New Pharmacological Targets and Biomarkers for the Treatment of Tuberculosis (TB)

Two decades of rigorous study and a unifying omics strategy to TB treatment. We are now confronted with several uncertainties as well as the unfathomable implications of multi-drug resistance. Outstanding prospective leads have emerged in recent years as a result of collaborative efforts. This includes academic research, pharmaceutical corporations, government programs, and non-profit organizations. Novel biomarkers have been identified as possible medication targets by new drug development pipelines that use machine learning methodologies.

Vidya Niranjan

Professor and Head of the Department, Department of Biotechnology Lead- Centre of Excellence Computational Genomics, R V College of Engineering

Mycobacterium tuberculosis (MTB), which has harmed people for more than 10 decades, is the cause of the chronic lung infectious disease known as pulmonary tuberculosis (TB). Modern chemotherapy has been crucial in the fight against TB, but the spread of HIV and the rise of drug-resistant TB pose a threat to its control. The success rate of the 6-month conventional treatment for developing TB is only 85%, despite the fact that the cure rate of TB has dramatically increased since the deployment of direct treatment short-course chemotherapy (DOTS), which was approved by the WHO.

The main disadvantage of the present chemotherapy is how long it takes to complete—up to two years for drug-resistant TB (DR-TB) and 6–9 months for drug–susceptible TB (DS–TB) patients. Patient nonadherence, treatment failure, and resurgence are frequently the results of this. According to 2017 WHO Global TB Report, there were 1.67 million deaths,

10.4 million new cases of active TB disease, 6,00,000 new cases of rifampicin resistance (RR-TB), of which 4,90,000 were multidrug resistant (MDR-TB), and 6.3 million new TB cases recorded in 2016.

Numerous novel compounds with anti-TB potential have been identified as a result of decades of worldwide study, and they are now being tested in both the pre-clinical and clinical phases of therapeutic development. It takes an hour to look for novel anti-TB medications (ATD) that can address the problems with the present TB treatment, however very few treatments reach the market. Hopefully, innovation in the quest for fresh and potent ATDs can reduce the global TB burden.

In order to highlight the impact of tuberculosis on human health worldwide, we begin this review by giving a succinct introduction to the disease. We started out by focusing on how current chemotherapy is used to treat TB and its effectiveness. The main difficulties or problems in TB chemotherapy are then discussed. The remainder of the review gives readers in-depth information on the drug targets now being used against M. tuberculosis, as well as updates on recently FDA-approved medications that can be used to improve the efficacy, bioavailability, and safety of current regimens. Since only a small percentage of compounds pass past the strict bottlenecks of TB medication development programs. This points to the urgent need for the development of new medications that can entirely.

Mycobacterium tuberculosis and host epigenetic alterations as new indicators and therapeutic targets.

The fact that MTB can divert the innate and adaptive immune systems of the human body in many ways is one of the key causes of tuberculosis' protracted dormancy period. In order to fend off the immune attack, pathogenic mycobacteria support a number of mechanisms, including suppression of phago-lysosomal maturation, inhibition of autophagy, activation and production of cytokines, inhibition of reactive oxygen and nitrogen species (ROS and RNS), manipulation of T cell antigen presentation, and epigenetics. During MTB infection, several miRNA levels are dysregulated. Similar to miR146a, the host's level rises

following infection. This miRNA can affect the expression of TRAF6 mRNA to affect MTB survival in macrophage. Conversely, the opposing regulation of certain miRNAs enhances the immune signaling pathway and promotes the immune cells' ability to recognize the pathogen. It is known that these epigenetic modifications affect the latent active and inactive phases of TB infection. MTB latency and the reactivation of pertinent transcription and translation are impacted by epigenetics. Ser/Thr protein kinase (STPK), a component of the Ser/Thr/Tyr kinase system found in MTB, has a significant impact on bacterial growth and engages in interactions with the host. In order to better adapt to the environment of the host, bacteria will occasionally modify their condition through phosphorylation. Bacterial replication can be aided by Ser/Thr protein kinase B (PknB), and its overexpression is detrimental to bacterial development. When MTB is active, latent, or reactivated, PknB can be phosphorylated to regulate the production of specific proteins.

In the realm of oncology or other disease models, the investigation of epigenetic medicines has advanced significantly. Malignant tumors can now be treated in a novel approach by using epigenetic targets to prevent or suppress the imbalance of epigenetic regulation. In the drug discovery process in different disease models, our aforementioned targets or biomarkers, particularly connected microRNA, have made some success. For instance, MRG-201, which imitates miR-29 and is used to treat individuals with Keloids, has passed clinical phase II. Similar to this, there are other medications in phase I, as well as miR-21 and miR-155 inhibitors for T-cell lymphoma and Alport syndromes, respectively. Finding epigenetic medicines for the treatment of tuberculosis is made possible by the development of treatments for related diseases.

For MTB, the novel epigenetic biomarkers/targets are MamA, Rv2966c, RV1988, Rv3204, Rv3763, Rv3423.1, Rv2416c, HsdM. Similarly, in humans (host) the novel epigenetic targets are SUV39H1, SET8, MiR-29, MiR-147, MiR-21, MiR-99b, MiR-126b, MiR-144, MiR-223, MiR-424, MiR-26b, MiR-132 and MiR-155.

Scientists from academic and industry domains undoubtedly have innovative strategies to address the problem of drug-resistant tuberculosis given the growing understanding of MTB

infection, which causes epigenetic changes in infected hosts. The development of modulators that target epigenetic changes occurring both before and after TB infection is both exciting and difficult.

Circular RNA as potential biomarkers and Regulate Anti-TB Defense as Potential Therapeutic Targets)

A type of non-coding protein RNA called circular RNAs (circRNAs) is expressed in the majority of eukaryotic cells. Circular RNAs can loop into a single-stranded, covalently closed structure for more stable and highly conserved properties, which helps them resist or evade RNAase digestion, in contrast to linear RNAs, which have three-prime tails and five-prime caps. The first circular RNA was discovered in the 1970s in plant viroids, which had great thermal stability and a single-stranded covalently closed structure. Sequence analysis verified this discovery two years later. Thus, the study of circRNAs in various species from a functional and mechanistic perspective is now possible because of this work in biology and medicine.

Sputum specimen smear microscopy and sputum culture are currently the major methods used in the laboratory to diagnose tuberculosis (TB). Sputum culture is constrained by its long detection time, which increases the risk of missing the right treatment in time, whereas sputum specimen smear microscopy is constrained by its low sensitivity and specificity values.

CircRNAs have been shown to play a significant role in a wide range of physiological and pathological processes. The circRNAs that are aberrantly expressed in patients may provide a clue as to the possible use of circRNAs in the diagnosis of various disorders. Regarding their vast distribution and durability, circRNAs can be easily found in bodily fluids like blood, urine, exosomes, and others. CircRNAs may be used as TB diagnostic biomarkers, according to the increasing number of research in recent years. To learn about the crucial functions of circRNAs following tuberculosis infection, which can improve our comprehension of TB pathogenesis and aid in the development of TB diagnostic or therapeutic approaches, there are still a lot of facets of the topic that need to be fully researched.

As the initial line of defense against the germs after MTB infection, host macrophages are activated. It's interesting to note that MTB can successfully adapt to a number of ways to evade the macrophages' bactericidal actions, securely surviving inside the cell host, and even developing into active TB. According to an increasing number of studies, circRNAs can operate as essential components in the immune defense response during TB infection by influencing the actions of macrophages with the goal of containing and eradicating MTB invading in macrophages. Determining the significance of circRNAs that are aberrantly

produced in TB and delineating their potential roles in the pathophysiology of TB infection is therefore crucial. For list of circular RNA’s reported to be It is crucial to find involved in regulating tuberculosis are as follows Hsa_circ_0001204, hsa_circ_0001747, hsa_new TB targets circ_0001204, hsa_circ_000174, hsa_circ_0001953 that are not only hsa_circ_0009024 hsa_circ_0001953; hsa_ crucial under host circ_0009024 hsa_circ_001937 hsa_circ_0043497 infection but are hsa_circ_0001204 hsa_circ_103017 hsa_ also susceptible to circ_059914 hsa_circ_0028883 hsa_circ_0005836 hsa_circ_0001380 hsa_circ_103571 circ_051239 pharmacological circ_029965 circ_404022 SAMD8_hsa_ inhibition circRNA994 TWF1_hsa_circRNA9897 circ_ TRAPPC6B hsa_circ_0003528 hsa_circ_101128 hsa_circ_0045474 circAGFG1 circ_0001490 cPWWP2A.

The majority of research has reported that different circRNAs are involved in TB through the miRNA-mRNA transcriptional regulatory axis, but their functions, such as interacting with RBPs or taking part in transcription or translation, have not been investigated. Uncovering the functions and mechanisms of circRNAs in TB will be crucial in the future study, making use of newly developed technologies. In order to discover new functions and underlying processes in TB, it would be advantageous and essential to continue developing a unique regulatory network analysis technique of circRNAs. This would ultimately be helpful and vital for the prevention, control, and treatment of TB.

To sum up, more research is still needed to determine whether circRNAs are safe to use as innovative tools. The immunogenicity and biosafety of circRNAs vaccines or medications need to be further verified in vivo and in vitro. CircRNAs drugs targeting immunological disorders or tumors can be manufactured using circRNAs technology. We expect that circRNAs will continue to be recognised as playing important roles in the management of TB as more research is done on their mechanisms and activities using successively upgraded methodologies.

MTB Enzyme complexes of the electron transport chain can be plyed as potential drug targets

Unlike other bacteria that rely on substrate-level phosphorylation, Mtb is an obligate aerobic

bacterium that primarily depends on Oxidative phosphorylation (OxPhos). The OxPhos process uses the Electron Transport Chain (ETC) to shuttle electrons through a sequence of ETC complexes in order to produce the required PMF.

Recently, numerous chemicals that are thought to be better regime tools have been reported against the Mtb energy production cycle. The development of possible therapeutic compounds using ETC complexes such as NDH-II, cyt bc1-aa3, cyd-bd MK, ATP synthase, and others has been suggested. Although BDQ (sirturo) and Q203 (telebace), which either directly or indirectly limit ATP production, are currently being tested in clinical trials against MDR-TB and XDR-TB.

The drug targets for ETC are NDH-I, NDH-II, Cytochrome bc-I, MenG, MKH2, SDH and ATP synthase. Based on their contributions to the creation of the PMF, each ETC complex has been targeted as a possible druggable target. ATP synthase draws its energy from the PMF. More exhaustive research is needed in order to pinpoint the pathway's potentially more sensitive and dependable target.

The MTB deftly alters its paths to suit its needs. Enzymatic assay, inhibitory assay, and genomic organization of the genes encoding these proteins have all been investigated for each of the complexes directly connected to ETC. Currently, the energy production cycle is affected by more than 30% of the medications undergoing clinical trials. Therefore, identifying the most appropriate target would benefit from a complete understanding of the system and its metabolic adaptability under changing settings.

The components' mechanistic and functional analysis will aid in the development of anti-tuberculosis inhibitors. This review comes to the conclusion that using inhibitory action against a single component will be less effective than using a combinatorial theory of inhibition. The present medications that target the ETC pathway are effective, but only for a short time due to altered pathways and the emergence of resistance. Therefore, it is important to find the appropriate scaffolds and potential inhibitors that could work well with present medications to treat tuberculosis.

A novel concept of bait drug synergism targeting AAC proteins

The four families of aminoglycoside acetyltransferases are AAC(1′), AAC(2′), AAC(3′), and AAC(6′), which are named by the position of modification on the 2-deoxystreptamine core. Aminoglycoside acetyltransferases (AACs) catalyze the synthesis of a physiologically stable amide with the aminoglycoside using intracellular acetyl-CoA as a co-substrate. O-acetylation occurs using the acetyltransferase domain of the bifunctional enzyme AAC(6′)APH(2′′) and the mycobacterial enzyme AAC(2′)-Ic, although AACs primarily change

amino groups (N-acetylation). The AAC family is found to not be prone to mutation over the years.

The novel idea works on the concept of “bait-drug synergism” wherein a biosimilar molecule with a similar interaction profile with AAC as that of aminoglycosides. This bait drug molecule will competitively bind to AAC against aminoglycosides, in-turn preventing the acetylation of aminoglycosides. These aminoglycosides can prevent ribosomal activity leading to the death of pathogens.

The concept of “bait drug synergism” has to be explored more in the coming years as a potential mode to overcome antimicrobial resistance in tuberculosis.

Conclusion

A resurgence in interest in TB medication development during the past ten years has led to numerous important scientific advancements. The present TB-drug pipeline contains innovative chemical scaffolds and a range of targets from a novelty perspective. But despite these improvements in chemotherapy, eliminating TB is still a major issue on a global scale. Therefore, it is crucial to find new TB targets that are not only crucial under host infection but are also susceptible to pharmacological inhibition, in addition to the aforementioned scientific research The new targets should also be focused on overcoming antimicrobial resistance. In the implementation of machine learning in pharmacological research new drug targets have been identified. The key message is that in order to develop a comprehensive control strategy against MTB, the scientific community should constantly engage the socio-political establishment, fill gaps within existing approaches, pursue newer chemotherapeutic approaches, and try to achieve a cumulative therapeutic outcome from various unrelated approaches.

AUTHOR BIO

Vidya Niranjan, PhD is a leading scientist and academic researcher excelling in computational biology. She has worked extensively on genome analysis, drug discovery, tools and database development. With an extensive research experience of over 20 years, she has published over 80 research articles. She has bagged research funding worth 40 million USD from various government agencies and pharmaceutical companies.