Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis.

The emergence of resistant Mycobacterium tuberculosis (Mtb) infection and the dearth of drugs against tuberculosis have made it imperative to identify and validate novel targets and classes of drugs for treatment. The pyrimidine operon regulatory protein (PyrR), a regulator of de novo pyrimidine synthesis, is an essential enzyme and a probable 5-fluorouracil (5-FU) target in Mtb, with mutations in PyrR attributable to 5-FU resistance. Here we report, for the first time, the co-crystal structure of the PyrR-5-FU complex along with mapping of spontaneous mutational sites of PyrR. A cluster of mutations in the presence of the drug usually indicates a plausible region of drug-target interaction. Notably, we observed that three of the mutated PyrR residues lie in close proximity to the 5-FU binding site, including the amino acid Val178, which is involved in water mediated hydrogen bonding contact with 5-FU. Computational modeling of the PyrR-5'-phosphoribosyl-α-1'-pyrophosphate (PRPP) complex revealed the location of several other mutations at the PRPP binding site of PyrR, indicating their probable role in resistance. Indeed, 5-FU-resistant strains harboring these mutations exhibited decreased susceptibility to 5-FU. Considering that pyrimidine analogs are predominantly regarded to inhibit PyrR, the present studies will be beneficial for the screening of appropriate inhibitors of PyrR and help provide insight into future TB drug design and development.

Mutations in genes for the F420 biosynthetic pathway and a nitroreductase enzyme are the primary resistance determinants in spontaneous in vitro-selected PA-824-resistant mutants of Mycobacterium tuberculosis.

Alleviating the burden of tuberculosis (TB) requires an understanding of the genetic basis that determines the emergence of drug-resistant mutants. PA-824 (pretomanid) is a bicyclic nitroimidazole class compound presently undergoing the phase III STAND clinical trial, despite lacking identifiable genetic markers for drug-specific resistant Mycobacterium tuberculosis. In the present study, we aimed to characterize the genetic polymorphisms of spontaneously generated PA-824-resistant mutant strains by surveying drug metabolism genes for potential mutations. Of the 183 independently selected PA-824-resistant M. tuberculosis mutants, 83% harbored a single mutation in one of five nonessential genes associated with either PA-824 prodrug activation (ddn, 29%; fgd1, 7%) or the tangential F420 biosynthetic pathway (fbiA, 19%; fbiB, 2%; fbiC, 26%). Crystal structure analysis indicated that identified mutations were specifically located within the protein catalytic domain that would hinder the activity of the enzymes required for prodrug activation. This systematic analysis conducted of genotypes resistant to PA-824 may contribute to future efforts in monitoring clinical strain susceptibility with this new drug therapy.

Structural basis of mapping the spontaneous mutations with 5-flurouracil in uracil phosphoribosyltransferase from Mycobacterium tuberculosis.

Tuberculosis (TB) remains the second leading cause of death from an infectious disease globally, despite the incessant efforts to control it. Research and development into new TB medicines is imperative for effective TB control; however, new strategies for the rational use of existing drugs, such as through the identification of new drug targets, could also significantly enhance this process. Key enzymes involved in the essential metabolic and regulatory pathways are usually sought in the pursuit of potential drug targets. Uracil phosphoribosyltransferase (UPRT) is a key salvage pathway enzyme in the synthesis of uridine 5'-monophosphate (UMP) and a probable target of 5-fluorouracil (5-FU) in Mycobacterium tuberculosis (Mtb). To date, there is no structure available for UPRT from Mtb (MtUPRT) that would assist in the identification of appropriate inhibitors for the enzyme. Here we report the structure of MtUPRT along with its spontaneous mutational studies in the presence of 5-FU. We further mapped these four single nucleotide polymorphisms (SNPs) onto the MtUPRT structure, with two residues found to be conserved among the MtUPRT homologs. Notably, none of these SNPs are located in the 5-FU binding pocket. However, the mutants harboring these mutations showed increased MICs (minimum inhibitory concentration) as compared to wild type strains. The present study will aid in the screening of inhibitors of MtUPRT and thus assist in TB drug design and development.

In-situ vaccination using dual responsive organelle targeted nanoreactors.

The poor translation of nanomedicines from bench to bedside can be attributed to (i) lack of a delivery system with precise drug compositions with no batch-to-batch variations, (ii) off-target or undesirable release of payload, and (iii) lack of a method to monitor the fate of the specific drug of interest, which often has to be modified with a fluorescent tag or replaced with a model drug which can be tracked. To overcome these translation hurdles, we developed dual responsive organelle targeted nanoreactors (DRONEs) with precise drug composition, site specific payload release and which enable accurate in-vivo monitoring. DRONEs consist of a polyprodrug inner core composed of a dual responsive backbone containing a photosensitizer (Protoporphyrin IX) grafted with functionalized polyethylene glycol (PEG) outer shell to prolong blood circulation and a tumour homing pro-apoptotic peptide (CGKRKD[KLAKLAK]2) (THP). DRONEs can significantly reduce the tumour burden in an orthotopic glioblastoma model due to its BBB penetrating and tumour homing capabilities. DRONEs exhibit good safety profile and biocompatibility along with a reliable route of elimination. DRONEs showed great potential as an in-situ vaccine which can not only eliminate the tumour but also trigger an adaptive immune response which would provide long-term anti-tumoural immunity.

Enhanced penetration of pro-apoptotic and anti-angiogenic micellar nanoprobe in 3D multicellular spheroids for chemophototherapy.

Light irradiation is considered an ideal non-invasive stimulus that enables precise tumour treatment with flexible, facile, and spatiotemporal control. Photodynamic therapy (PDT) is an important clinically relevant therapeutic modality that has proven to compensate for the reduced therapeutic efficacy of conventional chemotherapy. However, oxygen consumption during PDT can result in an inadequate oxygen supply which reduces photodynamic efficacy. In our quest to circumvent the limitations of chemotherapy and photodynamic therapy, we have engineered a robust and smart "all-in-one" nanoparticle-based drug delivery system capable of overcoming biological barriers and leveraging on several synergistic cancer cell killing mechanisms. The fabricated Targeted Micellar Nanoprobe (TMNP) had exceptionally high encapsulation efficiencies of a hydrophobic drug simvastatin (SV) and a photosensitizer protoporphyrin IX (PpIX) due to the ℼ-ℼ stacking of the aromatic groups of SV and PpIX and strong hydrophobic interactions with the alkyl chains of the carrier. In-vitro results demonstrated that TMNP exhibited excellent colloidal stability, biocompatibility and drug retaining capability in physiological condition. Under light irradiation, TMNP causes the accelerated generation of reactive oxygen species (ROS) which subsequently damages the mitochondria. On further evaluation of the mechanisms behind the superior anti-cancer effect of TMNP, we concluded that TMNP causes synergistic apoptosis and necrosis along with cell cycle arrest at the G1-S phase and elicits anti-angiogenic effects. Taking into consideration that these promising results on 2D monolayer cell cultures might not translate into similar results in animal models, we developed 3D multicellular tumour spheroids (MCs) as an intermediate step to bridge the gap between 2-D cell experiments and in-vivo studies. TMNPs showed enhanced penetration and growth inhibition on MCs. In addition, the modelling of the transport of TMNP in the tumour exhibited the improved effective delivery volume. Overall, TMNPs could potentially be used for image-guided delivery of the therapeutic payloads for precise cancer treatment.

Redox regulation of cell state and fate.

The failure in effective cancer treatment is thought to be attributed to a subpopulation of tumor cells with stem cell-like properties. These cancer stem cells (CSCs) are intimately linked to tumor initiation, heterogeneity, maintenance, recurrence and metastasis. Increasing evidence supports the view that a tight redox regulation is crucial for CSC proliferation, tumorigenicity, therapy resistance and metastasis in many cancer types. Since the distinct metabolic and epigenetic states of CSCs may influence ROS levels, and hence their malignancy, ROS modulating agents hold promise in their utility as anti-CSC agents that may improve the durability of current cancer treatments. This review will focus on (i) how ROS levels are regulated for CSCs to elicit their hallmark features; (ii) the link between ROS and metabolic plasticity of CSCs; and (iii) how ROS may interface with epigenetics that would enable CSCs to thrive in a stressful tumor microenvironment and survive therapeutic insults.