Design, synthesis, and evaluation of indole compounds as novel inhibitors targeting Gp41.

A series of indole ring containing compounds were designed based on the structure of the gp41 complex in the region of the hydrophobic pocket. These compounds were synthesized using a Suzuki Coupling reaction, and evaluated using a fluorescence binding assay and cell-cell fusion assay. The observed inhibition constant of compound 7 was 2.1microM, and the IC(50) for cell-cell fusion inhibition was 1.1microM. Assay data indicated that 7 is a promising lead compound for optimization into an effective low molecular weight fusion inhibitor.

Stable extended human immunodeficiency virus type 1 gp41 coiled coil as an effective target in an assay for high-affinity fusion inhibitors.

The human immunodeficiency virus type 1 (HIV-1) gp41 coiled-coil domain is an important target for fusion inhibitors, including the peptide T20, which has been approved as a drug against HIV-1. Research into nonpeptide fusion inhibitors has focused primarily on a hydrophobic pocket located within the coiled coil and has so far yielded compounds with relatively weak fusion inhibitory activity. Here, we describe metal ion-assisted stabilization of an extended 39-residue construct of gp41, which includes residues of the hydrophobic pocket and also of an extended groove N terminal to the hydrophobic pocket. We show that the presence of a metal ion and the high-affinity interaction between the receptor construct and cognate C-peptides result in a simple and highly selective assay for fusion inhibitors that may be used to scan large compound libraries. The long construct presents multiple potential binding sites along the extended coiled-coil groove. We demonstrate the modular use of assay probes to detect whether compounds bind in the hydrophobic pocket or elsewhere along the groove. Rapid detection and quantitation of hits can lead to the discovery of compounds binding to different sites along the groove and provide structure-activity relationship data for optimization. Compounds binding to adjacent sites could be linked to form more potent fusion inhibitors.

NMR second site screening for structure determination of ligands bound in the hydrophobic pocket of HIV-1 gp41.

The development of nonpeptide fusion inhibitors through rational drug design has been hampered by the limited accessibility of the gp41 coiled coil target, which is highly hydrophobic, and the absence of structural data defining details of small molecule interactions. Here we describe a new approach for obtaining structural information on small molecules bound in the hydrophobic pocket of gp41, using a paramagnetic probe peptide which binds adjacent to the pocket along an extended coiled coil. Ligand binding in the pocket leads to paramagnetic relaxation effects or pseudocontact shifts of ligand protons. These effects are distance and/or orientation dependent, permitting determination of ligand pose in the pocket. The method is demonstrated with a fast-exchanging ligand. Multiple measurements at different coiled coil and probe peptide ratios enabled accurate determination of the NMR parameters. Use of a labeled probe peptide stabilizes an otherwise aggregation-prone coiled coil and also enables modulation of the paramagnetic effect to study ligands of various affinities. Ultimately, this technique can provide essential information for structure-based design of nonpeptide fusion inhibitors.

Facile synthesis and relaxation properties of novel bispolyazamacrocyclic Gd3+ complexes: an attempt towards calcium-sensitive MRI contrast agents.

Three novel GdDO3A-type bismacrocyclic complexes, conjugated to Ca (2+) chelating moieties like ethylenediaminetetraacetic acid and diethylenetriamine pentaacetic acid bisamides, were synthesized as potential "smart" magnetic resonance imaging contrast agents. Their sensitivity toward Ca (2+) was studied by relaxometric titrations. A maximum relaxivity increase of 15, 6, and 32% was observed upon Ca (2+) binding for Gd 2L (1), Gd 2L (2), and Gd 2L (3), respectively (L (1) = N, N-bis{1-[{[({1-[1,4,7-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-10-yl]eth-2-yl}amino)carbonyl]methyl}-(carboxymethyl)amino]eth-2-yl}aminoacetic acid; L (2) = N, N-bis[1-({[({alpha-[1,4,7-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-10-yl]- p-tolylamino}carbonyl)methyl]-(carboxymethyl)}amino)eth-2-yl]aminoacetic acid; L (3) = 1,2-bis[{[({1-[1,4,7-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-10-yl]eth-2-yl}amino)carbonyl]methyl}(carboxymethyl)amino]ethane). The apparent association constants are log K A = 3.6 +/- 0.1 for Gd 2L (1) and log K A = 3.4 +/- 0.1 for Gd 2L (3). For the interaction between Mg (2+) and Gd 2L (1), log K A = 2.7 +/- 0.1 has been determined, while no relaxivity change was detected with Gd 2L (3). Luminescence lifetime measurements on the Eu (3+) complexes in the absence of Ca (2+) gave hydration numbers of q = 0.9 (Eu 2L (1)), 0.7 (Eu 2L (2)), and 1.3 (Eu 2L (3)). The parameters influencing proton relaxivity of the Gd (3+) complexes were assessed by a combined nuclear magnetic relaxation dispersion (NMRD) and (17)O NMR study. Water exchange is relatively slow on Gd 2L (1) and Gd 2L (2) ( k ex (298) = 0.5 and 0.8 x 10 (6) s (-1)), while it is faster on Gd 2L (3) (k ex (298) = 80 x 10 (6) s (-1)); in any case, it is not sensitive to the presence of Ca (2+). The rotational correlation time, tau R (298), differs for the three complexes and reflects their rigidity. Due to the benzene linker, the Gd 2L (2) complex is remarkably rigid, with a correspondingly high relaxivity despite the low hydration number ( r 1 = 10.2 mM (-1)s (-1) at 60 MHz, 298 K). On the basis of all available experimental data from luminescence, (17)O NMR, and NMRD studies on the Eu (3+) and Gd (3+) complexes of L (1) and L (3) in the absence and in the presence of Ca (2+), we conclude that the relaxivity increase observed upon Ca (2+) addition can be mainly ascribed to the increase in the hydration number, and, to a smaller extent, to the Ca (2+)-induced rigidification of the complex.

Monopropionate analogues of DOTA4- and DTPA5-: kinetics of formation and dissociation of their lanthanide(III) complexes.

The replacement of an acetate function of the macrocyclic DOTA4-(DO3A-Nprop4-) or the acyclic DTPA5- in terminal position (DTTA-Nprop5-) has been recently shown to result in a significant increase of the water exchange rate on the Gd3+ complexes, which makes these chelates potential contrast agents for MRI applications. Here, two novel and straightforward synthetic routes to H4DO3A-Nprop are described. Protonation constants of DO3A-Nprop4- and stability constants with several alkaline earth and transition metal ions have been determined by potentiometry. For each metal, the thermodynamic stability constant is decreased in comparison to the DOTA chelates. The formation reaction of LnDO3A-Nprop- complexes (Ln=Ce, Gd and Yb) proceeds via the rapid formation of a diprotonated intermediate and its subsequent deprotonation and rearrangement in a slow, OH- catalyzed process. The stability of the LnH2DO3A-Nprop* intermediates is similar to those reported for the corresponding DOTA analogues. The rate constants of the OH- catalyzed deprotonation step increase with decreasing lanthanide ion size, and are slightly higher than for DOTA complexes. The kinetic inertness of GdDTTA-Nprop2- was characterized by the rates of its exchange reactions with Zn2+ and Eu3+. The rate of the reaction between GdDTTA-Nprop2- and Zn2+ increases with Zn2+ concentration, while it is independent of pH, implying that the exchange takes place predominantly via direct attack of the metal ion on the complex. In the Eu3+ exchange, the rate decreases with increasing concentration of the exchanging ion which is accounted for by the transitional formation of a dinuclear GdDTTA-NpropEu+ species. The kinetic inertness of the monopropionate GdDTTA-Nprop2- is decreased in comparison to GdDTPA2-: all rate constants, characterizing the dissociation reaction via either proton- or metal-catalyzed pathways being higher by 1-2 orders of magnitude. Similarly, a study of the acid-catalyzed dissociation of the macrocyclic CeDO3A-Nprop- showed a partial loss of the kinetic inertness with regard to the tetraacetate derivative CeDOTA-.

Rates of ligand exchange between >FeIII-OH2 functional groups on a nanometer-sized aqueous cluster and bulk solution.

Variable-temperature 17O NMR experiments were conducted on the nanometer-sized Keplerate Mo72Fe30 cluster, with the stoichiometry [Mo72Fe30O252(CH3COO)12[Mo2O7(H2O)]2[H2Mo2O8(H2O)](H2O)91]. approximately 150H2O. This molecule contains on its surface 30 Fe(H2O) groups forming a well-defined icosidodecahedron, and we estimated the rates of exchange of the isolated >FeIII-OH2 waters with bulk aqueous solution. Both longitudinal and transverse 17O-relaxation times were measured, as well as chemical shifts, and these parameters were then fit to the Swift-Connick equations in order to obtain the rate parameters. Correspondingly, we estimate: k(ex)298 = 6.7(+/-0.8) x 106 s-1, which is about a factor of approximately 4 x 104 times larger than the corresponding rate coefficient for the Fe(OH2)63+ ion of k(ex)298 = 1.6 x 102 s-1 (Grant and Jordan, 1981; Inorg. Chem. 20, 55-60) and DeltaH and DeltaS are 26.3 +/- 0.6 kJ mol-1 and -26 +/- 0.9 J mol-1 K-1, respectively. High-pressure 17O NMR experiments were also conducted, but the cluster decomposed slightly under pressure, which precluded confident quantitative estimation of the DeltaV. However, the increase in the reduced transverse-relaxation time with pressure suggests a dissociative character, such as a D or Id mechanism. The enhanced reactivity of waters on the Mo72Fe30 cluster is associated with an increase in the FeIII-OH2 bond length in the solid state of approximately 0.1 A relative to the Fe(OH2)63+ ion, suggesting that a correlation exists between the FeIII-OH2 bond length and k(ex)298. Although there are only few high-spin Fe(III) complexes where both exchange rates and structural data are available, these few seem to support a general correlation.

Rates of oxygen-isotope exchange between sites in the [HxTa6O19](8-x)-(aq) Lindqvist ion and aqueous solutions: comparisons to [HxNb6O19](8-x)-(aq).

Rates of steady oxygen-isotope exchange differ in interesting ways for two sets of structural oxygens in the [HxTa6O19](8-x)-(aq) Lindqvist ion when compared to published data on the [HxNb6O19]8-x(aq) version. Because of the lanthanide contraction, the [HxTa6O19](8-x)-(aq) and [HxNb6O19](8-x)-(aq) ions are virtually isostructural and differ primarily in a full core (Kr vs Xe) and the 4f14 electrons in the [HxTa6O19](8-x)-(aq) ion. For both molecules, both pH-dependent and -independent pathways are evident in isotopic exchange of the 12 mu2-O(H) and 6 eta=O sites. Rate parameters for eta=O exchange at conditions where there is no pH dependence are, for the Ta(V) and Nb(V) versions respectively, K(298)(0) = 2.72 x 10(-5) s(-1) and 9.7 x 10(-6) s(-1), DeltaH = 83.6 +/- 3.2 and 89.4 kJ.mol(-1), and DeltaS = -51.0 +/- 10.6 and -42.9 J.mol(-1).K-1. For the mu2-O sites, K(298)(0) = 1.23 x 10(-6) s(-1), DeltaH = 70.3 +/- 9.7 and 88.0 kJ.mol(-1), and DeltaS = -116.1 +/- 32.7 and -29.4 J.mol(-1).K-1. Protonation of the 6 eta=O sites is energetically unfavored relative to the 12 mu2-O bridges in both molecules, although not equally so. Experimentally, protonation labilizes both the mu2-O(H) and eta=O sites to isotopic exchange in both molecules. Density-functional electronic-structure calculations indicate that proton affinities of structural oxygens in the two molecules differ with the [HxTa6O19](8-x)-(aq) anion having a smaller affinity to protonate than the [HxNb6O19]8-x(aq) ion. This difference in proton affinities is evident in the solution chemistry as pKa = 11.5 for the [HTa6O19]7-(aq) ion and pKa = 13.6 for the [HNb6O19]7-(aq) ion. Most striking is the observation that eta=O sites isotopically equilibrate faster than the mu2-O sites for the [HxTa6O19](8-x)-(aq) Lindqvist ion but slower for the [HxNb6O19](8-x)-(aq) ion, indicating that predictions about site reactivities in complicated structures, such as the interface of aqueous solutions and oxide solids, should be approached with great caution.

Dinuclear complexes formed with the triazacyclononane derivative ENOTA4-: high-pressure 17O NMR evidence of an associative water exchange on [MnII2(ENOTA)(H2O)2].

Mn2+ has five unpaired d-electrons, a long electronic relaxation time, and labile water exchange, all of which make it an attractive candidate for contrast agent application in medical magnetic resonance imaging. In the quest for stable and nonlabile Mn2+ complexes, we explored a novel dimeric triazacyclononane-based ligand bearing carboxylate functional groups, H4ENOTA. The protonation constants of the ligand and the stability constants of the complexes formed with some endogenously important metals (Ca2+, Cu2+, Zn2+), as well as with Mn2+ and Ce3+, have been assessed by NMR methods, potentiometry, and UV-vis spectrophotometry. Overall, the thermodynamic stability of the complexes is lower as compared to that of the corresponding NOTA analogues (H3NOTA, 1,4,7-triaazacyclononane-1,4,7-triacetic acid). The crystal structure of Mn2(ENOTA)(H2O) x 5H2O contains two six-coordinated Mn2+, in addition to the three amine nitrogens and the two oxygens from the pendent monodentate carboxylate groups, and one water (Mn2) or one bridging carboxylate oxygen (Mn1) completes the coordination sphere of the metal ion. In an aqueous solution, this bridging carboxylate is replaced by a water molecule, as evidenced by the 17O chemical shifts and proton relaxivity data that point to monohydration for both metal ions in the dinuclear complex. A variable-temperature and -pressure 17O NMR study has been performed on [Mn2(ENOTA)(H2O)2] to assess the rate and, for the first time on a Mn2+ chelate, also the mechanism of the water exchange. The inner sphere water is slightly more labile in [Mn2(ENOTA)(H2O)2] (k298ex = 5.5 x 107 s-1) than in the aqua ion (2.1 x 107 s-1, Merbach, A. E.; et al. Inorg. Chem. 1980, 19, 3696). The water exchange proceeds via an almost limiting associative mechanism, as evidenced by the large negative activation volume (deltaV = -10.7 cm3 mol-1). The proton relaxivities measured on [Mn2(ENOTA)(H2O)2] show a low-field dispersion at approximately 0.1 MHz arising from a contact interaction between the MnII electron spin and the water proton nuclear spins.

Pyridine and phosphonate containing ligands for stable lanthanide complexation. An experimental and theoretical study to assess the solution structure.

We report an experimental and theoretical study of the stability and solution structure of lanthanide complexes with two novel ligands containing pyridine units and phosphonate pendant arms on either ethane-1,2-diamine (L2) or cyclohexane-1,2-diamine (L3) backbones. Potentiometric studies have been carried out to determine the protonation constants of the ligands and the stability constants of the complexes with Gd(III) and the endogenous metal ions Zn(II) and Cu(II). While the stability constant of the GdL2 complex is too high to be determined by direct pH-potentiometric titrations, the cyclohexyl derivative GdL3 has a lower and assessable stability (log K(GdL3)=17.62). Due to the presence of the phosphonate groups, various protonated species can be detected up to pH approximately 8 for both ligands and all metal ions studied. The molecular clusters [Ln(L)(H2O)](3-).19H2O (Ln=La, Nd, Ho or Lu; L=L2 or L3) were characterized by theoretical calculations at the HF level. Our calculations provide two minimum energy geometries where the ligand adopts different conformations: twist-wrap (tw), in which the ligand wraps around the metal ion by twisting the pyridyl units relative to each other, and twist-fold (tf), where the slight twisting of the pyridyl units is accompanied by an overall folding of the two pyridine units towards one of the phosphonate groups. The relative free energies of the tw and tf conformations of [Ln(L)(H2O)]3- (L=L2, L3) complexes calculated in aqueous solution (C-PCM) by using the B3LYP model indicate that the tw form is the most stable one along the whole lanthanide series for the complexes of L3, while for those of L2 only the Gd(III) complex is more stable in the tf conformation by ca. 0.5 kcal mol-1. 1H NMR studies of the Eu(III) complex of L3 show the initial formation of the tf complex in aqueous solution, which slowly converts to the thermodynamically stable tw form. The structures calculated for the Nd(III) complexes are in reasonably good agreement with the experimental solution structures, as demonstrated by Nd(III)-induced relaxation rate enhancement effects in the 1H NMR spectra.

Pyridine- and phosphonate-containing ligands for stable Ln complexation. Extremely fast water exchange on the Gd(III) chelates.

Two novel ligands containing pyridine units and phosphonate pendant arms, with ethane-1,2-diamine (L2) or cyclohexane-1,2-diamine (L3) backbones, have been synthesized for Ln complexation. The hydration numbers obtained from luminescence lifetime measurements in aqueous solutions of the Eu(III) and Tb(III) complexes are q = 0.6 (EuL2), 0.7 (TbL2), 0.8 (EuL3), and 0.4 (TbL3). To further assess the hydration equilibrium, we have performed a variable-temperature and -pressure UV-vis spectrophotometric study on the Eu(III) complexes. The reaction enthalpy, entropy, and volume for the hydration equilibrium EuL <--> EuL(H2O) were calculated to be DeltaH degrees = -(11.6 +/- 2) kJ mol(-1), DeltaS degrees = -(34.2 +/- 5) J mol(-1) K(-1), and = 1.8 +/- 0.3 for EuL2 and DeltaH degrees = -(13.5 +/- 1) kJ mol(-1), DeltaS degrees = -(41 +/- 4) J mol(-1) K(-1), and = 1.7 +/- 0.3 for EuL3, respectively. We have carried out variable-temperature 17O NMR and nuclear magnetic relaxation dispersion (NMRD) measurements on the GdL2(H2O)q and GdL3(H2O)q systems. Given the presence of phosphonate groups in the ligand backbone, a second-sphere relaxation mechanism has been included for the analysis of the longitudinal (17)O and (1)H NMR relaxation rates. The water exchange rate on GdL2(H2O)q, = (7.0 +/- 0.8) x 10(8) s(-1), is extremely high and comparable to that on the Gd(III) aqua ion, while it is slightly reduced for GdL3(H2O)q, = (1.5 +/- 0.1) x 10(8) s(-1). This fast exchange can be rationalized in terms of a very flexible inner coordination sphere, which is slightly rigidified for L3 by the introduction of the cyclohexyl group on the amine backbone. The water exchange proceeds via a dissociative interchange mechanism, evidenced by the positive activation volumes obtained from variable-pressure 17O NMR for both GdL2(H2O)q and GdL3(H2O)q (DeltaV = +8.3 +/- 1.0 and 8.7 +/- 1.0 cm(3) mol(-1), respectively).

Unexpected aggregation of neutral, xylene-cored dinuclear GdIII chelates in aqueous solution.

We have synthesized ditopic ligands L(1), L(2), and L(3) that contain two DO3A(3-) metal-chelating units with a xylene core as a noncoordinating linker (DO3A(3-) = 1,4,7,10-tetraazacyclododecane-1,4,7-triacetate; L(1) = 1,4-bis{[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1-yl]methyl}benzene; L(2) = 1,3-bis{[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1-yl]methyl}benzene; L(3) = 3,5-bis{[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1-yl]methyl}benzoic acid). Aqueous solutions of the dinuclear Gd(III) complexes formed with the three ligands have been investigated in a variable-temperature, multiple-field (17)O NMR and (1)H relaxivity study. The (17)O longitudinal relaxation rates measured for the [Gd(2)L(1-3)(H2O)(2)] complexes show strong field dependence (2.35-9.4 T), which unambiguously proves the presence of slowly tumbling entities in solution. The proton relaxivities of the complexes, which are unexpectedly high for their molecular weight, and in particular the relaxivity peaks observed at 40-50 MHz also constitute experimental evidences of slow rotational motion. This was explained in terms of self-aggregation related to hydrophobic interactions, pi stacking between the aromatic linkers, or possible hydrogen bonding between the chelates. The longitudinal (17)O relaxation rates of the [Gd(2)L(1-3)(H2O)(2)] complexes have been analysed with the Lipari-Szabo approach, leading to local rotational correlation times tau(1)(298) of 150-250 ps and global rotational correlation times tau(g)(298) of 1.6-3.4 ns (c(Gd): 20-50 mM), where tau(1)(298) is attributed to local motions of the Gd segments, while tau(g)(298) describes the overall motion of the aggregates. The aggregates can be partially disrupted by phosphate addition; however, at high concentrations phosphate interferes in the first coordination sphere by replacing the coordinated water. In contrast to the parent [Gd(DO3A)(H2O)(1.9)], which presents a hydration equilibrium between mono- and dihydrated species, a hydration number of q = 1 was established for the [Ln(2)L(1-3)(H2O)(2)] chelates by (17)O chemical shift measurements on Ln = Gd and UV/Vis spectrophotometry for Ln = Eu. The exchange rate of the coordinated water is higher for [Gd(2)L(1-3)(H2O)(2)] complexes k(ex)(298) = 7.5-12.0 x 10(6) s(-1)) than for [Gd(DOTA)(H2O)](-). The proton relaxivity of the [Gd(2)L(1-3)(H2O)(2)] complexes strongly decreases with increasing pH. This is related to the deprotonation of the inner-sphere water, which has also been characterized by pH potentiometry. The protonation constants determined for this process are logK(OH) = 9.50 and 10.37 for [Gd(2)L(1)(H2O)(2)] and [Gd(2)L(3)(H2O)(2)], respectively.

The highest water exchange rate ever measured for a Gd(III) chelate.

The complex [Gd(L)(H2O)]3- (H(6)L =N,N'-bis(6-carboxy-2-pyridylmethyl)ethylenediamine-N,N'-methylenephosphonic acid) displays the highest water exchange rate ever measured for a Gd(III) chelate (k(298)(ex)= 8.8 x 10(8) s(-1)), which is attributed to the flexibility of the metal coordination environment.

Kinetics of formation and dissociation of lanthanide(III) complexes with the 13-membered macrocyclic ligand TRITA4-.

The tetraazamacrocyclic ligand TRITA(4-) is intermediate in size between the widely studied and medically used 12-membered DOTA(4-) and the 14-membered TETA(4-). The kinetic inertness of GdTRITA(-) was characterized by the rates of exchange reactions with Zn(2+) and Eu(3+). In the Zn(2+) exchange, a second order [H(+)] dependence was found for the pseudo-first-order rate constant (k(0)=(4.2 +/- 0.5) x 10(-7) s(-1); k'=(3.5 +/- 0.3) x 10(-1) M(-1)s(-1), k" =(1.4 +/- 0.4) x 10(3) M(-2)s(-1)). In the Eu(3+) exchange, at pH <5 the rate decreases with increasing concentration of the exchanging ion, which can be accounted for by the transitional formation of dinuclear GdTRITAEu(2+) species. At physiological pH, the kinetic inertness of GdTRITA(-) is considerably lower than that of GdDOTA(-)(t(1/2)= 444 h (25 degrees C) vs. 3.8 x 10(5) h (37 degrees C), respectively). However, GdTRITA(-) is still kinetically more inert than GdDTPA(2-), the most commonly used MRI contrast agent (t(1/2)= 127 h). The formation reactions of LnTRITA(-) complexes (Ln = Ce, Gd and Yb) proceed via the rapid formation of a diprotonated intermediate and its subsequent deprotonation and rearrangement in a slow, OH(-) catalyzed process. The stability of the LnH(2)TRITA* intermediates (log K(LnH2L*)= 3.1-3.9) is lower than that of the DOTA-analogues. The rate constants of the OH(-) catalyzed step increase with decreasing lanthanide ion size, and are about twice as high as for DOTA-complexes.