Synthesis, iron(III) complexation properties, molecular dynamics simulations and P. aeruginosa siderophore-like activity of two pyoverdine analogs

Ironing out pyoverdine’s chromophore structure: serendipity or design?

“…The larger HOMO-LUMO gap in Fe 3+ -PvdI compared to Fe 3+ -aPvd (similar to that of Fe 3+ (Aha -)3 vs Fe 3+ (Cat 2-)3) confirms the lower Fe 3+ binding affinity of PvdI; it also provides yet another confirmation of the remarkable similitude of PvdI and (Aha -)3 for the complexation of Fe 3+ . Intriguingly, upon solvation, stabilities are reversed and PvdI becomes the strongest binder by 40-50 kcal mol -1 , in agreement with the pFe values measured in our previous work [37] and hinting at particularly favorable interactions with water; however, as we will see below, the binding affinities of the analogs remain well within the range of efficient siderophores.…”

“…In our previous work, we had already concluded that the interaction of pyoverdine strains with water was more discriminating than their interactions with the FpvA transporter, and represented the dominant contribution to the binding free energy; [35] the same obviously holds true for the pFe of pyoverdines and analogs. However, despite their lower affinity for Fe 3+ than PvdI, the predicted pFe values of our analogs remain quite high -similar to that of tris-hydroxamate desferrioxamine B, native siderophore of Streptomyces (pFe=26.6) and much higher than the best analog considered in our previous study [37] (pFe=21) despite the theoretically greater Fe 3+ affinity of the latter's triscatecholate nature. aPvd1, aPvd2 and aPvd3 thus appear to meet the first of the criteria enumerated at the start of this section (which we will now strive to confirm experimentally).…”

“…Interestingly, when taking solvation into account, the picture is reversed: while the three proposed analogs can definitely chelate Fe 3+ in an aqueous medium (as attested by the short and stable Fe 3+ ×××O distances seen in MD simulations despite the absence of bonded interactions), they do so with less affinity than PvdI. In our previous work, [37] we have found a very good linear correlation between MM-GBSA binding free energies and experimental pFe values on similar pyoverdine analogs; applying this relationship to the binding free energies computed herein yields pFe values of 24 to 25 for all analogs under study, as compared to 27 for PvdI. The superior affinity of PvdI for iron arises from more favorable solvation electrostatic energies, linked to the better structuration of the water layers around the metal ion: the average number of water molecules in direct contact with Fe 3+ is 8.80 and 8.88 in aPvd1 and aPvd2, vs. 9.23 in PvdI.…”

“…Nonconventional residues (chromophores and analogs, ornithine, side-chainbranching lysine) required additional parameterization, which was achieved as described in our previous work. [35][36][37] In order to monitor the capacity of the different siderophores to bind and retain Fe 3+ , iron was treated noncovalently using the nonbonded parameters of Giammona. [55] The systems were solvated in a truncated octahedral TIP3P water box with a buffer distance of 10 Å and neutralized with a minimal number of Na + or Clions.…”

“…We build on the expertise of our group which has, in the past few years, palliated the dearth of computational studies on bacterial siderophores by combining quantum chemistry, forcefield design and state-of-the art free energy simulations to study the structural properties of pyoverdines and their impact on recognition by the FpvA transporter [35,36], and experimented with simple tris-catecholate ligands showing promising ironbinding affinities. [37] In this paper, we follow a stepwise approach: (i) we extract the individual iron chelation capabilities of catecholate and hydroxamate moieties, (ii) investigate possible synergistic effects in the metal-binding affinities of model monocatecholate-bis-hydroxamate systems, (iii) check the influence of the peptide chain linking the chelating groups in pyoverdine analogs built thereupon and (iv) study the interaction of these analogs with the FpvA transporter. We expect each step of the way to provide insights for the design of simple yet functional mimics of the pyoverdine PAO1 chromophore able to chelate Fe 3+ and be transported through FpvA for therapeutic purposes.…”