Development Of Anti-tuberculosis Drugs Research Articles

QSAR based therapeutic management of M. tuberculosis.

Mycobacterium tuberculosis is responsible for severe mortality and morbidity worldwide but, under-developed and developing countries are more prone to infection. In search of effective and wide-spectrum anti-tubercular agents, interdisciplinary approaches are being explored. Of the several approaches used, computer based quantitative structure activity relationship (QSAR) have gained momentum. Structure-based drug design and discovery implies a combined knowledge of accurate prediction of ligand poses with the good prediction and interpretation of statistically validated models derived from the 3D-QSAR approach. The validated models are generally used to screen a small combinatorial library of potential synthetic candidates to identify hits which further subjected to docking to filter out compounds as novel potential emerging drug molecules to address multidrug-resistant tuberculosis. Several newer models are integrated to QSAR methods which include different types of chemical and biological data, and simultaneous prediction of pharmacological activities including toxicities and/or other safety profiles to get new compounds with desired activity. In the process, several newer molecules have been identified which are now being assessed for their clinical efficacy. Present review deals with the advances made in the field highlighting overall future prospects of the development of anti-tuberculosis drugs.

Validation of Mycobacterium tuberculosis dihydroneopterin aldolase as a molecular target for anti-tuberculosis drug development

An early step of target validation in antimicrobial drug discovery is to prove that a gene coding for a putative target is essential for pathogen's viability. However, little attention has been paid to demonstrate the causal links between gene essentiality and a particular protein function that will be the focus of a drug discovery effort. This should be considered an important step in target validation since a growing number of proteins are found to exhibit multiple and unrelated tasks. Here, we show that the Mycobacterium tuberculosis (Mtb) folB gene is essential and that this essentiality depends on the dihydroneopterin aldolase/epimerase activities of its protein product, the FolB protein from the folate biosynthesis pathway. The wild-type (WT) MtFolB and point mutants K99A and Y54F were cloned, expressed, purified and monitored for the aldolase, epimerase and oxygenase activities using HPLC. In contrast to the WT MtFolB, both mutants have neither aldolase nor epimerase activities in the conditions assayed. We then performed gene knockout experiments and showed that folB gene is essential for Mtb survival under the conditions tested. Moreover, only the WT folB sequence could be used as a rescue copy in gene complementation studies. When the sequences of mutants K99A or Y54F were used for complementation, no viable colonies were obtained, indicating that aldolase and/or epimerase activities are crucial for Mtb survival. These results provide a solid basis for further work aiming to develop new anti-TB agents acting as inhibitors of the aldolase/epimerase activities of MtFolB.

Sclerotiorin inhibits protein kinase G from Mycobacterium tuberculosis and impairs mycobacterial growth in macrophages

As a eukaryotic-like Ser/Thr protein kinase, Mycobacterium tuberculosis virulent effector protein kinase G (PknG) mediates mycobacterial survival by regulating bacterial cell metabolic processes and preventing phagosome-lysosome fusion in host macrophages. Targeting PknG is an effective strategy for development of anti-tuberculosis (TB) drugs. In the study, we found that sclerotiorin, derived from marine fungi from the South China Sea, exhibited moderately strong inhibitory effects on recombinant PknG, with an IC50 value of 76.5 μM, and acted as a non-competitive inhibitor. The dissociation constant (KD) of sclerotiorin determined by MST was 11.4 μM, demonstrating a moderate binding strength between them. Sclerotiorin could substantially impair the mycobacterial survival in infected macrophages while the macrophage viability remained unaffected, though it did not inhibit the mycobacterial growth in culture. When sclerotiorin was used in combination with rifampicin, intracellular mycobacterial growth decreased as sclerotiorin concentration increased. Docking analysis suggested a binding mechanism of inhibition with performing interactions with the P-loop and catalytic loop of PknG. In summary, we reported that sclerotiorin had moderately strong PknG inhibitory activity, but no cytotoxicity, and it could substantially decrease the mycobacterial growth inside macrophages, suggesting that sclerotiorin has potential to supplement antibiotic therapy for TB.

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...

Synthesis, Inhibition of Mycobacterium tuberculosis Enoyl-acyl Carrier Protein Reductase and Antimycobacterial Activity of Novel Pentacyanoferrate(II)-isonicotinoylhydrazones

Tuberculosis remains among the top causes of death triggered by a single pathogen. Herein, a greener synthetic approach for isonicotinoylhydrazones is described using ultrasound energy. These compounds were used as starting materials for synthesizing pentacyanoferrate(II)-isonicotinoylhydrazones, which inhibited the reaction catalyzed by Mycobacterium tuberculosis 2-trans-enoyl-ACP(CoA) reductase (MtInhA) in a time-dependent manner. The most active coordination complex showed an increase of more than ten-fold in the MtInhA inhibition rate constant compared with lead pentacyano(isoniazid)ferrate(II) (IQG607). Additionally, the new series of metal-based compounds demonstrated antitubercular activity against a drug-susceptible Mycobacterium tuberculosis (Mtb) strain and was devoid of toxicity to mammalian cells (IC50 > 20 µmol L-1, half maximal inhibitory concentration). Finally, one of the synthesized compounds showed intracellular activity similar to isoniazid in a macrophage model of Mtb infection, indicating that this chemical class may furnish novel structures to embark on the preclinical phase of anti-tuberculosis drug development.

Delamanid in the treatment of multidrug-resistant tuberculosis.

Otsuka has been engaged in anti-tuberculosis drug development efforts for over 30 years, and is the leading private sector funder of tuberculosis (TB) research and development. Delamanid (DLM), discovered by Otsuka's scientists, has been shown to provide benefit with respect to short-term surrogate markers and long-term treatment outcomes, and it has received regulatory approval for treatment of adult pulmonary multidrug-resistant TB (MDR-TB) as one of only two new anti-tuberculosis drugs in the last 40 years. Lack of drug-drug interactions with major antiretrovirals and efficacy against MDR-TB allow DLM's applicability in a wide range of MDR-TB patients. Current and future efforts are focused on replacing less safe and less efficacious second-line drugs with DLM, its contribution to all-oral and/or shortened treatment regimens, and, ultimately, inclusion in a pan-TB regimen. This manuscript provides a brief review of DLM.

Molecular Diversity of Mycobacterium tuberculosis Strains in Northwestern Iran.

BackgroundYears after the development of antituberculosis (TB) drugs, many people continue to suffer from this disease. To control the spread of TB, strains of the Mycobacterium tuberculosis complex need to be determined, and sources of infection must be identified. Such steps should help to prevent transmission of the infection.ObjectivesThe aim of this study was to perform molecular genotyping of isolates of the M. tuberculosis complex obtained from patients in northwestern Iran.MethodsOne hundred ninety-four culture-positive M. tuberculosis isolates obtained from patients in northwestern Iran were analyzed using the mycobacterial interspersed repetitive unit-exact tandem repeats (MIRU-ETR) method.ResultsThe MIRU-ETR method distinguished 162 different patterns in the 194 isolates, comprising 23 clusters and 139 unique patterns. Its discriminatory power according to the Hunter-Gaston discriminatory index (HGDI) was 0.9978. The largest cluster contained six isolates.ConclusionsThis research indicated that various strains of M. tuberculosis were responsible for TB and that the majority of cases were due to reactivation.

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.

Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets.

Background: Glutamine synthetase (GS) is a crucial enzyme to the nitrogen cycle with great commercial and pharmaceutical value. Current inhibitors target the active site, affecting GS activity indiscriminately in all organisms. As the active site is located at the interface between two monomers, the protein-protein interface (PPI) of GSs gains a new role, by providing new targets for enzyme inhibition. Exploring GSs PPI could allow for the development of inhibitors selective for specific organisms. Here we map the PPI of three GSs—human (hsGS), maize (zmGS) and Mycobacterium tuberculosis (mtGS)—and unravel new drugable pockets. Methods: The PPI binding free energy coming from key residues on three GSs from different organisms were mapped by computational alanine scan mutagenesis, applying a multiple dielectric constant MM-PBSA methodology. The most relevant residues for binding are referred as hot-spots. Drugable pockets on GS were detected with the Fpocket software. Results and Conclusions: A total of 23, 19 and 30 hot-spots were identified on hsGS, zmGS and mtGS PPI. Even possessing differences in the hot-spots, hsGS and zmGS PPI are overall very similar. On the other hand, mtGS PPI differs greatly from hsGS and zmGS PPI. A novel drugable pocket was detected on the mtGS PPI. It seems particularly promising for the development of selective anti-tuberculosis drugs given its location on a PPI region that is highly populated with hot-spots and is completely different from the hsGS and zmGS PPIs. Drugs targeting this pockets should be inactive on eukaryotic GS II enzymes.

A Macrophage Infection Model to Predict Drug Efficacy Against Mycobacterium Tuberculosis.

In the last 40 years, only a single new antituberculosis drug was FDA approved. New tools that improve the drug development process will be essential to accelerate the development of next-generation antituberculosis drugs. The drug development process seems to be hampered by the inefficient transition of initially promising hits to candidate compounds that are effective in vivo. In this study, we introduce an inexpensive, rapid, and BSL-2 compatible infection model using macrophage-passaged Mycobacterium tuberculosis (Mtb) that forms densely packed Mtb/macrophage aggregate structures suitable for drug efficacy testing. Susceptibility to antituberculosis drugs determined with this Mtb/macrophage aggregate model differed from commonly used in vitro broth-grown single-cell Mtb cultures. Importantly, altered drug susceptibility correlated well with the reported ability of the respective drugs to generate high tissue and cerebrospinal fluid concentrations relative to their serum concentrations, which seems to be the best predictors of in vivo efficacy. Production of these Mtb/macrophage aggregates could be easily scaled up to support throughput efforts. Overall, its simplicity and scalability should make this Mtb/macrophage aggregate model a valuable addition to the currently available Mtb drug discovery tools.

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.

Viability, morphology, and proteome of Mycobacterium smegmatis MSMEG_0319 knockout strain.

Mycobacterium tuberculosis Rv0228, a membrane protein, is predicted as a drug target through computational methods. MSMEG_0319 (MS0319) in Mycobacterium smegmatis mc(2) 155 is the ortholog of Rv0228. To study the effect of MS0319 protein on M. smegmatis, an MS0319 gene knockout strain (ΔMS0319) was generated via a homologous recombination technique in this study. The results showed that the lack of MS0319 protein in mc(2) 155 cells led to the loss of viability at nonpermissive temperature. Scanning electron microscopy and transmission electron microscopy observations showed drastic changes in cellular shape especially cell wall disruption in ΔMS0319 cells. Proteomic analysis of ΔMS0319 cells through LC-MS/MS revealed that 462 proteins had changes in their expressions by lacking MS0319 protein. The M. tuberculosis orthologs of these 462 proteins were found through BLASTp search and functional clustering and metabolic pathway enrichment were performed on the orthologs. The results revealed that most of them were enzymes involved in metabolism of carbohydrates and amino acids, indicating that Rv0228 played an important role in cellular metabolism. All these results suggested Rv0228 as a potential target for development of antituberculosis drugs.

Defining New Drug Targets Through Protein-Protein Interaction: Interaction of Resuscitation Promoting Factors with SucA of TCA Cycle in M. tuberculosis H37Rv

Upon infection with Mycobacterium tuberculosis, only a small percentage causes active infection while the rest goes into latent infection. These latent bacilli can reactivate under immunocompromised conditions and cause active disease. Little is known about the mechanism by which the mycobacteria reactivate. A family of extracellular bacterial proteins, known as resuscitation promoting factors (Rpf) from Micrococcus luteus and M. tuberculosis has been shown to stimulate growth of dormant mycobacteria as well as reactivation of chronic tuberculosis in mice. Rpf is present as a single, essential gene in M. luteus and five homologues (rpfA-E) in M. tuberculosis. The ability to stimulate culturability and resuscitation appears to be related to muralytic activity of Rpf and they have been identified as peptidoglycan glycosidases. Rpf B has earlier been shown to interact and synergize with Rpf-interacting protein A (RipA), an endopeptidase to cleave bonds in bacterial peptidoglycan suggesting distinct role of Rpf B in cell wall hydrolysis. In order to further understand the role of other Rpfs in resuscitation of dormant mycobacteria, we used an E. coli two hybrid system to identify SucA of TCA cycle as an interacting partner of Rpf from M. tuberculosis (Rpf A, C and D) and M. luteus (RpfM). The in vivo protein-protein interaction was confirmed by M-PFC system in mycobacterial host, in vitro by FRET analysis. An enhanced expression of SucA and Rpf genes was observed during resuscitation phase. We hypothesize that during transition from nonculturable to resuscitation phase mycobacteria cleaves its hard breaking cell wall by endopeptidase RipA interacting with Rpf B and increases its metabolic energy generation by evoking TCA cycle, interacting with Rpf A, C and D and could serve as prospective target along with Rpfs and RipA for development of new anti-tuberculosis drugs preventing reactivation of dormant bacilli.

Accelerating clinical drug development for children with tuberculosis.

Despite urgent need, the development, approval and availability of child-friendly anti-tuberculosis drugs lag significantly behind that of adults, with children having been ignored in anti-tuberculosis drug development research. This paper outlines possible strategies for accelerating and better integrating the development of drugs and regimens for pediatric tuberculosis (TB) into existing drug development pathways for adults: initiation of pediatric studies of new treatments as soon as promising efficacy data have been generated in adults following successful phase II studies, shifting from the current age de-escalated approach to concomitant enrollment of children from the various age groups in studies, and leveraging the concepts of both the Unified Pathway and regimen development that have helped speed the study and development of novel regimens in adults.

Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria.

Fatty acid degradation protein D32 (FadD32), an enzyme required for mycolic acid biosynthesis and essential for mycobacterial growth, has recently been identified as a valid and promising target for anti-tuberculosis drug development. Here we report the crystal structures of Mycobacterium smegmatis FadD32 in the apo and ATP-bound states at 2.4 Å and 2.25 Å resolution, respectively. FadD32 consists of two globular domains connected by a flexible linker. ATP binds in a cleft at the interface between the N- and C-terminal domains and its binding induces significant local conformational changes in FadD32. The binding sites of meromycolic acid and phosphopantetheine are identified by structural comparison with other members of the adenylating enzyme superfamily. These results will improve our understanding of the catalytic mechanism of FadD32 and help in the design of inhibitors of this essential enzyme.

Structural basis for phosphatidylinositol-phosphate biosynthesis.

Phosphatidylinositol is critical for intracellular signalling and anchoring of carbohydrates and proteins to outer cellular membranes. The defining step in phosphatidylinositol biosynthesis is catalysed by CDP-alcohol phosphotransferases, transmembrane enzymes that use CDP-diacylglycerol as donor substrate for this reaction, and either inositol in eukaryotes or inositol phosphate in prokaryotes as the acceptor alcohol. Here we report the structures of a related enzyme, the phosphatidylinositol-phosphate synthase from Renibacterium salmoninarum, with and without bound CDP-diacylglycerol to 3.6 and 2.5 Å resolution, respectively. These structures reveal the location of the acceptor site, and the molecular determinants of substrate specificity and catalysis. Functional characterization of the 40%-identical ortholog from Mycobacterium tuberculosis, a potential target for the development of novel anti-tuberculosis drugs, supports the proposed mechanism of substrate binding and catalysis. This work therefore provides a structural and functional framework to understand the mechanism of phosphatidylinositol-phosphate biosynthesis.

Synthetic and Immunological Studies of Mycobacterial Lipoarabinomannan Oligosaccharides and Their Protein Conjugates.

Lipoarabinomannan (LAM) is one of the major constituents of the Mycobacterium tuberculosis cell wall and an attractive molecular scaffold for antituberculosis drug and vaccine development. In this paper, a convergent strategy was developed for the synthesis of LAM oligosaccharides with an α-1,2-linked dimannopyranose cap at the nonreducing end. The strategy was highlighted by efficient coupling of separately prepared nonreducing end and reducing end oligosaccharides. Glycosylations were mainly achieved with thioglycoside donors, which gave excellent yields and stereoselectivity even for reactions between complex oligosaccharides. The strategy was utilized to successfully synthesize tetra-, hepta-, and undecasaccharides of LAM from d-arabinose in 10, 15, and 14 longest linear steps and 7.84, 7.50, and 2.59% overall yields, respectively. The resultant oligosaccharides with a free amino group at their reducing end were effectively conjugated with carrier proteins, including bovine serum albumin and keyhole limpet hemocyanin (KLH), via a bifunctional linker. Preliminary immunological studies on the KLH conjugates revealed that they could elicit robust antibody responses in mice and that the antigen structure had some influence on their immunological property, thus verifying the potential of the oligosaccharides for vaccine development and other immunological studies.

Identification of chebulinic acid as potent natural inhibitor of M. tuberculosis DNA gyrase and molecular insights into its binding mode of action

Drug resistant tuberculosis has threatened all the advances that have been made in TB control at the global stage in the last few decades. DNA gyrase enzymes are an excellent target for antibacterial drug discovery as they are involved in essential functions like DNA replication. Here we report, a successful application of high throughput virtual screening (HTVS) to identify an inhibitor of Mycobacterium DNA gyrase targeting the wild type and the most prevalent three double mutants of quinolone resistant DNA gyrase namely A90V+D94G, A74S+D94G and A90V+S91P. HTVS of 179.299 compounds gave five compounds with significant binding affinity. Extra presicion (XP) docking and MD simulations gave a clear view of their interaction pattern. Among them, chebulinic acid (CA), a phytocompound obtained from Terminalia chebula was the most potent inhibitor with significantly high XP docking score, −14.63, −16.46, −15.94 and −15.11 against wild type and three variants respectively. Simulation studies for a period of 16ns indicated stable DNA gyrA–CA complex formation. This stable binding would result in inhibition of the enzyme by two mechanisms. Firstly, binding of CA causes displacement of catalytic Tyr129 away from its target DNA-phosphate molecule from 1.6Å to 3.8–7.3Å and secondly, by causing steric hindrance to the binding of DNA strand at DNA binding site of enzyme. The combined effect would result in loss of cleavage and religation activity of enzyme leading to bactericidal effect on tuberculosis. This phytocompound displays desirable quality for carrying forward as a lead compound for anti-tuberculosis drug development. The results presented here are solely based on computations and need to be validated experimentally in order to assert the proposed mechanism of action.

The Structure and Interactions of Periplasmic Domains of Crucial MmpL Membrane Proteins from Mycobacterium tuberculosis

Mycobacterium tuberculosis mycobacterial membrane protein large (MmpL) proteins are important in substrate transport across the inner membrane. Here, we show that MmpL proteins are classified into two phylogenetic clusters, where MmpL cluster II contains three soluble domains (D1, D2, and D3) and has two full-length members, MmpL3 and MmpL11. Significantly, MmpL3 is currently the most druggable M.tuberculosis target. We have solved the 2.4-Å MmpL11-D2 crystal structure, revealing structural homology to periplasmic porter subdomains of RND (multidrug) transporters. The resulting predicted cluster II MmpL membrane topology has D1 and D2 residing, and possibly interacting, within the periplasm. Crosslinking and biolayer interferometry experiments confirm that cluster II D1 and D2 bind with weak affinities, and guided D1-D2 heterodimeric model assemblies. The predicted full-length MmpL3 and MmpL11 structural models reveal key substrate binding and transport residues, and may serve as templates to set the stage for insilico anti-tuberculosis drug development.