Identification of Major Enzymes Involved in the Synthesis of Diadenosine Tetraphosphate and/or Adenosine Tetraphosphate in Myxococcus xanthus

Exploring actinomycetes natural products to identify potential multi-target inhibitors against Leishmania donovani

Visceral leishmaniasis (VL) is a neglected tropical disease that mainly affects the poor population of the Indian, African, and South American subcontinent. The increasing resistance to antimonial and miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an anti-leishmanial drug with excellent efficacy and safety profile. In this study, three sequential docking protocols (HTVS, SP, and XP) were performed to screen the secondary metabolites (n = 6519) from the actinomycetes source against five key proteins involved in the metabolic pathway of Leishmania donovani. Those proteins were adenine phosphoribosyltransferase (PDB ID: 1QB7), trypanothione reductase (PDB ID: 2JK6), N-myristoyl transferase (PDB ID: 2WUU), pteridine reductase (PDB ID: 2XOX), and MAP kinase (PDB ID: 4QNY). Although the binding energy of top ligands was predicted using the MM-GBSA module of the Schrödinger suite. SP and XP docking mode resulted in 55 multi-targeted ligands against L donovani. MM-GBSA analysis selected the top 18 ligands with good-binding affinity and the binding-free energy for four proteins, as mentioned earlier, when compared with the miltefosine, paromomycin, and a reference ligand selected for each target. Finally, molecular dynamics simulation, post-MD-binding-free energy (MM-PBSA), and principal component analysis (PCA) proposed three best ligands (Adenosine pentaphosphate, Atetra P, and GDP-4-keto-6-deoxymannose) qualifying the above screening parameters and confirmed as a potential drug candidate to fight against Leishmania donovani parasites.

Characterization of Agrobacterium tumefaciens PPKs reveals the formation of oligophosphorylated products up to nucleoside nona-phosphates

Agrobacterium tumefaciens synthesizes polyphosphate (polyP) in the form of one or two polyP granules per cell during growth. The A. tumefaciens genome codes for two polyphosphate kinase genes, ppk1_AT and ppk2_AT, of which only ppk1_AT is essential for polyP granule formation in vivo. Biochemical characterization of the purified PPK1_AT and PPK2_AT proteins revealed a higher substrate specificity of PPK1_AT (in particular for adenine nucleotides) than for PPK2_AT. In contrast, PPK2_AT accepted all nucleotides at comparable rates. Most interestingly, PPK2_AT catalyzed also the formation of tetra-, penta-, hexa-, hepta-, and octa-phosphorylated nucleosides from guanine, cytosine, desoxy-thymidine, and uridine nucleotides and even nona-phosphorylated adenosine. Our data-in combination with in vivo results-suggest that PPK1_AT is important for the formation of polyP whereas PPK2_AT has the function to replenish nucleoside triphosphate pools during times of enhanced demand. The potential physiological function(s) of the detected oligophosphorylated nucleotides await clarification. KEY POINTS: •PPK1_AT and PPK2_AT have different substrate specificities, •PPK2_AT is a subgroup 1 member of PPK2s, •PPK2_AT catalyzes the formation of polyphosphorylated nucleosides.

Enzymatic characteristics of two adenylate kinases, AdkA and AdkB, from Myxococcus xanthus

Adenylate kinase (Adk) plays a critical role in energy metabolism and adaptation of bacteria to environmental stresses. We have previously shown that Myxococcus xanthus expresses polyphosphate kinase 1 (Ppk1) that also has Adk activity in the absence of polyphosphates. In this study, we investigated the Adk activity of the other two M. xanthus enzymes, AdkA and AdkB. The activity of AdkA was increased by dithiothreitol (DTT), which also enhanced enzyme stability. Site-directed mutagenesis of three cysteine residues (C130, C150, and C153) present in the LID domain of AdkA revealed that the Adk activity and stability of C150S and C153S mutants were not affected by DTT addition, suggesting formation of a disulfide bond between C150 and C153 in AdkA. The Km of AdkA for AMP was 8 and 17 times lower than that for ADP and ATP, respectively. AdkB is a polyphosphate kinase 2 (Ppk2) homolog lacking the Ppk2 middle region and, consequently, Ppk activity. According to our analysis, AdkB also had Adk activity and its affinity for substrates was higher than that of AdkA. Thus, M. xanthus expresses three enzymes, AdkA, AdkB, and Ppk1, with Adk activity, which may function to support energy metabolism of the bacteria in different environmental conditions.