Function of the d-Alanine:d-Alanine Ligase Lid Loop: A Molecular Modeling and Bioactivity Study

Sustainable Production of Shinorine from Agricultural Wastes Using Engineered Saccharomyces cerevisiae Expressing Novel d-Alanine-d-alanine Ligase from Pseudonocardia pini

Shinorine, a compound known for its protective properties against UV radiation, is widely used in cosmetics and pharmaceuticals. Despite the construction of various recombinant Saccharomyces cerevisiae strains for shinorine production, achieving industrial-scale yields remains a challenge. In this study, genes encoding enzymes (DDGS, O-MT, and ATP-grasp enzyme) from Actinosynnema mirum were introduced into S. cerevisiae DXdT to enable the heterologous conversion of sedoheptulose 7-phosphate to mycosporine-glycine─the direct biosynthetic precursor of shinorine. Subsequently, a novel d-alanine-d-alanine ligase from Pseudonocardia pini was introduced to produce shinorine. The engineered strain (DXdT-MG-mi89-PP.ddl) produced 267.9 mg/L shinorine with a 48.6 mg/g dry cell weight (DCW) content in a medium supplemented with lignocellulosic hydrolysate derived from rice straw. Notably, the recombinant strain produced 1.7 g/L shinorine with a 79.1 mg/g DCW content from a corn steep liquor medium with a mixture of glucose and xylose. These results support the idea that sustainable shinorine production from agricultural wastes holds significant promise for industrial applications.

The Mycobacterium tuberculosis Cell Wall: An Alluring Drug Target for Developing Newer Anti-TB Drugs-A Perspective

The Mycobacterium cell wall is a capsule-like structure comprising of various layers of biomolecules such as mycolic acid, peptidoglycans, and arabinogalactans, which provide the Mycobacteria a sort of cellular shield. Drugs like isoniazid, ethambutol, cycloserine, delamanid, and pretomanid inhibit cell wall synthesis by inhibiting one or the other enzymes involved in cell wall synthesis. Many enzymes present across these layers serve as potential targets for the design and development of newer anti-TB drugs. Some of these targets are currently being exploited as the most druggable targets like DprE1, InhA, and MmpL3. Many of the anti-TB agents present in clinical trials inhibit cell wall synthesis. The present article covers a systematic perspective of developing cell wall inhibitors targeting various enzymes involved in cell wall biosynthesis as potential drug candidates for treating Mtb infection.

Discovery of a fragment hit compound targeting D-Ala:D-Ala ligase of bacterial peptidoglycan biosynthesis

Bacterial resistance is an increasing threat to healthcare systems, highlighting the need for discovering new antibacterial agents. An established technique, fragment-based drug discovery, was used to target a bacterial enzyme Ddl involved in the biosynthesis of peptidoglycan. We assembled general and focused fragment libraries that were screened in a biochemical inhibition assay. Screening revealed a new fragment-hit inhibitor of DdlB with a Ki value of 20.7 ± 4.5 µM. Binding to the enzyme was confirmed by an orthogonal biophysical method, surface plasmon resonance, making the hit a promising starting point for fragment development.

Efficient production of natural sunscreens shinorine, porphyra-334, and mycosporine-2-glycine in Saccharomyces cerevisiae

Mycosporine-like amino acids (MAAs) are promising natural sunscreens mainly produced in marine organisms. Until now, metabolic engineering efforts to produce MAAs in heterologous hosts have mainly focused on shinorine production, and the low production levels are still not suitable for industrial applications. In this study, we successfully developed Saccharomyces cerevisiae strains that can efficiently produce various disubstituted MAAs, including shinorine, porphyra-334, and mycosporine-2-glycine (M2G), which are formed by conjugating serine, threonine, and glycine to mycosporine-glycine (MG), respectively. We first generated an MG-producing strain by multiple integration of the biosynthetic genes from cyanobacteria and applying metabolic engineering strategies to increase sedoheptulose-7-phosphate pool, a substrate for MG production. Next, five mysD genes from cyanobacteria, which encode D-Ala-D-Ala ligase homologues that conjugate an amino acid to MG, were introduced into the MG-producing strain to determine the substrate preference of each MysD enzyme. MysDs from Lyngbya sp., Nostoclinckia, and Euhalothece sp. showed high specificity toward serine, threonine, and glycine, resulting in efficient production of shinorine, porphyra-334, and M2G, respectively. This is the first report on the production of porphyra-334 and M2G in S. cerevisiae. Furthermore, we identified that the substrate specificity of MysD was determined by the omega loop region of 43-45 amino acids predicted based on its structural homology to a D-Ala-D-Ala ligase from Thermus thermophilus involved in peptidoglycan biosynthesis. The substrate specificities of two MysD enzymes were interchangeable by swapping the omega loop region. Using the engineered strain expressing mysD from Lyngbya sp. or N. linckia, up to 1.53 g/L shinorine or 1.21 g/L porphyra-334 was produced by fed-batch fermentation in a 5-L bioreactor, the highest titer reported so far. These results suggest that S. cerevisiae is a promising host for industrial production of different types of MAAs, providing a sustainable and eco-friendly alternative for the development of natural sunscreens.

Structure based virtual screening, molecular dynamic simulation to identify the oxadiazole derivatives as inhibitors of Enterococcus D-Ala-D-Ser ligase for combating vancomycin resistance

Vancomycin resistance in enterococci mainly arises due to alteration in terminal peptidoglycan dipeptide. A comprehensive structural analysis for substrate specificity of dipeptide modifying d-Alanine: d-Serine ligase (Ddls) is essential to screen its inhibitors for combating vancomycin resistance. In this study modeled 3D structure of EgDdls from E. gallinarum was used for structure based virtual screening (SBVS) of oxadiazole derivatives. Initially, fifteen oxadiazole derivatives were identified as inhibitors at the active site of EgDdls from PubChem database. Further, four EgDdls inhibitors were evaluated using pharmacokinetic profile and molecular docking. The results of molecular docking showed that oxadiazole inhibitors could bind preferentially at ATP binding pocket with the lowest binding energy. Further, molecular dynamics simulation results showed stable behavior of EgDdls in complex with screened inhibitors. The residues Phe172, Lys174, Glu217, Phe292, and Asn302 of EgDdls were mainly involved in interactions with screened inhibitors. Furthermore, MM-PBSA calculation showed electrostatic and van der Waals interactions mainly contribute to overall binding energy. The PCA analysis showed motion of central domain and omega loop of EgDdls. This is involved in the formation of native dipeptide and stabilized after binding of 2-(1-(Ethylsulfonyl) piperidin-4-yl)-5-(furan-2-yl)-1,3,4-oxadiazole, which could be reason for the inhibition of EgDdls. Hence, in this study we have screened inhibitors of EgDdls which could be useful to alleviate the vancomycin resistance problem in enterococci, involved in hospital-acquired infections, especially urinary tract infections (UTI).

Metabolic Profiles of Clinical Isolates of Drug-Susceptible and Multidrug-Resistant Mycobacterium tuberculosis: A Metabolomics-Based Study

Background

Mycobacterium tuberculosis (MTB) is a global and highly deleterious pathogen that creates an enormous pressure on global public health. Although several effective drugs have been used to treat tuberculosis, the emergence of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) has further increased the public health burden. The aim of this study was to describe in depth the metabolic changes in clinical isolates of drug-susceptible Mycobacterium tuberculosis (DS-MTB) and MDR-MTB and to provide clues to the mechanisms of drug resistance based on metabolic pathways.

Methods

Based on the minimum inhibition concentration (MIC) of multiple anti-tuberculosis drugs, two clinical isolates were selected, one DS-MTB isolate (isoniazid MIC=0.06 mg/L, rifampin MIC=0.25 mg/L) and one MDR-MTB isolate (isoniazid MIC=4 mg/L, rifampin MIC=8 mg/L). Through high-throughput metabolomics, the metabolic profiles of the DS-MTB isolate and the MDR-MTB isolate and their cultured supernatants were revealed.

Results

Compared with the DS-MTB isolate, 128 metabolites were significantly altered in the MDR-MTB isolate and 66 metabolites were significantly altered in the cultured supernatant. The differential metabolites were significantly enriched in pyrimidine metabolism, purine metabolism, nicotinate and nicotinamide metabolism, arginine acid metabolism, and phenylalanine metabolism. Furthermore, metabolomics analysis of the bacterial cultured supernatants showed a significant increase in 10 amino acids (L-citrulline, L-glutamic acid, L-aspartic acid, L-norleucine, L-phenylalanine, L-methionine, L-tyrosine, D-tryptophan, valylproline, and D-methionine) and a significant decrease in 2 amino acids (L-lysine and L-arginine) in MDR-MTB isolate.

Conclusion

The present study provided a metabolite alteration profile as well as a cultured supernatant metabolite alteration profile of MDR-MTB clinical isolate, providing clues to the potential metabolic pathways and mechanisms of multidrug resistance.

Discovery of novel antibacterial agents: Recent developments in D-alanyl-D-alanine ligase inhibitors

Bacterial infections can cause serious problems that threaten public health over a long period of time. Moreover, the continuous emergence of drug-resistant bacteria necessitates the development of novel antibacterial agents. D-alanyl-D-alanine ligase (Ddl) is an indispensable adenosine triphosphate-dependent bacterial enzyme involved in the biosynthesis of peptidoglycan precursor, which catalyzes the ligation of two D-alanine molecules into one D-alanyl-D-alanine dipeptide. This dipeptide is an essential component of the intracellular peptidoglycan precursor, uridine diphospho-N-acetylmuramic acid (UDP-MurNAc)-pentapeptide, that maintains the integrity of the bacterial cell wall by cross-linking the peptidoglycan chain, and is crucial for the survival of pathogens. Consequently, Ddl is expected to be a promising target for the development of antibacterial agents. In this review, we present a brief introduction regarding the structure and function of Ddl, as well as an overview of the various Ddl inhibitors currently being used as antibacterial agents, specifically highlighting their inhibitory activities, structure-activity relationships and mechanisms of action.

Insights into the Inhibition of Aeromonas hydrophila d-Alanine-d-Alanine Ligase by Integration of Kinetics and Structural Analysis

Aeromonas hydrophila, a pathogenic bacterium, is harmful to humans, domestic animals, and fishes and, moreover, of public health concern due to the emergence of multiple drug-resistant strains. The cell wall has been discovered as a novel and efficient drug target against bacteria, and d-alanine-d-alanine ligase (Ddl) is considered as an essential enzyme in bacterial cell wall biosynthesis. Herein, we studied the A. hydrophila HBNUAh01 Ddl (AhDdl) enzyme activity and kinetics and determined the crystal structure of AhDdl/d-Ala complex at 2.7 Å resolution. An enzymatic assay showed that AhDdl exhibited higher affinity to ATP (K_m: 54.1 ± 9.1 μM) compared to d-alanine (K_m: 1.01 ± 0.19 mM). The kinetic studies indicated a competitive inhibition of AhDdl by d-cycloserine (DCS), with an inhibition constant (K_i) of 120 μM and the 50% inhibitory concentrations (IC₅₀) value of 0.5 mM. Meanwhile, structural analysis indicated that the AhDdl/d-Ala complex structure adopted a semi-closed conformation form, and the active site was extremely conserved. Noteworthy is that the substrate d-Ala occupied the second d-Ala position, not the first d-Ala position. These results provided more insights for understanding the details of the catalytic mechanism and resources for the development of novel drugs against the diseases caused by A. hydrophila.

Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action

The pharmacological activity of Acacia nilotica's phytochemical constituents was confirmed with evidence-based studies, but the determination of exact targets that they bind and the mechanism of action were not done; consequently, we aim to identify the exact targets that are responsible for the pharmacological activity via the computational methods. Furthermore, we aim to predict the pharmacokinetics (ADME) properties and the safety profile in order to identify the best drug candidates. To achieve those goals, various computational methods were used including the ligand-based virtual screening and molecular docking. Moreover, pkCSM and SwissADME web servers were used for the prediction of pharmacokinetics and safety. The total number of the investigated compounds and targets was 25 and 61, respectively. According to the results, the pharmacological activity was attributed to the interaction with essential targets. Ellagic acid, Kaempferol, and Quercetin were the best A. nilotica's phytochemical constituents that contribute to the therapeutic activities, were non-toxic as well as non-carcinogen. The administration of Ellagic acid, Kaempferol, and Quercetin as combined drug via the novel drug delivery systems will be a valuable therapeutic choice for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic disease.

Exploration of factors in response to low acid tolerance using random mutagenesis in Cronobacter malonaticus

Cronobacter species are associated with rare but severe infections in newborns, and their tolerance to environmental stress such as acid stress has been described. However, the factors involved in low acid tolerance in Cronobacter are poorly understood. Here, a transposon mutagenesis approach was used to explore the factors involved in acid tolerance in C. malonaticus. Eight mutants from mutant library (n = 215) were successfully screened through a comparison of growth with wild type (WT) strain under acid stress (pH 4.0). Eight mutating sites including glucosyltransferase MdoH, extracellular serine protease, sulfate transporter, phosphate transporter permease subunit PstC, lysine transporter, nitrogen regulation protein NR (II), D-alanine-D-alanine ligase, glucan biosynthesis protein G were successfully identified by arbitrary polymerase chain reaction and sequencing. The biomass of biofilm of eight mutants were significantly reduced using crystal violet staining (CVS) compared with that of WT. furthermore, the more compact biofilms of WT was observed than those of eight mutants through scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). Disassembly of biofilms appeared among mutants and WT strain from 48 h to 72 h through the increasing of dead cells and reduction of viable cells and exopolysaccharide. The study reveals the molecular basis involved in acid tolerance of C. malonaticus and a possible relationship between biofilm formation and acid tolerance, which provides valuable information for survival of C. malonaticus under acid stress.

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.