTS-EVs), have garnered attention for their unique biogenesis and molecular composition because they enable highly targeted cell-specific communication. Various studies have outlined the roles that CTS-EVs play in the signaling for physiological function and the maintenance of homeostasis, including immune modulation, tissue regeneration, and organ development. These properties are also exploited for disease propagation, such as in cancer, neurological disorders, infectious diseases, autoimmune conditions, and more. The insights gained from analyzing CTS-EVs in different biological roles not only enhance our understanding of intercellular signaling and disease pathogenesis but also open new avenues for innovative diagnostic biomarkers and therapeutic targets for a wide spectrum of medical conditions. This review comprehensively outlines the current understanding of CTS-EV origins, function within normal physiology, and implications in diseased states.

Methyltrifluoromethanesulfonate Catalyst in Direct Nucleophilic Substitution of Alcohols; One-Pot Synthesis of 4H-Chromene Derivatives.

The catalytic activity of methyltrifluoromethanesulfonate (MeOTf) has been explored toward direct nucleophilic substitution of the hydroxyl group of nonmanipulated alcohols such as benzylic, allylic, propargylic, and tertiary alcohols with a wide range of uncharged nucleophiles such as 1,3-dicarbonyl compounds, amides, alkynes, and indoles to generate functionalized 1,3-dicarbonyl compounds, amides, alkynes, and indoles, respectively. Thus, the present protocol defines an alternate pathway to construct new C-C, C-N, and C-O bonds with the formation of water as the byproduct under mild conditions without any acids or metals. A completely different mechanism was established through several control experiments to explain the reaction methodology. As an application of the reported protocol, 1H-indene derivatives have been synthesized in one pot when benzylic alcohols were subjected to react with internal alkynes. The scope of the reaction has been further extended toward a tandem benzylation-cyclization-dehydration of 1,3-dicarbonyl compounds with 2-hydroxybenzyl alcohols, which furnish biologically important 4H-chromene derivatives.

Regioselective Transition Metal-Free Catalytic Ring Opening of 2H-Azirines by Phenols and Naphthols; One-Pot Access to Benzo- and Naphthofurans.

Benzofuran and naphthofuran derivatives are synthesized from readily available phenols and naphthols. Regioselective ring openings of 2H-azirine followed by in situ aromatization using a catalytic amount of Brønsted acid have established the novelty of the methodology. The involvement of a series of 2H-azirines with a variety of phenols, 1-naphthols, and 2-naphthols showed the generality of the protocol. In-depth density functional theory calculations revealed the reaction mechanism with the energies of the intermediates and transition states of a model reaction. An alternate pathway of the mechanism has also been proposed with computer modeling.

Effects of microRNA-mediated negative feedback on gene expression noise.

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in eukaryotes by binding with target mRNAs and preventing translation. miRNA-mediated feedback motifs are ubiquitous in various genetic networks that control cellular decision making. A key question is how such a feedback mechanism may affect gene expression noise. To answer this, we have developed a mathematical model to study the effects of a miRNA-dependent negative-feedback loop on mean expression and noise in target mRNAs. Combining analytics and simulations, we show the existence of an expression threshold demarcating repressed and expressed regimes in agreement with earlier studies. The steady-state mRNA distributions are bimodal near the threshold, where copy numbers of mRNAs and miRNAs exhibit enhanced anticorrelated fluctuations. Moreover, variation of negative-feedback strength shifts the threshold locations and modulates the noise profiles. Notably, the miRNA-mRNA binding affinity and feedback strength collectively shape the bimodality. We also compare our model with a direct auto-repression motif, where a gene produces its own repressor. Auto-repression fails to produce bimodal mRNA distributions as found in miRNA-based indirect repression, suggesting the crucial role of miRNAs in creating phenotypic diversity. Together, we demonstrate how miRNA-dependent negative feedback modifies the expression threshold and leads to a broader parameter regime of bimodality compared to the no-feedback case.

Exploring and exploiting the host cell autophagy during Mycobacterium tuberculosis infection.

Tuberculosis, caused by Mycobacterium tuberculosis, is a fatal infectious disease that prevails to be the second leading cause of death from a single infectious agent despite the availability of multiple drugs for treatment. The current treatment regimen involves the combination of several drugs for 6 months that remain ineffective in completely eradicating the infection because of several drawbacks, such as the long duration of treatment and the side effects of drugs causing non-adherence of patients to the treatment regimen. Autophagy is an intracellular degradative process that eliminates pathogens at the early stages of infection. Mycobacterium tuberculosis's unique autophagy-blocking capability makes it challenging to eliminate compared to usual pathogens. The present review discusses recent advances in autophagy-inhibiting factors and mechanisms that could be exploited to identify autophagy-inducing chemotherapeutics that could be used as adjunctive therapy with the existing first-line anti-TB agent to shorten the duration of therapy and enhance cure rates from multidrug-resistant tuberculosis (MDR-TB) and extreme drug-resistant tuberculosis (XDR-TB).

GC-MS-Guided Antimicrobial Defense Responsive Secondary Metabolites from the Endophytic Fusarium solani Isolated from Tinospora cordifolia and Their Multifaceted Biological Properties.

Medicinal plants are hosts to an infinite number of microorganisms, commonly referred to as endophytes which are rich in bioactive metabolites yielding favorable biological activities. The endophytes are known to have a profound impact on their host plant by promoting the accumulation of secondary metabolites which are beneficial to humankind. In the present study, the fungal endophyte, Fusarium solani (ABR4) from the medicinal plant Tinospora cordifolia, was assessed for its bioactive secondary metabolites employing fermentation on a solid rice medium. The crude ABR4 fungal extract was sequentially purified using the solvent extraction method and characterized using different spectroscopic and analytical techniques namely TLC, UV spectroscopic analysis, HRESI-MS, FTIR, and GC-MS analysis. The GC-MS analysis revealed the presence of pyridine, benzoic acid, 4-[(trimethylsilyl)oxy]-trimethylsilyl ester, hexadecanoic acid trimethylsilyl ester, and oleic acid trimethylsilyl ester. The cytotoxic ability of ABR4 was evaluated by MTT assay against lung cancer (A549) and breast cancer (MCF-7) cell lines. The compounds did not exhibit significant cytotoxicity against the tested cell lines. The endophytic ABR4 extract was evaluated for its antimicrobial potential against human pathogens (S. aureus, B. cereus, E. coli, S. typhimurium, P. aeruginosa, and C. albicans) by recording 47 to 54% inhibition. Taken together, the endophytic fungal strain ABR4 demonstrated a remarkable antimicrobial activity against the tested pathogens. Furthermore, the functional metabolites isolated from the endophytic strain ABR4 reveal its broader usage as antimicrobial agents for newer drug development in the pharmaceutical industry.

Tweaking host immune responses for novel therapeutic approaches against Mycobacterium tuberculosis.

In TB, combat between the human host and Mycobacterium tuberculosis involves intricate interactions with immune cells. M. tuberculosis has evolved a complex evasion system to circumvent immune cells, leading to persistence and limiting its clearance by the host. Host-directed therapies are emerging approaches to modulate host responses, including inflammatory responses, cytokine responses, and autophagy, by using small molecules to curb mycobacterial infections. Targeting host immune pathways reduces the chances of antibiotic resistance to M. tuberculosis because, unlike antibiotics, this approach acts directly on the cells of the host. In this review, we discuss the role of immune cells during M. tuberculosis proliferation, provide a updated understanding of immunopathogenesis, and explore the range of host-modulating options for the clearance of this pathogen.

Unravelling the flexibility of Mycobacterium tuberculosis: an escape way for the bacilli.

The persistence of Mycobacterium tuberculosis makes it difficult to eradicate the associated infection from the host. The flexible nature of mycobacteria and their ability to adapt to adverse host conditions give rise to different drug-tolerant phenotypes. Granuloma formation restricts nutrient supply, limits oxygen availability and exposes bacteria to a low pH environment, resulting in non-replicating bacteria. These non-replicating mycobacteria, which need high doses and long exposure to anti-tubercular drugs, are the root cause of lengthy chemotherapy. Novel strategies, which are effective against non-replicating mycobacteria, need to be adopted to shorten tuberculosis treatment. This not only will reduce the treatment time but also will help prevent the emergence of multi-drug-resistant strains of mycobacteria.

Role of transcription termination factor Rho in anti-tuberculosis drug discovery.

Mycobacterial infections, including multidrug and extreme drug-resistant (MDR and XDR) infections, are a severe challenge and create a virtual antibiotic-deficient era. Bacterial transcription is an established antimicrobial drug target. In mycobacteria, efficient transcription termination relies on the ATP-dependent RNA helicase factor Rho. Rho factor is essential for Mycobacterium tuberculosis (Mtb) survival, and is a valid antibacterial drug target with no homolog in eukaryotes. Rho maintains genomic stability and virulence and prevents pervasive transcription in Mtb. In this review, we provide an overview of the essentiality of Rho in Mtb, which makes it an attractive drug target for inhibitor discovery.

(3 + 2) cycloaddition of 2-alkoxynaphthalenes with azaoxyallyl cations: access to benzo[e]indolones.

A reaction between 2-alkoxynaphthalene and an in situ formed azaoxyallyl cation has been reported under ambient reaction conditions. The (3 + 2) cycloaddition reaction followed by aryl C-OMe/C-OEt bond cleavage produces a variety of benzo[e]indolone derivatives. Based on the isolated intermediate from the control experiment and previous results, a possible mechanism has been drawn. Reduction of the N-O bond of the benzo[e]indolone derivative manifests the possibility of further functionalization of the products towards biologically important heterocyclic molecules.

An evolutionary divergent thermodynamic brake in ZAP-70 fine-tunes the kinetic proofreading in T cells.

T cell signaling starts with assembling several tyrosine kinases and adapter proteins to the T cell receptor (TCR), following the antigen binding to the TCR. The stability of the TCR-antigen complex and the delay between the recruitment and activation of each kinase determines the T cell response. Integration of such delays constitutes a kinetic proofreading mechanism to regulate T cell response to the antigen binding. However, the mechanism of these delays is not fully understood. Combining biochemical experiments and kinetic modeling, here we report a thermodynamic brake in the regulatory module of the tyrosine kinase ZAP-70, which determines the ligand selectivity, and may delay the ZAP-70 activation upon antigen binding to TCR. The regulatory module of ZAP-70 comprises of a tandem SH2 domain that binds to its ligand, doubly-phosphorylated ITAM peptide (ITAM-Y2P), in two kinetic steps: a fast step and a slow step. We show the initial encounter complex formation between the ITAM-Y2P and tandem SH2 domain follows a fast-kinetic step, whereas the conformational transition to the holo-state follows a slow-kinetic step. We further observed a thermodynamic penalty imposed during the second phosphate-binding event reduces the rate of structural transition to the holo-state. Phylogenetic analysis revealed the evolution of the thermodynamic brake coincides with the divergence of the adaptive immune system to the cell-mediated and humoral responses. In addition, the paralogous kinase Syk expressed in B cells does not possess such a functional thermodynamic brake, which may explain the higher basal activation and lack of ligand selectivity in Syk.

Binary matrix factorization on special purpose hardware.

Many fundamental problems in data mining can be reduced to one or more NP-hard combinatorial optimization problems. Recent advances in novel technologies such as quantum and quantum-inspired hardware promise a substantial speedup for solving these problems compared to when using general purpose computers but often require the problem to be modeled in a special form, such as an Ising or quadratic unconstrained binary optimization (QUBO) model, in order to take advantage of these devices. In this work, we focus on the important binary matrix factorization (BMF) problem which has many applications in data mining. We propose two QUBO formulations for BMF. We show how clustering constraints can easily be incorporated into these formulations. The special purpose hardware we consider is limited in the number of variables it can handle which presents a challenge when factorizing large matrices. We propose a sampling based approach to overcome this challenge, allowing us to factorize large rectangular matrices. In addition to these methods, we also propose a simple baseline algorithm which outperforms our more sophisticated methods in a few situations. We run experiments on the Fujitsu Digital Annealer, a quantum-inspired complementary metal-oxide-semiconductor (CMOS) annealer, on both synthetic and real data, including gene expression data. These experiments show that our approach is able to produce more accurate BMFs than competing methods.

Similar immunogenicity profiles between the proposed biosimilar MYL-1501D and reference insulin glargine in patients with diabetes mellitus: the phase 3 INSTRIDE 1 and INSTRIDE 2 studies.

BACKGROUND: MYL-1501D is a proposed biosimilar to insulin glargine. The noninferiority of MYL-1501D was demonstrated in patients with type 1 diabetes and type 2 diabetes in 2 phase 3 trials. Immunogenicity of MYL-1501D and reference insulin glargine was examined in both studies. METHODS: INSTRIDE 1 and INSTRIDE 2 were multicenter, open-label, randomized, parallel-group studies. In INSTRIDE 1, patients with type 1 diabetes received MYL-1501D or insulin glargine over a 52-week period. In INSTRIDE 2, patients with type 2 diabetes treated with oral antidiabetic drugs, insulin naive or not, received MYL-1501D or reference insulin glargine over a 24-week period. Incidence rates and change from baseline in relative levels of antidrug antibodies (ADA) and anti-host cell protein (anti-HCP) antibodies in both treatment groups were determined by a radioimmunoprecipitation assay and a bridging immunoassay, respectively. Results were analyzed using a mixed-effects model (INSTRIDE 1) or a nonparametric Wilcoxon rank sum test (INSTRIDE 2). RESULTS: Total enrollment was 558 patients in INSTRIDE 1 and 560 patients in INSTRIDE 2. The incidence of total and cross-reactive ADA was comparable between treatment groups in INSTRIDE 1 and INSTRIDE 2 (P > 0.05 for both). A similar proportion of patients had anti-HCP antibodies in both treatment groups in INSTRIDE 1 at week 52 (MYL-1501D, 93.9 %; reference insulin glargine, 89.6 %; P = 0.213) and in INSTRIDE 2 at week 24 (MYL-1501D, 87.3 %; reference insulin glargine, 86.9 %; P > 0.999). CONCLUSIONS: In INSTRIDE 1 and INSTRIDE 2, similar immunogenicity profiles were observed for MYL-1501D and reference insulin glargine in patients with type 1 diabetes and type 2 diabetes, respectively. TRIAL REGISTRATION: ClinicalTrials.gov, INSTRIDE 1 ( NCT02227862 ; date of registration, August 28, 2014); INSTRIDE 2 ( NCT02227875 ; date of registration, August 28, 2014).

Altered neural oscillations within and between sensorimotor cortex and parietal cortex in chronic jaw pain.

Pain perception is associated with priming of the motor system and the orienting of attention in healthy adults. These processes correspond with decreases in alpha and beta power in the sensorimotor and parietal cortices. The goal of the present study was to determine whether these findings extend to individuals with chronic pain. Individuals with chronic jaw pain and pain-free controls anticipated and experienced a low pain or a moderate pain-eliciting heat stimulus. Although stimuli were calibrated for each subject, stimulus temperature was not different between groups. High-density EEG data were collected during the anticipation and heat stimulation periods and were analyzed using independent component analyses, EEG source localization, and measure projection analyses. Direct directed transfer function was also estimated to identify frequency specific effective connectivity between regions. Between group differences were most evident during the heat stimulation period. We report three novel findings. First, the chronic jaw pain group had a relative increase in alpha and beta power and a relative decrease in theta and gamma power in sensorimotor cortex. Second, the chronic jaw pain group had a relative increase in power in the alpha and beta bands in parietal cortex. Third, the chronic jaw pain group had less connectivity strength in the beta and gamma bands between sensorimotor cortex and parietal cortex. Our findings show that the effect of chronic pain attenuates rather than magnifies neural responses to heat stimuli. We interpret these findings in the context of system-level changes in intrinsic sensorimotor and attentional circuits in chronic pain.

Multimodal dopaminergic and free-water imaging in Parkinson's disease.

INTRODUCTION: When using free-water diffusion imaging or positron emission tomography (PET), it is established that substania nigra microstructure and presynaptic dopamine activity are impaired in early PD. It is not well understood if these two forms of degeneration are redundant, or if they each provide a unique contribution to the clinical motor and cognitive symptoms. METHODS: A total of 129 PD and 75 control individuals underwent motor and cognitive evaluations, and in vivo [11C]dihydrotetrabenazine (DTBZ) monoaminergic brain PET imaging and diffusion imaging. Correlations between free-water in the substantia nigra and striatal PET measures were analyzed. Unbiased multiple regression using a backward elimination method was performed between clinical severity and all imaging measures. RESULTS: Inverse correlations were found between free-water in posterior substantia nigra and DTBZ binding in putamen and caudate. Multiple regression revealed that increased free-water in the posterior substantia nigra, decreased DTBZ binding in putamen, and age were predictors of higher Hoehn and Yahr stage, MDS-UPDRS III scores, and posture and gait sub-scores. Increased posterior substantia nigra free-water alone was associated tremor scores. Free-water in caudate and putamen did not predict measures of motor performance. Decreased DTBZ binding in caudate, increased free-water in caudate and posterior substantia nigra were associated with higher dementia ratings. CONCLUSIONS: These findings suggest that free-water in the posterior substantia nigra and presynaptic dopamine imaging in striatum are uniquely associated with the clinical symptoms of PD, indicating that each imaging modality may be measuring a unique mechanism relevant to nigrostriatal degeneration.

Cortical dynamics within and between parietal and motor cortex in essential tremor.

BACKGROUND: Evidence from functional imaging in essential tremor suggests that activity within parietal and motor cortices may be associated with worsening of tremor at increased visual feedback. OBJECTIVES: Examine how cortical oscillations within these regions and the connectivity between these regions is associated with worsening of tremor in essential tremor in response to high visual feedback. METHOD: The study included 24 essential tremor participants and 17 controls. We measured cortical activity and tremor magnitude at low and high feedback conditions. Cortical activity was measured using high-density electroencephalogram and isolated using source localization. RESULTS: Changes in power across feedback in the 4-12 Hz and 12-30 Hz bands were reduced within the contralateral motor cortex of essential tremor patients compared to controls. The 12-30 Hz bidirectional connectivity between the parietal and contralateral motor cortex was decreased in essential tremor patients. Worsening of tremor from low to high visual feedback was associated with 4-12 Hz activity in contralateral motor cortex. The greatest separation between groups was found when using the difference of the contralateral motor cortex activity at high and low feedback, rather than either feedback condition alone. CONCLUSION: Our findings provide new evidence that tremor in essential tremor is associated with reduced power across feedback in the motor cortex and reduced connectivity between the parietal and motor cortices. Combined with previous work on the cerebellar-thalamo-cortical motor circuit, our findings suggest that the network level disturbances associated with essential tremor extend to the cortico-cortical pathway between the parietal cortex and motor cortex. © 2018 International Parkinson and Movement Disorder Society.

Functional brain activity during motor control and pain processing in chronic jaw pain.

Changes in brain function in chronic pain have been studied using paradigms that deliver acute pain-eliciting stimuli or assess the brain at rest. Although motor disability accompanies many chronic pain conditions, few studies have directly assessed brain activity during motor function in individuals with chronic pain. Using chronic jaw pain as a model, we assessed brain activity during a precisely controlled grip force task and during a precisely controlled pain-eliciting stimulus on the forearm. We used multivariate analyses to identify regions across the brain whose activity together best separated the groups. We report 2 novel findings. First, although the parameters of grip force production were similar between the groups, the functional activity in regions including the prefrontal cortex, insula, and thalamus best separated the groups. Second, although stimulus intensity and pain perception were similar between the groups, functional activity in brain regions including the dorsal lateral prefrontal cortex, rostral ventral premotor cortex, and inferior parietal lobule best separated the groups. Our observations suggest that chronic jaw pain is associated with changes in how the brain processes motor and pain-related information even when the effector producing the force or experiencing the pain-eliciting stimulus is distant from the jaw. We also demonstrate that motor tasks and multivariate analyses offer alternative approaches for studying brain function in chronic jaw pain.

Correction: The evolution of cost-efficiency in neural networks during recovery from traumatic brain injury.

[This corrects the article DOI: 10.1371/journal.pone.0170541.].