Identification of Genes Encoded Toxin-Antitoxin System in Mycobacterium Tuberculosis Strains from Clinical Sample.

BACKGROUND: The toxin-antitoxin system is a genetic element that is highly present in Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis. The toxin-antitoxin sys-tem comprises toxin protein and antitoxin protein or non-encoded RNA interacting with each other and inhibiting toxin activity. M. Tuberculosis has more classes of TA loci than non-tubercle bacilli and other microbes, including VapBC, HigBA, MazEF, ParDE, RelBE, MbcTA, PemIK, DarTG, MenTA, one tripartite type II TAC chaperone system, and hypothetical proteins. AIMS: The study aims to demonstrate the genes encoded toxin-antitoxin system in mycobacterium tuberculosis strains from clinical samples. MATERIALS AND METHODS: The pulmonary and extra-pulmonary tuberculosis clinical samples were collected, and smear microscopy (Ziehl-Neelsen staining) was performed for the detection of high bacilli (3+) count, followed by nucleic acid amplification assay. Bacterial culture and growth assay, genomic DNA extraction, and polymerase chain reaction were also carried out. RESULTS: The positive PTB and EPTB samples were determined by 3+ in microscopy smear [20], and the total count of tubercle bacilli determined by NAAT assay was 8.0×1005 in sputum and 1.3×1004 CFU/ml in tissue abscess. Moreover, the genomic DNA was extracted from culture, and the amplification of Rv1044 and Rv1045 genes in 624 and 412 base pairs (between 600-700 and 400-500 in ladder), respectively, in the H37Rv and clinical samples was observed. CONCLUSION: It has been found that Rv1044 and Rv1045 are hypothetical proteins with 624 and 882 base pairs belonging to the AbiEi/AbiEii family of toxin-antitoxin loci. Moreover, the signifi-cant identification of TA-encoded loci genes may allow for the investigation of multidrug-resistant and extensively drug-resistant tuberculosis.

Harnessing the combined effect of antivirulence agent trans-chalcone with bactericidal curcumin against sortase A enzyme to tackle Gram-positive bacterial infections.

Gram-positive bacteria are responsible for a wide range of infections in humans. In most Gram-positive bacteria, sortase A plays a significant role in attaching virulence factors to the bacteria's cell wall. These cell surface proteins play a significant role in virulence and pathogenesis. Even though antibiotics are available to treat these infections, there is a continuous search for an alternative strategy due to an increase in antibiotic resistance. Thus, using anti-sortase drugs to combat these bacterial infections may be a promising approach. Here, we describe a method for targeting Gram-positive bacterial infection by combining curcumin and trans-chalcone as sortase A inhibitors. We have used curcumin and trans-chalcone alone and in combination as a sortase A inhibitor. We have seen ~78%, ~43%, and ~94% inhibition when treated with curcumin, trans-chalcone, and a combination of both compounds, respectively. The compounds have also shown a significant effect on biofilm formation, IgG binding, protein A recruitment, and IgG deposition. We discovered that combining curcumin and trans-chalcone is more effective against Gram-positive bacteria than either compound alone. The present work demonstrated that a combination of these natural compounds could be used as an antivirulence therapy against Gram-positive bacterial infection.

Targeting Staphylococcal Cell-Wall Biosynthesis Protein FemX Through Steered Molecular Dynamics and Drug-Repurposing Approach.

Staphylococcus aureus-mediated infection is a serious threat in this antimicrobial-resistant world. S. aureus has become a "superbug" by challenging conventional as well as modern treatment strategies. Nowadays, drug repurposing has become a new trend for the discovery of new drug molecules. This study focuses on evaluating FDA-approved drugs that can be repurposed against S. aureus infection. Steered molecular dynamics (SMD) has been performed for Lumacaftor and Olaparib against staphylococcal FemX to understand their binding to the active site. A time-dependent external force or rupture force has been applied to the ligands to calculate the force required to dislocate the ligand from the binding pocket. SMD analysis indicates that Lumacaftor has a high affinity for the substrate binding pocket in comparison to Olaparib. Umbrella sampling exhibits that Lumacaftor possesses a higher free energy barrier to displace it from the ligand-binding site. The bactericidal activity of Lumacaftor and Olaparib has been tested, and it shows that Lumacaftor has moderate activity along with biofilm inhibition potential (MIC value with conc. 128 µg/mL). Pharmacokinetic and toxicology evaluations indicate that Lumacaftor has higher pharmacokinetic potential with lower toxicity. This is the first experimental report where staphylococcal FemX has been targeted for the discovery of new drugs. It is suggested that Lumacaftor may be a potential lead molecule against S. aureus.

"Toehold Switches; a foothold for Synthetic Biology".

Toehold switches are de novo designed riboregulators that contain two RNA components interacting through linear-linear RNA interactions, regulating the gene expression. These are highly versatile, exhibit excellent orthogonality, wide dynamic range, and are highly programmable, so can be used for various applications in synthetic biology. In this review, we summarized and discussed the design characteristics and benefits of toehold switch riboregulators over conventional riboregulators. We also discussed applications and recent advancements of toehold switch riboregulators in various fields like gene editing, DNA nanotechnology, translational repression, and diagnostics (detection of microRNAs and some pathogens). Toehold switches, therefore, furnished advancement in synthetic biology applications in various fields with their prominent features.

Sortase A: A chemoenzymatic approach for the labeling of cell surfaces.

Sortase A, a transpeptidase enzyme is present in many Gram-positive bacteria and helps in the recruitment of the cell surface proteins. Over the last two decades, Sortase A has become an attractive tool for performing in vivo and in vitro ligations. Sortase A-mediated ligation has continuously been used for its specificity, robustness, and highly efficient nature. These properties make it a popular choice among protein engineers as well as researchers from different fields. In this review, we give an overview of Sortase A-mediated ligation of various molecules on the cell surfaces, which can have diverse applications in interdisciplinary fields.

Current status of nanoscale drug delivery and the future of nano-vaccine development for leishmaniasis - A review.

The study of tropical diseases like leishmaniasis, a parasitic disease, has not received much attention even though it is the second-largest infectious disease after malaria. As per the WHO report, a total of 0.7-1.0 million new leishmaniasis cases, which are spread by 23 Leishmania species in more than 98 countries, are estimated with an alarming 26,000-65,000 death toll every year. Lack of potential vaccines along with the cost and toxicity of amphotericin B (AmB), the most common drug for the treatment of leishmaniasis, has raised the interest significantly for new formulations and drug delivery systems including nanoparticle-based delivery as anti-leishmanial agents. The size, shape, and high surface area to volume ratio of different NPs make them ideal for many biological applications. The delivery of drugs through liposome, polymeric, and solid-lipid NPs provides the advantage of high biocomatibilty of the carrier with reduced toxicity. Importantly, NP-based delivery has shown improved efficacy due to targeted delivery of the payload and synergistic action of NP and payload on the target. This review analyses the advantage of NP-based delivery over standard chemotherapy and natural product-based delivery system. The role of different physicochemical properties of a nanoscale delivery system is discussed. Further, different ways of nanoformulation delivery ranging from liposome, niosomes, polymeric, metallic, solid-lipid NPs were updated along with the possible mechanisms of action against the parasite. The status of current nano-vaccines and the future potential of NP-based vaccine are elaborated here.

Sortase A Mediated Bioconjugation of Common Epitopes Decreases Biofilm Formation in Staphylococcus aureus.

Staphylococcus aureus is one of the most notorious pathogens and is frequently associated with nosocomial infections imposing serious risk to immune-compromised patients. This is in part due to its ability to colonize at the surface of indwelling medical devices and biofilm formation. Combating the biofilm formation with antibiotics has its own challenges like higher values of minimum inhibitory concentrations. Here, we describe a new approach to target biofilm formation by Gram positive bacteria. Sortase A is a transpeptidase enzyme which is responsible for tagging of around ∼22 cell surface proteins onto the outer surface. These proteins play a major role in the bacterial virulence. Sortase A recognizes its substrate through LPXTG motif. Here, we use this approach to install the synthetic peptide substrates onS. aureus. Sortase A substrate mimic, 6His-LPETG peptide was synthesized using solid phase peptide chemistry. Incorporation of the peptide on the cell surface was measured using ELISA. Effect of peptide incubation on Staphylococcus aureus biofilm was also studied. 71.1% biofilm inhibition was observed with 100 µM peptide while on silicon coated rubber latex catheter, 45.82% inhibition was observed. The present work demonstrates the inability of surface modified S. aureus to establish biofilm formation thereby presenting a novel method for attenuating its virulence.

Studies on the production of shikimic acid using the aroK knockout strain of Bacillus megaterium.

Shikimic acid has various pharmaceutical and industrial applications. It is the sole chemical building block for the antiviral drug oseltamivir (Tamiflu(®)) and one of the potent pharmaceutical intermediates with three chiral centres. Here we report a modified strain of Bacillus megaterium with aroK (shikimate kinase) knock out to block the aromatic biosynthetic pathway downstream of shikimic acid. Homologous recombination based gene disruption approach was used for generating aroK knock out mutant of B. megaterium. Shake flask cultivation showed shikimic acid yield of 2.98 g/L which is ~6 times more than the wild type (0.53 g/L). Furthermore, the shikimate kinase activity was assayed and it was 32 % of the wild type. Effect of various carbon sources on the production of shikimic acid was studied and fructose (4 %, w/v) was found to yield maximum shikimic acid (4.94 g/L). The kinetics of growth and shikimic acid production by aroK knockout mutant was studied in 10 L bioreactor and the yield of shikimic acid had increased to 6 g/L which is ~12 fold higher over the wild type. It is evident from the results that aroK gene disruption had an immense effect in enhancing the shikimic acid production.

A protein transduction domain with cell uptake and selectivity profiles that are controlled by multivalency effects.

Protein transduction domains (PTDs) are reagents that facilitate the delivery of diverse cargo to the interior of mammalian cells. We identified a PTD called "Ypep" (N-YTFGLKTSFNVQ-C), with cell penetration selectivity and potency profiles that are tightly controlled by multivalency effects. Pentavalent display of Ypep on M13 bacteriophage enables selective uptake of this phage in PC-3 human prostate cancer cells at low picomolar concentration and in the presence of human blood. All Ypep-dependent delivery is nontoxic and proceeds through energy-dependent endocytosis. Collectively, our results establish Ypep-displaying phage as a cell-penetrating platform with selectivity and potency profiles that compare to, or exceed, antibodies and their fragments. Our findings may have broader implications on the design of PTD technologies generated from phage display, as well as the use of Ypep-displaying phage as a prostate cancer cell-selective delivery platform.

In vitro evolution of a Friedel-Crafts deoxyribozyme.

We report the in vitro selection of a single-stranded 72-nucleotide DNA enzyme (deoxyribozyme) that catalyzes a Friedel-Crafts reaction between an indole and acyl imidazole in good yield and in aqueous solvent. Appreciable Friedel-Crafts product requires addition of copper nitrate and the deoxyribozyme. We observe deoxyribozyme-mediated bond formation for both in cis and in trans Friedel-Crafts reactions.

Exploring residues crucial for nitrilase function by site directed mutagenesis to gain better insight into sequence-function relationships.

Nitrilases represent a very important class of enzymes having an array of applications. In the present scenario, where the indepth information about nitrilases is limited, the present work is an attempt to shed light on the residues crucial for the nitrilase activity. The nitrilase sequences demonstrating varying degree of identity with P. putida nitrilase were explored. A stretch of residues, fairly conserved throughout the range of higher (96%) to lower (27%) sequence identity among different nitrilases was selected and investigated for the possible functional role in nitrilase enzyme system. Subsequently, the alanine substitution mutants (T48A, W49A, L50A, P51A, G52A, Y53A and P54A) were generated. Substitution of the rationally selected conserved residues altered the substrate recognition ability, catalysis and affected the substrate specificity but had very little impact on enantioselectivity and pattern of nitrile hydrolysis.

Cross-linked enzyme aggregates of recombinant Pseudomonas putida nitrilase for enantioselective nitrile hydrolysis.

The cross-linked enzyme aggregate (CLEA) method is used for the dual purpose of combining both the purification and immobilization of enzyme in one step. The present work involved the preparation of a carrier-free, highly active reusable biocatalyst (nitrilase) which encounters least mass-transfer limitations with higher thermal and storage stability. The effect of type of aggregating agent, its concentration as well as that of cross-linking agent was studied. Nitrilase aggregates were prepared using ammonium sulphate (35%) precipitation followed by cross-linking with glutaraldehyde (125 mM) which rendered 70% activity retention. The various cross-linking parameters were optimized in order to increase the activity retention. Stability in terms of temperature, reusability and leaching were also examined. The CLEA preparation showed residual nitrilase activity on repeated use. A highly stable CLEA of nitrilase was finally prepared with maximum activity recovery.

Molecular evolution of a defined DNA sequence with accumulation of mutations in a single round by a dual approach to random chemical mutagenesis (DuARCheM).

Directed evolution has paved the way to a new era of protein and nucleic acid molecules with improved and enhanced properties. The utmost important component of directed evolution is random mutations in a defined DNA sequence. The utility of random chemical mutagenesis in directed evolution studies is dwindling due to the inherent flaws with whole-organism mutagenesis and the in vitro approach. Here, we report a novel Dual Approach to Random Chemical Mutagenesis (DuARCheM) to introduce random mutations in a defined DNA fragment. DuARCheM involves in vivo chemical mutagenesis and in vitro genetic manipulations. The resulting library revealed an accumulation of mutations in its members. These results imply that the parent mutation is carried in the further generations within the same library. This method might help to change random chemical mutagenesis because the combination of in vivo and in vitro approaches mimics the amplification and mutation that is performed by PCR-based mutagenesis, and at the same time the mutations are confined to the desired gene. Moreover, the mutagen pressure is greater in chemical mutagenesis than in a Taq-polymerase-based error-prone system. Concomitant amplification and mutation in the DuARCheM method leads to a better spectrum of mutants because the plasmid construct is exponentially amplified in the presence of mutagen pressure, unlike in the in vitro chemical mutagenesis system in which the template molecule does not replicate. This work is able to nullify all the disadvantages that are associated with random chemical mutagenesis, and could make random chemical mutagenesis an indispensable tool in directed evolution studies.

Development and validation of HPLC method for the resolution of drug intermediates: DL-3-Phenyllactic acid, DL-O-acetyl-3-phenyllactic acid and (+/-)-mexiletine acetamide enantiomers.

Sensitive and specific, high-performance liquid chromatography (HPLC) methods have been developed and validated for linearity, accuracy and precision for the quantification of dl-3-phenyllactic acid, dl-O-acetyl-3-phenyllactic acid and (+/-)-mexiletine acetamide enantiomers. Chromatographic separations were performed on a Chiralcel OJ-H column (0.46 mm x 250 mm, 5 microm, Daicel Chemical Industries, Japan) based on cellulose tris-(4-methyl benzoate) chiral stationary phase. The mobile phase consists of hexane and isopropanol (IPA) in the ratio of 90:10 containing 0.1% trifluoroacetic acid (in case of dl-3-phenyllactic acid and dl-O-acetyl-3-phenyllactic acid) and hexane and IPA (95:5) containing 0.1% triethylamine (in case of (+/-)-mexiletine acetamide) and the flow rate was set at 0.5 ml/min at 25 degrees C. The detection was carried out at 261 nm for dl-3-phenyllactic acid and dl-O-acetyl-3-phenyllactic acid and at 254 nm for (+/-)-mexiletine acetamide. The developed methods were utilized for monitoring the progress of lipase catalyzed enantioselective synthesis of O-acetyl-3-phenyllactic acid and mexiletine acetamide from dl-3-phenyllactic acid and (+/-)-mexiletine, respectively.