Development Of New Antituberculosis Drugs Research Articles

Cryo-EM structures of Mycobacterium tuberculosis polynucleotide phosphorylase suggest a potential mechanism for its RNA substrate degradation

As one of the oldest infectious diseases in the world, tuberculosis (TB) is the second most deadly infectious disease after COVID-19. Tuberculosis is caused by Mycobacterium tuberculosis (Mtb), which can attack various organs of the human body. Up to now, drug-resistant TB continues to be a public health threat. Pyrazinamide (PZA) is regarded as a sterilizing drug in the treatment of TB due to its distinct ability to target Mtb persisters. Previously we demonstrated that a D67N mutation in Mycobacterium tuberculosis polynucleotide phosphorylase (MtbPNPase, Rv2783c) confers resistance to PZA and Rv2783c is a potential target for PZA, but the mechanism leading to PZA resistance remains unclear. To gain further insight into the MtbPNPase, we determined the cryo-EM structures of apo Rv2783c, its mutant form and its complex with RNA. Our studies revealed the Rv2783c structure at atomic resolution and identified its enzymatic functional groups essential for its phosphorylase activities. We also investigated the molecular mechanisms underlying the resistance to PZA conferred by the mutation. Our research findings provide structural and functional insights enabling the development of new anti-tuberculosis drugs.

Free Energy Barriers for Passive Drug Transport through the Mycobacterium tuberculosis Outer Membrane: A Molecular Dynamics Study.

The emergence of multi-drug-resistant tuberculosis strains poses a significant challenge to modern medicine. The development of new antituberculosis drugs is hindered by the low permeability of many active compounds through the extremely strong bacterial cell wall of mycobacteria. In order to estimate the ability of potential antimycobacterial agents to diffuse through the outer mycolate membrane, the free energy profiles, the corresponding activation barriers, and possible permeability modes of passive transport for a series of known antibiotics, modern antituberculosis drugs, and prospective active drug-like molecules were determined using molecular dynamics simulations with the all-atom force field and potential of mean-force calculations. The membranes of different chemical and conformational compositions, density, thickness, and ionization states were examined. The typical activation barriers for the low-mass molecules penetrating through the most realistic membrane model were 6-13 kcal/mol for isoniazid, pyrazinamide, and etambutol, and 19 and 25 kcal/mol for bedaquilin and rifampicin. The barriers for the ionized molecules are usually in the range of 37-63 kcal/mol. The linear regression models were derived from the obtained data, allowing one to estimate the permeability barriers from simple physicochemical parameters of the diffusing molecules, notably lipophilicity and molecular polarizability.

Research progress on Mycobacterium tuberculosis acetyltransferase

The protein acetylation of Mycobacterium tuberculosis(MTB) plays an important role in virulence, drug resistance, regulation of metabolism and host anti-tuberculosis immune response. The proteins acetylation of MTB and host protein could be induced by the MTB acetyltransferase, which is related to the occurrence, development and prognosis of tuberculosis (TB). A clear understanding of the function of MTB acetyltransferase and identification of its targeted regulatory protein acetylation modification is critical to elucidate the pathogenic mechanism and drug resistance mechanism of TB, and then this could then provide new targets for the development of anti-tuberculosis drugs. This article systematically reviewed the research progress on MTB acetyltransferase related functions, which will provide a theoretical basis for further research on its mediated protein acetylation modification, further development of new anti-tuberculosis drugs and elucidation of drug resistance mechanism.

Discovery of novel reversible inhibitor of DprE1 based on benzomorpholine for the treatment of tuberculosis.

About a quarter of the world's population is infected with Mycobacterium tuberculosis, equivalent to about two billion people. With the emergence of multidrug-resistant tuberculosis, those existing anti-tuberculosis drugs no longer meet the demand for cure anymore; there is an urgent need for the development of new anti-tuberculosis drugs. Decaprenylphosphoryl-β-D-ribose 2´-epimerase (DprE1) has been proven to be a potential antimycobacterial target, and several inhibitors have entered clinical trial. Herein, we designed and synthesized a series of compounds based on the indole and benzomorpholine by using the strategy of scaffold hopping. The preferred compound B18 showed strong antimycobacterial activity in H37Rv and drug-resistant clinical isolates. In addition, compound B18 did not exhibit antimycobacterial efficacy against other species of strains. Subsequently, the target of B18 was identified as DprE1 by analyzing spontaneous compound-resistant mutation data, and a docking study was performed to illustrate the binding mode between B18 and DprE1. In general, compound B18 is compatible to current DprE1 inhibitors, even higher phosphodiesterase 6C selectivity and plasma protein binding rate, which represent a new type of effective reversible DprE1 inhibitor. IMPORTANCE Drug therapy remains the cornerstone of tuberculosis (TB) treatment, yet first-line anti-tuberculosis drugs are associated with significant adverse effects that can compromise patient outcomes. Moreover, prolonged and widespread use has led to an alarming rise in drug-resistant strains of Mycobacterium tuberculosis, including multidrug-resistant [MDR-tuberculosis (TB)] and extensively drug-resistant (XDR-TB) forms. Urgent action is needed to develop novel anti-tuberculosis agents capable of overcoming these challenges. We report that compound B18, a decaprenylphosphoryl-β-D-ribose 2´-epimerase inhibitor with a benzomorpholine backbone, exhibits potent activity against not only the non-pathogenic strain H37Ra, but also the pathogenic strain H37Rv and clinical MDR and XDR strains. Preliminary druggability studies indicate that B18 possesses high safety and acceptable pharmacokinetic properties, rendering it a promising candidate for further development as a novel anti-tuberculosis agent.

К вопросу об актуальности разработки новых противотуберкулезных препаратов

К вопросу об актуальности разработки новых противотуберкулезных препаратов

3D-QSAR study of adenosine 5’-phosphosulfate (APS) analouges as ligands for APS reductase

Metabolism of sulfur (sulfur assimilation pathway, SAP) is one of the key pathways for the pathogenesis and survival of persistant bacteria, such as Mycobacterium tuberculosis (Mtb), in the latent period. Adenosine 5'-phosphosulfate reductase (APSR) is an important enzyme involved in the SAP, absent from the human body, so it might represent a valid target for development of new antituberculosis drugs. This work aimed to develop 3D-QSAR model based on the crystal structure of APSR from Pseudomonas aeruginosa, which shows high degree of homology with APSR from Mtb, in complex with its substrate, adenosine 5'-phosphosulfate (APS). 3D-QSAR model was built from a set of 16 nucleotide analogues of APS using alignment-independent descriptors derived from molecular interaction fields (MIF). The model improves the understanding of the key characteristics of molecules necessary for the interaction with target, and enables the rational design of novel small molecule inhibitors of Mtb APSR.

Andrographolide exerts anti-inflammatory effects in Mycobacterium tuberculosis-infected macrophages by regulating the Notch1/Akt/NF-κB axis.

Tuberculosis is a serious public health problem aggravated by the slow progress in the development of newanti-tuberculosisdrugs. The hyper-reactive TB patients have suffered from chronic inflammation which could cause deleterious effects on their bodies. Therefore, it is imperative to develop an adjunctive therapy based on inflammatory modulation during Mycobacterium tuberculosis (Mtb) infection. The present study aims to investigate the immune regulatory effects of Andrographolide (Andro) on Mtb-infected macrophages and its underlying mechanisms. The results showed that Andro inhibits the production of IL-1β and other inflammatory cytokines in a dose-dependent manner. The down-regulation of IL-1β expression causes the declining expression of IL-8 and MCP-1 in lung epithelial cells which were co-cultured with Mtb-infected macrophages. The inhibition of the activation of NF-κB pathway, but not the inhibition of MAPK signaling pathway, accounts for the anti-inflammatory role of Andro. Further studies elucidated that Andro could evoke the activation of autophagy to degrade NLRP3, which ultimately inhibited inflammasome activation and subsequent IL-1β production. Finally, the relevant results demonstrated that Andro inhibited the Notch1 pathway to down-regulate the phosphorylation of Akt/mTOR and NF-κB p65 subunit. Taken together, Andro has been found to suppress the Notch1/Akt/NF-κB signaling pathway. Both Akt inhibition-induced autophagy and inhibition of the NF-κB pathway contributed to restraining the activation of NLRP3 inflammasome and subsequent IL-1β production. Then, the decreased production of IL-1β influenced chemokine expression in lung epithelial cells. Based on these results, anti-inflammatory effect of Andro in TB infection is merit further investigation.

Development of new antituberculosis drugs among of 1,3- and 1,4-diazines. Highlights and perspectives

The properties of pyrimidine and pyrazine derivatives responsible for the existence of antituberculosis activity are considered. Examples of synthesis and biological activity of the most promising compounds containing the pyrimidine or pyrazine rings in the molecular structure are presented.

CAMP-Dependent Transcription Factor in Mycobacterium tuberculosis Coded by the Rv3676 Gene as a Possible Target for the Development of Antituberculosis Drugs

Adenylate cyclase Rv2212 plays a key role in the growth of Mycobacterium tuberculosis (Mtb) and its reactivation from the dormant state. This enzyme could potentially be a good target for the development of new antituberculosis drugs. However, enzymes of this type are also important for the metabolism of the host organism, which makes it doubtful that their inhibitors can be used for treatment of the disease. In the Mtb genome, the cAMP-dependent transcription factor (cAMP-TF), which is encoded by the Rv3676 gene, is annotated and absent in the human organism. The Mtb strain with an overexpression of this gene was designed. This strain rapidly grew in vitro and in vivo under stress conditions. Bacteria of the new strain retained the plasmid with the Rv3676 gene in vivo even in the absence of a selection agent, which indicated the advantages for survival with increased cAMP-TF expression. These results demonstrate the importance of Rv3676 for maintenance of the viability of Mtb cells under unfavorable in vitro conditions and their virulence in vivo and were similar to those obtained by overexpression of the adenylate cyclase Rv2212. Transcription factor Rv3676 may be a new target for the development of new antituberculosis drugs.

Quinoline Derivatives Kill Mycobacterium tuberculosis by Activating Glutamate Kinase

There is a great need for identification and development of new anti-tuberculosis drugs with novel targets. Recent drug-discovery efforts typically focus on identifying inhibitors but not activators that perturb metabolic enzymes' functions as a means to kill Mycobacterium tuberculosis (Mtb). Here, we describe a class of quinoline compounds, Z0933/Z0930, which kill Mtb by acting as activators of glutamate kinase (GK), a previously untargeted enzyme catalyzing the first step of proline biosynthesis. We further show that Z0933/Z0930 augment proline production and induce Mtb killing via proline-derived redox imbalance and production of reactive oxygen species. This work highlights the effectiveness of gain-of-function probes against Mtb and provides a framework for the discovery of next-generation allosteric activators of GK.

Molecular Docking, Dynamics Simulation, and Scanning Electron Microscopy (SEM) Examination of Clinically Isolated <i>Mycobacterium tuberculosis</i> by Ursolic Acid: A Pentacyclic Triterpenes

The purpose of this study was to analyze the inhibitory action of ursolic acid (UA) as an antitubercular agent by computational docking studies and molecular dynamics simulations. The effect of UA on the cell wall of Mycobacterium tuberculosis (MTB) was evaluated by using Scanning Electron Microscopy (SEM). UA was used as a ligand for molecular interaction and investigate its binding activities to a group of proteins involved in the growth of MTB and the biosynthesis of the cell wall. Computational docking analysis was performed by using autodock 4.2.6 based on scoring functions. UA binding was confirmed by 30 ns molecular dynamics simulation using gromacs 5.1.1. H37Rv sensitive strain and isoniazid-resistant strain were used in the SEM study. UA showed to have the optimum binding affinity to inhA (Two-trans-enoyl-ACP reductase enzyme involved in elongation of fatty acid) with the binding energy of -9.2 kcal/mol. The dynamic simulation showed that the UA-inhA complex relatively stable and found to establish hydrogen bond with Thr196 and Ile194. SEM analysis confirms that UA treatment in both sensitive strain and resistant strain affected the morphology cell wall of MTB. This result indicated that UA could be one of the potential ligands for the development of new antituberculosis drugs.

Tuberculosis Epidemiology, Pathogenesis, Drugs and Drug Resistance Development: A Review

Tuberculosis is a chronic infectious disease caused by Mycobacterium tuberculosis and classified as pulmonary and extrapulmonary based on their site of infection. Antituberculosis drugs developed since the 1940s and as their discovery resistance also developed against them. World health organization recognized tuberculosis as emergency public health in 1993. Acquired and primary drug resistances are the common pathways for the development of anti-tuberculosis drug resistance. Acquired drug resistance is the result of inappropriate treatment, poor quality of the drugs and inadequate drug intake and primary drug resistance is due to exposure to the drug-resistant anti-tuberculosis. Types of anti-tuberculosis drug-resistant are multidrug-resistant tuberculosis is the result of resistance to isoniazid and rifampicin, extensively drug-resistant tuberculosis a consequence of resistance to isoniazid, rifampicin, fluoroquinolones and one of the second-line injectable drugs and totally drug-resistant tuberculosis is a resistance to all first and second-line anti-tuberculosis drugs. Anti-tuberculosis drugs primarily actions are on protein synthesis, mycolic acid synthesis, DNA synthesis, folic acid synthesis, and ATP synthase. These drugs could produce bacteriostatic or bactericidal effects on the mycobacteria. The main resistance mechanism to the anti-tuberculosis drug is the mutation of the target gene accountable for the action of anti-tuberculosis drugs. This resistance to the antituberculosis drug produces a devastating effect on public health. Therefore, further study should be conducted in the areas of finding a new target for the development of new anti-tuberculosis drugs.

Genetic Aspects of Drug Resistance and Virulence in Mycobacterium tuberculosis

Drug-resistant Mycobacterium tuberculosis and its high virulence new strains present a global health threat. The solution of this problem requires the development of new anti-tuberculosis drugs. Investigation of the genetic mechanisms associated with the development of multidrug resistant M. tuberculosis strains is the basis for the search for new biotargets of anti-tuberculosis drugs. To date, the molecular genetic relationships between genes controlling drug resistance and virulence remain poorly investigated and require special attention. In the present study, genetic mechanisms of interaction of genetic systems of drug resistance and virulence of M. tuberculosis are considered.

Development of new anti-tuberculosis drugs: the strategy of unconventional microbial culture and silencing gene activation

Tuberculosis (TB), caused by Mycobacterium tuberculosis, has become a major human infectious disease. The existing first-line and second-line TB drugs have poor treatment outcomes in patients with MDR-TB and XDR-TB. There is an urgent need for new and better drugs to treat tuberculosis due to lengthy and complex treatment regimens and a rising problem of drug resistance. Microbial-derived natural products have revealed enormous reservoirs of as yet untapped lead compounds. In this review, we discuss the strategies that have been developed in bacteria and fungi to isolation of non-culturable microorganisms and activation of silent biosynthetic gene clusters involved in the study of microbial-derived natural products. This review also highlights recent advances in microbial-derived natural products with anti-tuberculosis activity using these methods.

<italic>Mycobacterium tuberculosis</italic> biofilm matrix and potential drug targets and treatment strategies

As one of the most successful pathogens, Mycobacterium tuberculosis adopts distinct mechanisms to survive drug exposure and to relapse. One example of such a mechanism is by generating persisters. Abundant evidence indicates that the generating persisters of Mycobacterium tuberculosis is influenced by their ability to grow as surface-associated multicellular communities called biofilms. Therefore, the research on the biofilm composition will contribute to the development of new antituberculosis drugs. The extracellular matrix of Mycobacterium tuberculosis biofilm is primarily composed of extracellular polysaccharide, as well as protein, DNA and lipid. This paper describes the composition of Mycobacterium tuberculosis biofilm matrix, based on which we discuss potential drug targets and treatment strategies, hoping to shed light on the biological function of Mycobacterium tuberculosis biofilm matrix.

Anti-Mycobacterial Evaluation of 7-Chloro-4-Aminoquinolines and Hologram Quantitative Structure-Activity Relationship (HQSAR) Modeling of Amino-Imino Tautomers.

In an ongoing research program for the development of new anti-tuberculosis drugs, we synthesized three series (A, B, and C) of 7-chloro-4-aminoquinolines, which were evaluated in vitro against Mycobacterium tuberculosis (MTB). Now, we report the anti-MTB and cytotoxicity evaluations of a new series, D (D01–D21). Considering the active compounds of series A (A01–A13), B (B01–B13), C (C01–C07), and D (D01–D09), we compose a data set of 42 compounds and carried out hologram quantitative structure–activity relationship (HQSAR) analysis. The amino–imino tautomerism of the 4-aminoquinoline moiety was considered using both amino (I) and imino (II) forms as independent datasets. The best HQSAR model from each dataset was internally validated and both models showed significant statistical indexes. Tautomer I model: leave-one-out (LOO) cross-validated correlation coefficient (q2) = 0.80, squared correlation coefficient (r2) = 0.97, standard error (SE) = 0.12, cross-validated standard error (SEcv) = 0.32. Tautomer II model: q2 = 0.77, r2 = 0.98, SE = 0.10, SEcv = 0.35. Both models were externally validated by predicting the activity values of the corresponding test set, and the tautomer II model, which showed the best external prediction performance, was used to predict the biological activity responses of the compounds that were not evaluated in the anti-MTB trials due to poor solubility, pointing out D21 for further solubility studies to attempt to determine its actual biological activity.

Development of new antituberculosis drugs from natural products.

The three major infectious diseases (AIDS, malaria, and tuberculosis) and neglected tropical diseases (NTDs: 17 diseases) unevenly affect more people in developing countries and have been overlooke...

Antimycobacterial Natural Products from Marine Pseudopterogorgia elisabethae

Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), which has been and still remains a serious disease to the global human population causing millions of deaths worldwide. The recent increase in the number of multi-drug resistant clinical isolates of M. tuberculosis has created an urgent need for the discovery and development of new antituberculosis drugs. The recent researches focusing on natural products have shown potential to obtain a potentially rich source of drug candidates. The natural products can be isolated from many sources, such as fungi, bacteria, plants and marine organisms. Among marine organisms, Pseudopterogorgia elisabethae is capable of performing a great diversity of compounds with remarkable biological activities. Many compounds of serrulatane, amphilectane, elisabethane, and elisapterane type are produced by this organism, as well as further derivatives which exhibit antituberculosis activity. This review covers all the compounds produced by this organism that has demonstrated moderate to high activity in bioassays realized in vitro against M. tuberculosis. Keywords: Tuberculosis, antitubercular natural products, Pseudopterogorgia elisabethae.

Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis.

The transcriptional regulator PhoP is an essential virulence factor in Mycobacterium tuberculosis, and it presents a target for the development of new anti-tuberculosis drugs and attenuated tuberculosis vaccine strains. PhoP binds to DNA as a highly cooperative dimer by recognizing direct repeats of 7-bp motifs with a 4-bp spacer. To elucidate the PhoP-DNA binding mechanism, we determined the crystal structure of the PhoP-DNA complex. The structure revealed a tandem PhoP dimer that bound to the direct repeat. The surprising tandem arrangement of the receiver domains allowed the four domains of the PhoP dimer to form a compact structure, accounting for the strict requirement of a 4-bp spacer and the highly cooperative binding of the dimer. The PhoP-DNA interactions exclusively involved the effector domain. The sequence-recognition helix made contact with the bases of the 7-bp motif in the major groove, and the wing interacted with the adjacent minor groove. The structure provides a starting point for the elucidation of the mechanism by which PhoP regulates the virulence of M. tuberculosis and guides the design of screening platforms for PhoP inhibitors.

Identification of Bostrycin Derivatives as Potential Inhibitors of Mycobacterium tuberculosis Protein Tyrosine Phosphatase (MptpB).

As a virulence factor secreted into host cells, the Mycobacterium tuberculosis protein tyrosine phosphatase (MptpB) mediates the intracellular survival of M. tuberculosis. MptpB has become an attractive target for the development of new anti-tuberculosis drugs. In the present study, we assessed the inhibitory activity of marine fungus-derived bostrycin and its derivatives against MptpB in vitro. The compounds were tested for their inhibitory effects on MptpB in vitro and the inhibition mode. The binding characteristics of inhibitors and MptpB were determined by microscale thermophoresis (MST). Our data showed that one of the derivatives, compound 25 (IC50 = 64.6 ± 9.1 µM), possessed a greater inhibitory activity compared with bostrycin (IC50 = 327.6 ± 60.4 µM) and behaved as a non-competitive inhibitor. The binding characteristic of MptpB and compound 25 was determined by MST, exhibiting a moderate affinity with a KD constant of 5200 ± 1020 nM. We, for the first time, reported that bostrycin and one of its analogues exhibited inhibitory activity against MptpB, which possessed potential as novel agents against tuberculosis.