Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM

Dynamic Measurement of Protein Translation in Mycobacteria Using Nontargeted Stable Isotope Labeling in Combination with MALDI-TOF Mass Spectrometry-Based Readout

Understanding the metabolic pathways of mycobacteria is essential to identify novel antibiotics and to compose synergistic antibiotic regimens against tuberculosis, one of the world's most deadly infectious diseases with >1.7 Mio yearly deaths. We present a novel proteomics approach for the dynamic measurement of the nascent fractions of specific proteins. We use nontargeted stable isotope incorporation to label the nascent proteins after adding glycerol-1,3-13C2. The analysis is performed using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) with a self-programmed script, allowing quantitative data. We compared the de novo synthesis of proteins under regular growth conditions and the effect of four antimicrobials, including rifampicin as a first-line drug, linezolid and bedaquiline as second-line drugs, and benzithiazinone-043 as promising drug candidates against tuberculosis. Changes in the synthesis of individual proteins, either due to antimicrobial action or due to regulations in the organism, can be followed in high temporal resolution within the 1/2 doubling cycle of mycobacteria. The analysis of de novo protein synthesis offers a fast screening and testing tool, allowing assessment of the onset and extent of antimycobacterial activity or regulatory phenotypes in different organisms. Due to the untargeted approach, it can be used in model strains and clinical isolates alike and does not require genetic modifications. The dynamic readout and labeling reveal the onset of action of drugs or drug candidates and allow for the prediction of synergistic effects of several substances.

Potential of Mycobacterium tuberculosis Type II NADH-Dehydrogenase in Antitubercular Drug Discovery

The type II NADH-dehydrogenase enzyme in Mycobacterium tuberculosis plays a critical role in the efficient functioning of the oxidative phosphorylation pathway. It acts as the entry point for electrons in the electron transport chain, which is essential for fulfilling the energy requirements of both replicating and nonreplicating mycobacterial species. Due to the absence of the type II NADH-dehydrogenase enzyme in mammalian mitochondria, targeting the type II NADH-dehydrogenase enzyme for antitubercular drug discovery could be a vigilant approach. Utilizing type II NADH-dehydrogenase inhibitors in antitubercular therapy led to bactericidal response, even in monotherapy. However, the absence of the cryo-EM structure of Mycobacterium tuberculosis type II NADH-dehydrogenase has constrained drug discovery efforts to rely on high-throughput screening methods, limiting the use of structure-based drug discovery. Here, we have delineated the literature-reported Mycobacterium tuberculosis type II NADH-dehydrogenase inhibitors and the rationale behind selecting this specific enzyme for antitubercular drug discovery, along with shedding light on the architecture of the enzyme structure and functionality. The gap in the current research and future research direction for TB treatment have been addressed.

Constructing protein-functionalized DNA origami nanodevices for biological applications

In living systems, proteins participate in various physiological processes and the clustering of multiple proteins is essential for efficient signaling. Therefore, understanding the effects of the number, distance and orientation of proteins is of great significance. With programmability and addressability, DNA origami technology has enabled fabrication of sophisticated nanostructures with precise arrangement and orientation control of proteins to investigate the effects of these parameters on protein-involved cellular processes. Herein, we highlight the construction and applications of protein-functionalized DNA origami nanodevices. After the introduction of the structural design principles of DNA origami and the strategies of protein-DNA conjugation, the emerging applications of protein-functionalized DNA origami nanodevices with controlled key parameters are mainly discussed, including the regulation of enzyme cascade reactions, modulation of cellular behaviours, drug delivery therapy and protein structural analysis. Finally, the current challenges and potential directions of protein-functionalized DNA origami nanodevices are also presented, advancing their applications in biomedicine, cell biology and structural biology.

A Novel Bi-Directional Channel for Nutrient Uptake across Mycobacterial Outer Envelope

Nutrients are absorbed by special transport proteins on the cell membrane; however, there is less information regarding transporters across the mycobacterial outer envelope, which comprises dense and intricate structures. In this study, we focus on the model organism Mycolicibacterium smegmatis, which has a cell envelope similar to that of Mycobacterium tuberculosis, as well as on the TiME protein secretion tube across the mycobacterial outer envelope. We present transcriptome results and analyze the protein compositions of a mycobacterial surface envelope, determining that more transporters and porins are induced to complement the deletion of the time gene in Mycolicibacterium smegmatis. The TiME protein is essential for nutrient utilization, as demonstrated in the uptake experiments and growth on various monosaccharides or with amino acids as the sole carbon source. Its deletion caused bacteria to be more sensitive to anti-TB drugs and to show a growth defect at an acid pH level, indicating that TiME promotes the survival of M. smegmatis in antibiotic-containing and acidic environments. These results suggest that TiME tubes facilitate bi-directional processes for both protein secretion and nutrient uptake across the mycobacterial outer envelope.

Mutations and insights into the molecular mechanisms of resistance of Mycobacterium tuberculosis to first-line

Genetically antimicrobial resistance in Mycobacterium tuberculosis is currently one of the most important aspects of tuberculosis, considering that there are emerging resistant strains for almost every known drug used for its treatment. There are multiple antimicrobials used for tuberculosis treatment, and the most effective ones are the first-line drugs, which include isoniazid, pyrazinamide, rifampicin, and ethambutol. In this context, understanding the mechanisms of action and resistance of these molecules is essential for proposing new therapies and strategies of treatment. Additionally, understanding how and where mutations arise conferring a resistance profile to the bacteria and their effect on bacterial metabolism is an important requisite to be taken in producing safer and less susceptible drugs to the emergence of resistance. In this review, we summarize the most recent literature regarding novel mutations reported between 2017 and 2022 and the advances in the molecular mechanisms of action and resistance against first-line drugs used in tuberculosis treatment, highlighting recent findings in pyrazinamide resistance involving PanD and, additionally, resistance-conferring mutations for novel drugs such as bedaquiline, pretomanid, delamanid and linezolid.

Unraveling Major Proteins of Mycobacterium tuberculosis Envelope

Abstract:

Although treatable, resistant form of tuberculosis (TB) has posed a major impediment to the effective TB control programme. As the Mycobacterium tuberculosis cell envelope is closely associated with its virulence and resistance, it is very important to understand the cell envelope for better treatment of causative pathogens. Cell membrane plays a crucial role in imparting various cell functions. Proteins being the functional moiety, it is impossible to characterize the functional properties based on genetic analysis alone. Proteomic based research has indicated mycobacterial envelope as a good source of antigens/proteins. Envelope/membrane and associated proteins have an anticipated role in biological processes, which could be of vital importance to the microbe, and hence could qualify as drug targets. This review provides an overview of the prominent and biologically important cell envelope and highlights the different functions offered by the proteins associated with it. Selective targeting of the mycobacterial envelope offers an untapped opportunity to address the problems associated with the current drug regimen and also will lead to the development of more potent and safer drugs against all forms of tuberculous infections.

A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets

Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.

Tuberculosis: Past, present and future of the treatment and drug discovery research

Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. Despite decades of research driving advancements in drug development and discovery against TB, it still leads among the causes of deaths due to infectious diseases. We are yet to develop an effective treatment course or a vaccine that could help us eradicate TB. Some key issues being prolonged treatment courses, inadequate drug intake, and the high dropout rate of patients during the treatment course. Hence, we require drugs that could accelerate the elimination of bacteria, shortening the treatment duration. It is high time we evaluate the probable lacunas in research holding us back in coming up with a treatment regime and/or a vaccine that would help control TB spread. Years of dedicated and focused research provide us with a lead molecule that goes through several tests, trials, and modifications to transform into a ‘drug’. The transformation from lead molecule to ‘drug’ is governed by several factors determining its success or failure. In the present review, we have discussed drugs that are part of the currently approved treatment regimen, their limitations, vaccine candidates under trials, and current issues in research that need to be addressed. While we are waiting for the path-breaking treatment for TB, these factors should be considered during the ongoing quest for novel yet effective anti-tubercular. If these issues are addressed, we could hope to develop a more effective treatment that would cure multi/extremely drug-resistant TB and help us meet the WHO's targets for controlling the global TB pandemic within the prescribed timeline.

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Despite numerous drugs and vaccines undergoing clinical trials, we have not been able to control TB.

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Majority of articles list the advancements in the TB drug-discovery; here we review the limitations of existing treatments.

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Brief description of aspects to be considered for the development of one but effective drug/preventive vaccine.

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A glance at pediatric tuberculosis: the most neglected area of TB research which requires dedicated research efforts.

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A concise narrative for research aspects to be re-evaluated by both academia and pharmaceutical R&D teams.