Taming Conformational Heterogeneity on Ion Racetrack to Unveil Principles that Drive Membrane Permeation of Cyclosporines.

Our study reveals the underlying principles governing the passive membrane permeability in three large N-methylated macrocyclic peptides (N-MeMPs): cyclosporine A (CycA), Alisporivir (ALI), and cyclosporine H (CycH). We determine a series of conformers required for robust passive membrane diffusion and those relevant to other functions, such as binding to protein targets or intermediates, in the presence of solvent additives. We investigate the conformational interconversions and establish correlations with the membrane permeability. Nuclear magnetic resonance (NMR) and cyclic ion-mobility spectrometry-mass spectrometry (cIMS-MS) are employed to characterize conformational heterogeneity and identify cis-amides relevant for good membrane permeability. In addition, ion mobility selected cIMS-MS and infrared (IR) multiple-photon dissociation (IRMPD) spectroscopy experiments are conducted to evaluate the energy barriers between conformations. We observe that CycA and ALI, both cyclosporines with favorable membrane permeabilities, display multiple stable and well-defined conformers. In contrast, CycH, an epimer of CycA with limited permeability, exhibits fewer and fewer stable conformers. We demonstrate the essential role of the conformational shift from the aqueous cis MeVal11-MeBmt1 state (A1) to the closed conformation featuring cis MeLeu9-MeLeu10 (C1) in facilitating membrane permeation. Additionally, we highlight that the transition from A1 to the all-trans open conformation (O1) is specifically triggered by the presence of CaCl2. We also capture a set of conformers with cis Sar3-MeLeu4, MeLeu9-MeLeu10, denoted as I. Conformationally selected cIMS-MS and IRMPD data of [CycA+Ca]2+ show immediate repopulation of the original population distribution, suggesting that CaCl2 smooths out the energy barriers. Finally, our work presents an improved sampling molecular dynamics approach based on a refined force field that not only consistently and accurately captures established conformers of cyclosporines but also exhibits strong predictive capabilities for novel conformers.

Entropy stabilized cubic Li7La3Zr2O12 with reduced lithium diffusion activation energy: studied using solid-state NMR spectroscopy.

Stabilizing cubic polymorph of Li7La3Zr2O12 at low temperatures is challenging and currently limited to mono- or dual-ion doping with aliovalent ions. Herein, a high-entropy strategy at the Zr sites was deployed to stabilize the cubic phase and lower the lithium diffusion activation energy, evident from the static 7Li and MAS 6Li NMR spectra.

Syntheses of Group 5 Amide Amidinates and Their Reactions with Water: Different Reactivities of Nb(V) and Ta(V) Complexes.

Chemistries of Nb(V) and Ta(V) compounds are essentially identical as a result of lanthanide contraction. Hydrolysis of M(NMe2)5 (M = Nb, Ta), for example, yields [M(µ3-O)(NMe2)3]4 (M = Nb, 1; Ta, 2) reported earlier. The similar reactivities of Nb(V) and Ta(V) compounds make it challenging, for example, to separate the two metals from their minerals. We have found that the reactions of H2O with amide amidinates M(NMe2)4[MeC(NiPr)2] (M = Nb, 3; Ta, 4) show that the niobium and tantalum analogues take different principal paths. For the Nb(V) complex 3, the amidinate and one amide ligand are liberated upon treatment with water, yielding [Nb(µ3-O)(NMe2)3]4 (1). For the Ta(V) complex 4, the amide ligands are released in the reaction with H2O, leaving the amidinate ligand intact. [Ta(µ3-O)(NMe2)3]4 (2), the analogue of 1, was not observed as a product in the reaction of 4 with H2O. To our knowledge, this is the first example of the formation of two different complexes that maintain the (V) oxidation state in both metals. The new complexes M(NMe2)4[MeC(NiPr)2] (M = Nb, 3; Ta, 4) have been prepared by the aminolysis of M(NMe2)5 (M = Nb, Ta) with iPrN(H)C(Me)=NiPr (5). The hydrolysis of 3 and 4 has been investigated by DFT electronic structure calculations. The first step in each hydrolysis reaction involves the formation of a hydrogen-bonded complex that facilitates a proton transfer to the amidinate ligand in 3 and protonation of an axial dimethylamide ligand in 4. Both proton transfers furnish an intermediate metal-hydroxide species. The atomic charges in 3 and 4 have been computed by Natural Population Analysis (NPA), and these data are discussed relative to which of the ancillary ligands is protonated initially in the hydrolysis sequence. Ligand exchanges in 3 and 4 as well as the exchange in iPrN(H)C(Me)=NiPr (5) were probed by EXSY NMR spectroscopy, giving rate constants of the exchanges: 0.430(13) s-1 (3), 0.033(6) s-1 (4), and 2.23(7) s-1 (5), showing that the rate of the Nb complex Nb(NMe2)4[MeC(NiPr)2] (3) is 13 times faster than that of its Ta analogue 4.

Atomic View of Aqueous Cyclosporine A: Unpacking a Decades-Old Mystery.

An atomic view of a main aqueous conformation of cyclosporine A (CycA), an important 11-amino-acid macrocyclic immunosuppressant, is reported. For decades, it has been a grand challenge to determine the conformation of free CycA in an aqueous-like solution given its poor water solubility. Using a combination of X-ray and single-crystal neutron diffraction, we unambiguously resolve a unique conformer (A1) with a novel cis-amide between residues 11 and 1 and two water ligands that stabilize hydrogen bond networks. NMR spectroscopy and titration experiments indicate that the novel conformer is as abundant as the closed conformer in 90/10 (v/v) methanol/water and is the main conformer at 10/90 methanol/water. Five other conformers were also detected in 90/10 methanol/water, one in slow exchange with A1, another one in slow exchange with the closed form and three minor ones, one of which contains two cis amides Abu2-Sar3 and MeBmt1-MeVal11. These conformers help better understand the wide spectrum of membrane permeability observed for CycA analogues and, to some extent, the binding of CycA to protein targets.

Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis-Trans Isomerization and the Chameleonic Roles of Calcium.

Falling outside of Lipinski's rule of five, macrocyclic drugs have accessed unique binding sites of their target receptors unreachable by traditional small molecules. Cyclosporin(e) A (CycA), an extensively studied macrocyclic natural product, is an immunosuppressant with undesirable side effects such as electrolytic imbalances. In this work, a comprehensive view on the conformational landscape of CycA, its interactions with Ca2+, and host-guest interactions with cyclophilin A (CypA) is reported through exhaustive analyses that combine ion-mobility spectrometry-mass spectrometry (IMS-MS), nuclear magnetic resonance (NMR) spectroscopy, distance-geometry modeling, and NMR-driven molecular dynamics. Our IMS-MS data show that CycA can adopt extremely compact conformations with significantly smaller collisional cross sections than the closed conformation observed in CDCl3. To adopt these conformations, the macrocyclic ring has to twist and bend via cis-trans isomerization of backbone amides, and thus, we termed this family of structures the "bent" conformation. Furthermore, NMR measurements indicate that the closed conformation exists at 19% in CD3OD/H2O and 55% in CD3CN. However, upon interacting with Ca2+, in addition to the bent and previously reported closed conformations of free CycA, the CycA:Ca2+ complex is open and has all-trans peptide bonds. Previous NMR studies using calcium perchlorate reported only the closed conformation of CycA (which contains one cis peptide bond). Here, calcium chloride, a more biologically relevant salt, was used, and interestingly, it helps converting the cis-MeLeu9-MeLeu10 peptide bond into a trans bond. Last, we were able to capture the native binding of CycA and CypA to give forth evidence that IMS-MS is able to probe the solution-phase structures of the complexes and that the Ca2+:CycA complex may play an essential role in the binding of CycA to CypA.

Syntheses and characterization of hepta-coordinated Group 4 amidinate complexes.

Tri-amidinate chloride complexes M[MeC(NiPr)2]3Cl [M = Zr (1), Hf (2)] have been prepared from MCl4 and lithium amidinate Li[MeC(NiPr)2]. The uncommon hepta-coordinated complexes Zr-Cl (1) and Hf-Cl (2) undergo metathesis reactions with 1 equiv. of MeLi and EtMgCl to give alkyl derivatives M[MeC(NiPr)2]3R [R = Me, M = Zr (3), Hf (4); R = Et, M = Zr (5), Hf (6)]. The dynamic behaviors of Zr-Cl (1) and Hf-Cl (2) in solution have been studied using variable-temperature 1H NMR (VT 1H NMR), giving activation parameters ΔH‡, ΔS‡, and ΔG‡ for several exchange processes in Zr-Cl (1) and Hf-Cl (2). 1H-15N gHMBC NMR spectroscopy gives the chemical shifts of the N atoms in 1-6. The 1H-15N gHMBC NMR spectra of 1-4 at elevated temperatures are needed to obtain signals. Crystal structures of Zr-Cl (1), Hf-Cl (2), Zr-Et (5), and Hf-Et (6) have been determined via X-ray diffraction. DART-MS studies of Zr-Cl (1) and Hf-Cl (2) in air give MS of 1-2, cations M[MeC(NiPr)2]3+ [M = Zr (7), Hf (8)], and hydroxyl complexes M[MeC(NiPr)2]3OH [M = Zr (9), Hf (10)]. In comparison, DART-MS spectra of 3-6 in air show only 7-8 and 9-10, indicating lability of the alkyl ligands and/or their fast hydrolysis by moisture.

Synthesis, structural characterization and NMR studies of group 10 metal complexes with macrocyclic amine N-heterocyclic carbene ligands.

A series of Ni(ii), Pd(ii) and Pt(ii) complexes [ML][PF6]2 [L = L1, M = Ni (1), Pd (2), Pt (3); L = L2, M = Ni (4), Pd (5), Pt (6)] and [Pt(L2)(acac)] (7) have been prepared by the reactions of two tetradentate macrocyclic amine-NHC ligand precursors, [H2L1][PF6]2 and [H2L2][PF6]2, with Ni(OAc)2·4H2O, Pd(OAc)2 and Pt(acac)2 in the presence of NaOAc. Complex 7 is isolated along with 6 from the same reaction between [H2L2][PF6]2 and Pt(acac)2. There are two atropisomers in 1-3 and two achiral conformers in 4-6. The crystal structures of 1-3 and one conformer of 4-6 (4a-6a) have been determined by single-crystal X-ray diffraction studies. The metal ion is found to reside in the cavity of the macrocyclic ring and adopts a square-planar configuration. Detailed NMR studies including variable-temperature NMR spectroscopy reveal a dynamic interconverting process between two atropisomers of 1-3 in the solutions via a ring twisting mechanism. Two conformers in the equilibrated solution of 4-6, probably arising from the orientation of two amine N-H bonds with respect to the coordination plane, exchange slowly. Time-dependent 1H NMR spectra show that one conformer (4a-6a) in solution converts into the other (4b-6b) via the inversion of the nitrogen atom.

C-H bond activation during and after the reactions of a metallacyclic amide with silanes: formation of a µ-alkylidene hydride complex, its H-D exchange, and ß-H abstraction by a hydride ligand.

Metallacyclic complex [(Me2N)3Ta(η(2)-CH2SiMe2NSiMe3)] (3) undergoes C-H activation in its reaction with H3SiPh to afford a Ta/µ-alkylidene/hydride complex, [(Me2N)2{(Me3Si)2N}Ta(µ-H)2(µ-C-η(2)-CHSiMe2NSiMe3)Ta(NMe2)2] (4). Deuterium-labeling studies with [D3]SiPh show H-D exchange between the Ta-D-Ta unit and all methyl groups in [(Me2N)2{(Me3Si)2N}Ta(µ-D)2(µ-C-η(2)-CHSiMe2NSiMe3)Ta(NMe2)2] ([D2]-4) to give the partially deuterated complex [Dn]-4. In addition, 4 undergoes ß-H abstraction between a hydride and an NMe2 ligand and forms a new complex [(Me2N){(Me3 Si)2N}Ta(µ-H)(µ-N-η(2)-C,N-CH2NMe)(µ-C-η(2)-C,N-CHSiMe2NSiMe3)Ta(NMe2)2] (5) with a cyclometalated, η(2)-imine ligand. These results indicate that there are two simultaneous processes in [Dn]-4:1) H-D exchange through σ-bond metathesis, and 2) H-D elimination through ß-H abstraction (to give [Dn]-5). Both 4 and 5 have been characterized by single-crystal X-ray diffraction studies.

Reactions of Group 4 amide guanidinates with dioxygen or water. Studies of the formation of oxo products.

Reactions of the zirconium amide guanidinates (R2N)2M[(i)PrNC(NR2)N(i)Pr]2 (R = Me, M = Zr, 1; M = Hf, 2; R = Et, M = Zr, 3) with O2 or H2O give products that are consistent with the oxo dimers {M(µ-O)[(i)PrNC(NR2)N(i)Pr]2}2 (R = Me, M = Zr, 4; M = Hf, 5; R = Et, M = Zr, 6) and polymers {M(µ-O)[(i)PrNC(NR2)N(i)Pr]2}n (R = Me, M = Zr, 7; M = Hf, 8; R = Et, M = Zr, 9). Mass spectrometric (MS) analyses of the reactions of water in air with 1 and 2 show formation of the Zr monomer Zr(═O)[(i)PrNC(NMe2)N(i)Pr]2 (10), oxo dimers 4 and 5, and dihydroxyl complexes M(OH)2[(i)PrNC(NMe2)N(i)Pr]2 (M = Zr, 11; Hf, 12). Similar MS analyses of the reaction of diethylamide guanidinate 3 with water in air show the formation of Zr(═O)[(i)PrNC(NEt2)N(i)Pr]2 (13), Zr(OH)2[(i)PrNC(NEt2)N(i)Pr]2 (14), 6, and {(Et2N)Zr[(i)PrNC(NEt2)N(i)Pr]2}(+) (15). Kinetic studies of the reaction between 1 and a continuous flow of 1.0 atm of O2 at 80-105 °C indicate that it follows pseudo-first-order kinetics with ΔH(‡) = 8.7(1.1) kcal/mol, ΔS(‡) = -54(3) eu, ΔG(‡)(358 K) = 28(2) kcal/mol, and a half-life of 213(1) min at 85 °C.

Unexpected formation of a trinuclear complex containing a Ta(IV)-Ta(IV) bond in the reactions of Bu(t)N=Ta(NMe2)3 with silanes.

A new trinuclear species containing a Ta(IV)-Ta(IV) bond, Ta(3)(µ-H)(µ-NMe(2))(µ=NBu(t))(2)(=NBu(t))(NMe(2))(5), has been formed by reductive elimination of H(2). Ta(2)H(2)(µ-NMe(2))(2)(NMe(2))(2)(=NBu(t))(2) has also been isolated. O(2) oxidizes the Ta(IV)-Ta(IV) bond to yield Ta(3)(µ(3)-O)(H)(µ=NBu(t))(µ-NMe(2))(2)(NMe(2))(4)(=NBu(t))(2) under ligand exchange. Delocalization of d electrons is discussed.

Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach.

ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.

Defining an inhibitory domain in the alpha-subunit of the epithelial sodium channel.

Epithelial sodium channels (ENaC) are processed by proteases as they transit the biosynthetic pathway. We recently observed that furin-dependent processing of the alpha-subunit of ENaC at two sites within its extracellular domain is required for channel activation due to release of a 26-residue inhibitory domain. While channels with alpha-subunits lacking the furin sites are not cleaved and have very low activity, channels lacking the furin consensus sites as well as the tract between these sites (alphaD206-R231) are active. We analyzed channels with a series of deletions in the tract alphaD206-R231 and lacking the alpha-subunit furin consensus sites in Xenopus laevis oocytes. We found an eight-residue tract that, when deleted, restored channel activity to the level found in oocytes expressing wild-type ENaC. A synthetic peptide, LPHPLQRL, representing the tract alphaL211-L218, inhibited wild-type ENaC expressed in oocytes with an IC(50) of 0.9 microM, and inhibited channels expressed in collecting duct cells and human primary airway epithelial cells with an IC(50)s of between approximately 50 and 100 microM. Analyses of peptides with deletions within this inhibitory tract indicate that eight residues is the minimal backbone length that is required for ENaC inhibition. Analyses of 8-mer peptides with conserved and nonconserved substitutions suggest that L(1), P(2), H(3), P(4), and L(8) are required for inhibitory activity. Our findings suggest that this eight-residue tract is a key conserved inhibitory domain that provides epithelial cells with a reserve of inactive channels that can be activated as required by proteases.