Theoretical investigation of hydroxylated analogues of valinomycin as potassium transporter.

Valinomycin is a potent ionophore known for its ability to transport potassium ions across biological membranes. The study focuses on the hydroxylated analogues of valinomycin (HyVLMs) and compares their energy profiles and capabilities for transporting potassium ions across phospholipid membranes. Using metadynamics, we investigated the energy profiles of wildtype valinomycin (VLM_1) and its three hydroxylated analogues (VLM_2, VLM_3, and VLM_4). We observed that all analogues exhibited energy maxima in the centre of the membrane and preferred positions below the phospholipid heads. Furthermore, the entry barriers for membrane penetration were similar among the analogues, suggesting that the hydroxyl group did not significantly affect their passage through the membrane. Transition state calculations provided insights into the ability of valinomycin analogues to capture potassium ions, with VLM_4 showing the lowest activation energy and VLM_2 displaying the highest. Our findings contribute to understanding the mechanisms of potassium transport by valinomycin analogues and highlight their potential as ionophores. The presence of the hydroxyl group is of particular importance because it paves the way for subsequent chemical modifications and the synthesis of new antiviral agents with reduced intrinsic toxicity.

Anti-Infective and Antiviral Activity of Valinomycin and Its Analogues from a Sea Cucumber-Associated Bacterium, Streptomyces sp. SV 21.

The manuscript investigated the isolation, characterization and anti-infective potential of valinomycin (3), streptodepsipeptide P11A (2), streptodepsipeptide P11B (1), and one novel valinomycin analogue, streptodepsipeptide SV21 (4), which were all produced by the Gram-positive strain Streptomycescavourensis SV 21. Although the exact molecular weight and major molecular fragments were recently reported for compound 4, its structure elucidation was not based on compound isolation and spectroscopic techniques. We successfully isolated and elucidated the structure based on the MS2 fragmentation pathways as well as 1H and 13C NMR spectra and found that the previously reported structure of compound 4 differs from our analysis. Our findings showed the importance of isolation and structure elucidation of bacterial compounds in the era of fast omics technologies. The here performed anti-infective assays showed moderate to potent activity against fungi, multi drug resistant (MDR) bacteria and infectivity of the Hepatitis C Virus (HCV). While compounds 2, 3 and 4 revealed potent antiviral activity, the observed minor cytotoxicity needs further investigation. Furthermore, the here performed anti-infective assays disclosed that the symmetry of the valinomycin molecule is most important for its bioactivity, a fact that has not been reported so far.

Metal-Assisted Folding of Prolinomycin Allows Facile Design of Functional Peptides.

Cyclic peptides have been proposed as privileged scaffolds that might mimic the folding and function of natural proteins. However, simple cyclic peptides typically cannot fold into well-defined structures. Herein, we describe a foldable cyclic peptide scaffold on which functional side chains can be displayed for targeted recognition of biomolecules. The foldable scaffold is based on prolinomycin, a proline-rich analogue of valinomycin. We report synthetic mutants of prolinomycin that retain the metal-assisted folding behavior under physiological conditions. The predictable structure formation of prolinomycin makes it a powerful platform to enable the development of synthetic receptors for biomolecules of interest. We demonstrate the potential of this scaffold by creating prolinomycin mutants that selectively bind anionic vesicles and bacterial cells.

Site-dependent biological activity of valinomycin analogs bearing derivatizable hydroxyl sites.

Valinomycin (VLM, 1) is a K(+) ionophore cyclodepsipeptide capable of depolarizing mitochondria and inducing apoptosis to several mammalian cell types, including a number of tumor cell lines. With the aim of creating VLM-based ligand-targeted anticancer drugs that may selectively convey VLM to pathological cells, we have previously introduced derivatizable hydroxyl handles into the VLM structure, allowing to access a three-entity library of monohydroxyl VLMs (HyVLMs) bearing the OH group at the isopropyl side chain of a D-Hyi, D-Val, or L-Val residue (analogs 2-4, respectively). Herein, the levels of bioactivity retained by the conjugable HyVLMs have been assessed on the basis of their ability to alter the functionality of isolated rat-liver mitochondria. Experiments run with HyVLMs in the range 1-10 nM and in 20 or 125 mM KCl medium show that the hydroxyl group reduces the potency of HyVLMs relative to VLM to an extent that depends upon the molecular site involved in the hydroxylation. On the other hand, estimation of the stability constants of complexes (in methanol at 25 °C) of each analog with Na(+), K(+), and Cs(+) reveals that HyVLMs nicely retain the VLM binding features, except for a moderate increase in the stability of Na(+) complexes. These findings, along with pertinent structural considerations, suggest that the incorporation of OH into the VLM structure might actually have altered its K(+) transporting ability across mitochondrial membranes. Besides facing new aspects of VLM structure-activity relationship, these studies set the basis for the rational design of ligand-HyVLMs conjugates through derivatization of hanging OH group.

Selective synthesis of hydroxy analogues of valinomycin using dioxiranes.

A synthesis of representative monohydroxy derivatives of valinomycin (VLM) was achieved under mild conditions by direct hydroxylation at the side chains of the macrocyclic substrate using dioxiranes. Results demonstrate that the powerful methyl(trifluoromethyl)dioxirane 1b should be the reagent of choice to carry out these key transformations. Thus, a mixture of compounds derived from the direct dioxirane attack at the ß-(CH(3))(2)C-H alkyl chain of one Hyi residue (compound 3a) or of one Val moiety (compounds 3b and 3c) could be obtained. Following convenient mixture separation, each of the new oxyfunctionalized macrocycles became completely characterized.

Determination of stability constants of valinomycin complexes with ammonium and alkali metal ions by capillary affinity electrophoresis.

Capillary affinity electrophoresis (CAE) has been employed to investigate quantitatively the interactions of valinomycin, macrocyclic depsipeptide antibiotic ionophore, with univalent cations, ammonium and alkali metal ions, K(+), Cs(+), Na(+), and Li(+), in methanol. The study involved measuring the change in effective electrophoretic mobility of valinomycin while the cation concentrations in the BGE were increased. The corresponding apparent stability (binding) constants of the valinomycin-univalent cation complexes were obtained from the dependence of valinomycin effective mobility on the cation concentration in BGE using a nonlinear regression analysis. The calculated apparent stability constants of the above-mentioned complexes show the substantially higher selectivity of valinomycin for K(+) and Cs(+) ions over Li(+), Na(+), and NH(4)(+) ions. CAE proved to be a suitable method for the investigation of both weak and strong interactions of valinomycin with small ions.

A hybrid minimal principle for the crystallographic phase problem.

Simulated annealing is used to solve the X-ray phase problem formulated as a minimization problem. The cost function consists of two parts, one represents the discrepancy between measured and calculated intensities while the other monitors the probability distribution of the triplets. From a random real-space structure at the start, the atoms are moved one by one to gradually reduce the cost function until the best structure emerges. Trial calculations for structures including hexadecaisoleucinomycin (HEXIL) are presented. Comparison of this method with other related methods is made.

The X-ray structure of the monoclinic crystal form of [D-Hyi2, L-Hyi4] meso-valinomycin.

The conformation and intermolecular association of [D-Hyi2, L-Hyi4] meso-valinomycin [cyclo[-D-Val-D-Hyi-L-Val-L-Hyi-(D-Val-L-Hyi-L-Val-D-+ ++Hyi)2-], C60H102N6O18] in a crystal form obtained from ethanol solution has been determined by x-ray crystallography. Two depsipeptides and one ethanol molecule per asymmetric unit crystallize in space group P2(1) (Z = 4); a = 14.579, b = 39.795, c = 13.928 A, beta = 116.90, Rl = 0.0757. The molecular conformation is very similar to that observed in the trigonal P3(2) crystal form obtained from acetone solution [V. Z. Pletnev et al. (1991) Biopolymers, Vol. 31, pp. 409-415]. Both independent molecules in the crystal adopt a similar distorted bracelet structure with a sterically inaccessible, partially formed, ion-binding center that is stabilized by six 4-->1 type H bonds. The observed conformation accounts for the inability of the molecule to complex ions. Close examination of the three crystallographically independent molecules reveals that differences in the backbone conformation associated with solvent interaction are significantly larger than those associated with hydrophobic van der Waals interactions of crystal packing.

The crystal and molecular structure of a valinomycin analogue cyclo[(D-Val-L-Lac-L-Ala-D-Hyi)2(D-Val-L-Lac-L-Val-D-Hyi)]. H2O(C50H82N6 O18.H2O).

The crystal and molecular structure of the valinomycin analogue, cyclo[(D-Val-L-Lac-L-Ala-D-Hyi)2(D-Val-L-Lac-L-Val-D-Hyi)] has been solved by x-ray direct methods using the "Shake and Bake" procedure. The crystals, grown from a mixture of octane/CH2Cl2, belong to space group P2(1) (Z = 4) with cell parameters a = 10.29, b = 32.08, c = 18.73 A, beta = 97.05 degrees, and contain two molecules per asymmetric unit. After anisotropic refinement the standard reliability factor was Rl = 0.058. The conformations of both independent molecules is similar to that observed for isoleucinomycin, cyclo[-(D-Ile-L-Lac-L-Ile-D-Hyi)3] [V. Z. Pletnev et al. (1980) Biopolymers, Vol. 19, pp. 1517-1534]. The structure has an asymmetric conformation stabilized by six intramolecular H bonds, five bonds being of the 4-->1 type and one bond being of the 5-->1 type. One water molecule is caged in the internal cavity of each cyclodepsipeptide. This conformation could represent an intermediate state between free and complexed forms of valinomycin.

Crystal and molecular structure of the centrosymmetric meso-valinomycin analogue--cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi-L-Val-D-Hyi-D-Val-L-Hy i) (C60H102N6O18).

The crystal structure of cyclo (D-Val-D-Hyi-D-Val-L-Hyi-L-Val-D-Hyi-L-Val-L-Hyi -L-Val-D-Hyi-D-Val-L-Hyi).2H2O has been solved by x-ray direct methods. The crystals (grown from a mixture of octane/CH2Cl2) are an orthorhombic, centrosymmetric space group Pbca, cell parameters a = 11.458 (2), b = 25.613 (3), c = 23.691 (3) A, Z = 4; therefore the molecule lies on a center of inversion in the cell. The atomic coordinates for the C, N, and O atoms were refined in the anisotropic thermal motion approximation (allowing for H-atom contribution to Fcal) to a standard R-factor value of 0.081. In contrast to meso-valinomycin, the analogue under study does not adopt an octahedral cage bracelet conformation. It has an unusual centrosymmetric elongated form with two type II terminal beta-bends formed by N-H ... C=O 4-->1 type intramolecular H bonds. Two symmetry-related water molecules reside in the elongated molecular cavity of the centrosymmetric depsipeptide ring.

Molecular structure of cyclo[-(D-Val-L-Hyi-L-Val-D-Hyi)2-] revealed by x-ray analysis.

The crystal structure of a synthetic analogue of valinomycin, cyclo[-(D-Val-L-Hyi-L-Val-D-Hyi)2-] (octa-meso-valinomycin) (I) (C40H68N4O12.1.5.C4H8O2, M(r) = 937.01 + 88.10), has been determined. Crystals grown from dioxane are monoclinic, space group P2(1)/a, with cell parameters a = 21.487 (8), b = 16.836 (5), c = 16.089 (4) A, beta = 111.70 (4), and Z = 4. The atomic coordinates for nonhydrogen atoms were refined in the anisotropic thermal motion approximation. H atom positions were included in the structure factor calculations at their geometrically expected positions. Values of the standard and weighted R factors after refinement are 0.11 and 0.13, respectively. The conformation of the depsipeptide crystallized from dioxane is different from that crystallized from chloroform (II). The molecule adopts a rectangular shape with two type IV beta-turns containing a hydrogen bond and possesses pseudorotational symmetry. The side chains are located on the molecular periphery. The orientation of the carbonyl groups of the molecule is not conducive for efficient metal-ion coordination and in the observed conformation cannot behave as an ionophore. In the crystal the molecules form infinite chains parallel to the c axis, and are stabilized by two intermolecular hydrogen bonds that are shorter and have better geometry than the intramolecular hydrogen bonds. A phi/psi plot for dodecadepsipeptides with a (DLLD)3 sequence has well-defined areas for Val and Hyi residues only in cases when the crystals have been grown from nonpolar or medium-polar solvents. The phi/psi plot for octadepsipeptides crystallized from chloroform (II) shows this behavior also.(ABSTRACT TRUNCATED AT 250 WORDS)

Crystal and molecular structure of the depsipeptide ionophore hexadecaisoleucinomycin, cyclo-[(D-Ile-L-Lac-L-Ile-D-Hyi)4-] (C80H136N8O24).

The crystal structure of a synthetic depsipeptide ionophore hexadecaisoleucinomycin, cyclo [-(D-Ile-L-Lac-L-Ile-D-Hyi)4-] (C80H136N8O24), has been determined by single crystal x-ray diffraction techniques. The crystals are orthorhombic, space group P2(1)2(1)2(1), number of molecules per unit cell z = 4, and cell parameters a = 11,195, b = 17.853, c = 54.835 A. The values of the standard (R) and weighted (Rw) discrepancy factors after refinement are 0.122 and 0.135, respectively. The structure is characterized by an elongated bracelet form with a twofold axis of pseudosymmetry. It is stabilized by eight intramolecular 4----1 hydrogen bonds between the amide C = O and N - H groups. The ester carbonyls are directed toward the inside of the molecule, their oxygen atoms forming an ellipsoidal internal cavity. The side chains are located on the molecular periphery. The conformational states of hexadecaisoleucinomycin in solution are discussed in the light of the data obtained.

[Structure of macrocyclic K+, Rb+-complexon of meso-valinomycin monohydrate, cyclo[-(D-Val-Hyi-Val-D-Hyi)3-].H2O, in a crystalline complex with dioxane by x-ray structural data]. / Struktura makrotsiklicheskogo K+, Rb+-kompleksona mezo-valinomitsina- monogidrata, cyclo]-(D-Val-Hyi-Val-D-Hyi)3-].H2O, v kristallicheskom komplekse s dioksanom po dannym rentgenostrukturnogo analiza.

The crystal structure of a valinomycin analogue, cyclo[-(D-Val-Hyi-Val-D-Hyi)3-]x(C60H102N6O18) crystallized with dioxane and water molecules, has been solved by X-ray direct methods. The conformation found is analogous to one established for free meso-valinomycin crystallized from other organic solvents. It is characterized by a centrosymmetric bracelet form, stabilized by six intramolecular 4----1 type hydrogen bonds between amide N-H and C = O groups. One water molecule is fixed asymmetrically by hydrogen bonds in the internal negatively charged cavity of the complexon. The meso-valinomycin molecule "bracelets" in the crystal form stacks alternatively with dioxane molecules.

[Crystallization and molecular structure of cyclic dodecadepsipeptide cyclo]D-Val-D-Hyi-Val-Hyi-(D-Val-Hyi-Val-D-Hyi)2-].2C3H60]. / Kristallicheskaia i molekuliarnaia struktura tsiklicheskogo dodekadepsipeptida cyclo[D-Val-D-Hyi-(D-Val-Hyi-Val-D-Hyi)2-].2C3H6O.

The crystal structure of a synthetic analogue of meso-valinomycin, crystallized with two acetone molecules, has been solved by X-ray direct methods. The trigonal crystals belong to the P32 space group, with the number of molecules in the unit cell z = 3, and cell dimensions a = b = 15,2085 A, c = 29,3250 A, alpha = beta = 90 degrees, gamma = 120 degrees. The standard (R) and weighted (Rw) factors after the structure refinement of atoms C, N, O in anisotropic thermal motion approximation and with the contribution from H atoms taken into account are 0,070 and 0,082, respectively. The molecule adopts an asymmetric conformations stabilized by six amide intramolecular hydrogen bonds NH ... OC of the 4----4 type; one of those is strong and the other are weakened in different extent. The side chains occupy the external pseudoaxial positions towards the cyclic frame of the molecule, whereas six free ester carbonyl groups have different orientations. In contrast to meso-valinomycin, the analogue under study has no specific binding site for metal ions. The isopropyl side chains of D-Hyi(2) and Hyi(4) residues effectively shield, from both sides, the access to the inner molecular cavity.

Molecular conformation and ion transport of cyclic and linear ionophores.

X-ray crystal structure determinations and energy-minimization techniques provide conformational data on the complexed and uncomplexed forms of ion transport antibiotics of the shuttle and channel types. In the solid state, hexadecaisoleucinomycin (HEXIL), an analogue of valinomycin, is observed as an asymmetric macrocycle stabilized by eight intramolecular (4----1) hydrogen bonds. The structure obtained from energy-minimization procedures exhibits a greater variation in phi and psi angles of chemically equivalent residues than does the crystallographically observed structure. The structure has eight carbonyl groups directed toward its interior and is capable of providing flexible coordination to a positively charged ion or molecule. These structural findings are consistent with the observed capacity of HEXIL to complex cesium ions, tetramethyl ammonium ions and acetylcholine. Gramicidin A is a pentadecapeptide that functions as a transmembrane channel for transporting monovalent cations. Uncomplexed gramicidin A crystallizes as a left-handed, antiparallel, double-stranded, helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 A and an average inner channel diameter of 4.8 A. The channel of this crystalline form does not contain ions or solvent molecules. Transporting ions through this channel could be achieved only by some expansion of the channel opening that would involve breaking and reforming hydrogen bonds that stabilize the double-stranded helix.

Ion transport mediated by the valinomycin analogue cyclo(L-Lac-L-Val-D-Pro-D-Val)3 in lipid bilayer membranes.

Cyclo(L-Lac-L-Val-D-Pro-D-Val)3 (PV-Lac) a structural analogue of the ion-carrier valinomycin, increases the cation permeability of lipid bilayer membranes by forming a 1:1 ion-carrier complex. The selectively sequence for PV-Lac is identical to that of valinomycin; i.e., Rb+ greater than K+ greater than Cs+ greater than or equal to NH+4 greater than Na+ greater than Li+. The steady-state zero-voltage conductance, G(0), is a saturating function of KCl concentration. A similar behavior was found for Rb+, Cs+, and NH+4. However, the ion concentration at which G(0) reaches a plateau strongly depends on membrane composition. The current-voltage curves present saturating characteristics, except at low ion concentrations of Rb+, K+, or Cs+. The ion concentration at which the saturating characteristics appear depends on membrane composition. These and other results presented in this paper agree with a model that assumes complexation between carrier and ion at the membrane-water interface. Current relaxation after voltage-jump studies were also performed for PV-Lac. Both the time constant and the amplitude of the current after a voltage jump strongly depend on ion concentration and membrane composition. These results, together with the stationary conductance data, were used to evaluate the rate constants of the PV-Lac-mediated K+ transport. In glycerolmonooleate they are: association rate constant, 2 x 10(6) M-1 s-1; dissociation rate constant, 4 x 10(5) s-1; translocation rate constant for complex, 5 x 10(4) s-1; and the rate of translocation of the free carrier (ks), 55 s-1. ks is much smaller for PV-Lac than for valinomycin and thus limits the efficiency with which the carrier is able to translocate cations across the membrane.

Kinetics of ion transport in lipid membranes induced by lysine-valinomycin and derivatives.

Lysine-valinomycine and two N epsilon-acyl derivatives are compared with respect to their potency to transport Rb+ ions across thin lipid membranes. Lysine-valinomycin acts as a neutral ion carrier only above a pH of about 7 of the aqueous solutions, while at lower pH the molecules seem to be positively charged due to a protonation of the epsilon-NH2 group of the lysine residue. A kinetic analysis based on voltage jump relaxation experiments and on the nonlinearity of the current-voltage characteristics showed that the conductance increment delta per carrier molecule for uncharged lysine-valinomycin is similar to that of natural valinomycin. The attachment of a rather bulky side group such as the dansyl or para-nitrobenzyloxycarbonyl group reduced delta by approximately one order of magnitude. Some of the relaxation data of the valinomycin analogues were influenced by an unspecific relaxation of the pure lipid membrane. This structural relaxation represents a limitation to the possibility of analyzing specific transport systems in thin lipid membranes by the voltage jump or charge pulse techniques. It is shown that the time dependence of this structural relaxation--which was first published by Sargent (1975)--is at variance with a three capacitor equivalent circuit of the membrane, which was suggested by Coster and Smith (1974) on the basis of a.c. measurements. A modified equivalent circuit has been found to represent a satisfactory analogue for the current relaxation in the presence of valinomycin. It turned out, however, that such an equivalent circuit provides little insight into the molecular mechanism of transport.

Synthesis of lysine-valinomycin by solid-phase segment condensation.

In order to obtain a readily derivatized analog of the ionophore antibiotic valinomycin, [1-lysine] valinomycin (Lys-VAL) was synthesized. The compound was built up on a polystyrene support by stepwise segment condensation and was cyclized in solution. The segments used were didepsipeptides protected by the t-butyloxycarbonyl and p-nitrobenzyloxycarbonyl groups. Derivatives prepared by acylation of the epsilon-amino group of Lys-VAL included [14C]acetyl-Lys-VAL, dansyl-Lys-VAL, palmitoyl-Lys-VAL and dithiodiglycoyl-bis-Lys-VAL. These derivatives had a high potassium binding capacity but were in general much less active than VAL in mediating ion transport in membranes.

Conformations of an ion-binding cyclic peptide analogue of valinomycin, cyclo(L-Val-Gly-Gly-L-Pro)3.

A 270-MHz 1H nuclear magnetic resonance investigation of an ion-binding cyclic peptide analogue of valinomycin, cyclo(L-Val-Gly-Gly-L-Pro)3, and its cation complexes is reported. In CD2Cl2 and CDCl3, the peptide is proposed to occur in a C3-symmetric conformer with the N--H's of all six glycine residues intramolecularly hydrogen bonded. This conformation is different from the familiar valinomycin bracelet structure and lacks any "cavity". Cations do not bind, or bind only weakly, to the peptide in these solvents. Uncomplexed cyclo(L-Val-Gly-Gly-L-Pro)3 in acetonitrile appears to be averaging among several conformations with no evidence found for any preferred intramolecular hydrogen bonds. The strong 1:1 complexes of cyclo(L-Val-Gly-Gly-L-Pro)3 with K+ ANd Ba2+ in acetonitrile are structurally analogous to the bracelet conformation of valinomycin and involve the N--H's of the Val residues and of the Gly's preceding Pro in intramolecular hydrogen bonding. Tl+ was also found to form strong 1:1 complexes with the dodecapeptide.