Spatial structure of cyclosporin A and insight into its flexibility

Bio-synthesis, purification and structural analysis of Cyclosporine-A produced by Tolypocladium inflatum with valorization of agro-industrial wastes

Cyclosporine A (CyA) holds significant importance as a strategic immunosuppressive drug for organ transplant patients. In this study, we aimed to produce pure and cost-effective Cyclosporine A (CyA) by fermenting a culture medium containing dairy sludge, using Tolypocladium inflatum PTCC 5253. Following the fermentation stage, ethyl acetate extraction and fast protein liquid chromatography were employed for sample purification. The initial evaluation of the effectiveness of CyA obtained from these processes was performed through bioassay, wherein the antimicrobial clear zone diameter was found to be larger compared to the sample obtained from the fermentation culture. The concentration of CyA was determined using high-performance liquid chromatography, yielding values of 334 mg/L, 456 mg/L, and 578 mg/L for the fermented, extracted, and purified samples, respectively. Further analysis utilizing liquid chromatography tandem mass spectrometry (LC/MS/MS) confirmed a purity of 91.9% and proper agreement with the standard sample based on the ion intensity of Z/m 1205. To validate the structure of CyA, nuclear magnetic resonance spectroscopy, Fourier-transform infrared (FT-IR), and Raman spectroscopy were employed. X-ray diffraction and differential scanning calorimetry analyses demonstrated that the purified CyA exhibited a crystal structure similar to the standard sample, characterized by two broad peaks at 2θ = 9° and 20°, and comparable glass transition temperatures (57-68 °C for the purified sample; 53-64 °C for the standard sample). Dynamic light scattering analysis confirmed a uniform particle size distribution in both the purified and standard samples. The zeta potentials of the purified and standard samples were determined to be - 25.8 ± 0.16 and - 23.63 ± 0.12 mV, respectively. Our results demonstrate that dairy sludge can serve as a suitable culture medium for the production of (CyA).

Cis-trans isomerization in cyclosporin C dissolved in acetonitrile

Cyclosporin is an 11-amino acid cyclic peptide with pharmacologically valuable properties which has a variety of actual and potential applications. Its activity relies on the cell membrane permeability which, in turn, depends on the structure of cyclosporin and its ability to change the conformation. In this work, conformational exchange processes occurring in cyclosporin C were studied using one- and two-dimensional nuclear magnetic resonance spectroscopy. The free energy barrier separating two major conformers observed in polar solution (acetonitrile) was found to be 77 ± 2 kJ/mol. Less populated conformation states are also present in the solution, which agrees with the ease of formation of multiple forms revealed by MD simulations of cyclosporin C.

Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets

Establishing a technological platform for creating clinical compounds inhibiting intracellular protein-protein interactions (PPIs) can open the door to many valuable drugs. Although small molecules and antibodies are mainstream modalities, they are not suitable for a target protein that lacks a deep cavity for a small molecule to bind or a protein found in intracellular space out of an antibody's reach. One possible approach to access these targets is to utilize so-called middle-size cyclic peptides (defined here as those with a molecular weight of 1000-2000 g/mol). In this study, we validated a new methodology to create oral drugs beyond the rule of 5 for intracellular tough targets by elucidating structural features and physicochemical properties for drug-like cyclic peptides and developing library technologies to afford highly N-alkylated cyclic peptide hits. We discovered a KRAS inhibitory clinical compound (LUNA18) as the first example of our platform technology.

Co(III)-tetra(4-sulfonatophenyl)porphyrin complexes with bidentate ligands in aqueous buffer media

The processes of hydrophilic Co(III)-tetra(4-sulfonatophenyl)porphyrin supramolecular assembly with 4,4-bipyridyl in aqueous buffer media have been studied by UV-vis, 1D and 2D 1H NMR-spectroscopy. In the case of 1,4-diazabicyclo[2.2.2]octane, pyrazine and piperazine in aqueous solutions, no assembly was observed. Interactions of the hydrophilic Co(III)-tetraarylporphyrin with ionic micelles (cationic surfactants with different alkyl tail lengths) in buffer media were investigated. These studies were performed by the UV-vis, 1D NOESY-spectroscopy and dynamic lightscattering (DLS) methods. The metalloporphyrins were incorporated into the hydrophobic part of micelles, which led to Co(III) reduction to Co(II) in the Co-porphyrinate composition. The rate of Co(III) reduction accompanied by detachment of additional ligands coordinated on Co(III)-porphyrins or disruption of supramolecular dimers and depends on the surfactant concentration and nature. The results obtained indicate the possibility of creating supramolecular porphyrin-based assemblies with the preprogrammed lifetime (from several hours to several days) and could be used in the creation of host-guest systems for recognition, selective binding and the prolonged release of bioactive substrates as the means in the designing of biomimetic systems with effective binding affinities to heterocycles, DNA base pairs and RNA.

Cyclosporin A: Conformational Complexity and Chameleonicity

The chameleonic behavior of cyclosporin A (CsA) was investigated through conformational ensembles employing multicanonical molecular dynamics simulations that could sample the cis and trans isomers of N-methylated amino acids; these assessments were conducted in explicit water, dimethyl sulfoxide, acetonitrile, methanol, chloroform, cyclohexane (CHX), and n-hexane (HEX) using AMBER ff03, AMBER10:EHT, AMBER12:EHT, and AMBER14:EHT force fields. The conformational details were discussed employing the free-energy landscapes (FELs) at T = 300 K; it was observed that the experimentally determined structures of CsA were only a part of the conformational space. Comparing the ROESY measurements in CHX-d12 and HEX-d14, the major conformations in those apolar solvents were essentially the same as that in CDCl₃ except for the observation of some sidechain rotamers. The effects of the metal ions on the conformations, including the cis/trans isomerization, were also investigated. Based on the analysis of FELs, it was concluded that the AMBER ff03 force field best described the experimentally derived conformations, indicating that CsA intrinsically formed membrane-permeable conformations and that the metal ions might be the key to the cis/trans isomerization of N-methylated amino acids before binding a partner protein.

Cyclosporin Structure and Permeability: From A to Z and Beyond

Cyclosporins are natural or synthetic undecapeptides with a wide range of actual and potential pharmaceutical applications. Several members of the cyclosporin compound family have remarkably high passive membrane permeabilities that are not well-described by simple structural metrics. Here we review experimental studies of cyclosporin structure and permeability, including cyclosporin-metal complexes. We also discuss models for the conformation-dependent permeability of cyclosporins and similar compounds. Finally, we identify current knowledge gaps in the literature and provide recommendations regarding future avenues of exploration.

Gradient selected pure shift EASY-ROESY techniques facilitate the quantitative measurement of 1H,1H-distance restraints in congested spectral regions

For elucidating molecular structure and dynamics in solution, NMR experiments such as NOESY, ROESY and EXSY have been used excessively over the past decades, to provide interatomic distance restraints or rates for chemical exchange. The extraction of such information, however, is often prohibited by signal overlap in these spectra. To reduce this problem, pure shift methods for improving the spectral resolution have become popular. We report on pure shift EASY-ROESY experiments and their application to extract cross-relaxation rates, proton-proton distances and exchange rates. Homonuclear decoupling (pure shift) is applied in the indirect dimension using the PSYCHE or the perfectBASH technique, to enhance the spectral resolution of severely overcrowded spectral regions. The spectral quality is further improved by using a gradient selected F1-PSYCHE-EASY-ROESY, which produces significantly less t₁-noise than the experiment used previously, as also demonstrated by employing the recently introduced SAN (signal-artefact-noise) plots. Applications include the quantification of distance restraints in a peptide organocatalyst and the extraction of a number of distance restraints in cyclosporine A, which were previously not available for analysis, because they were either located in overcrowded spectral regions or hidden under t₁-noise. Distances extracted and exchange rates obtained are accurate. Also, the 2D gradient-selected F1-perfectBASH-EASY-ROESY with the additional gradient selection proposed herein, which is superior in terms of sensitivity, can be used to accurately quantify cross-relaxation.

Exposing Hidden Conformations of Carbamazepine Appearing Due to Interaction With the Solid Phase by 2D 1H-15N HMBC NMR Spectroscopy

Two-dimensional ¹H-¹⁵N HMBC NMR spectra of the well-known anticonvulsant carbamazepine dissolved in different organic solvents, recorded on an NMR spectrometer prove the existence of hidden conformers in saturated solutions. Obtained conformer distribution arises due to the presence of the solid phase in saturated solution. A weak influence of ring currents was revealed for different molecular conformations of carbamazepine dissolved in a saturated solution, which provides a simple approach to discovering hidden conformations. Hidden conformers were found in three different solvents: dimethyl sulfoxide, chloroform, and dichloromethane.

Cyclic Peptide Design Guided by Residual Dipolar Couplings, J-Couplings, and Intramolecular Hydrogen Bond Analysis

Cyclic peptides have long tantalized drug designers with their potential ability to combine the best attributes of antibodies and small molecules. An ideal cyclic peptide drug candidate would be able to recognize a protein surface like an antibody while achieving the oral bioavailability of a small molecule. It has been hypothesized that such cyclic peptides balance permeability and solubility using their solvent-dependent conformational flexibility. Herein we report a conformational deconvolution NMR methodology that combines residual dipolar couplings, J-couplings, and intramolecular hydrogen bond analysis along with conformational analysis using molecular dynamics simulations and density functional theory calculations for studying cyclic peptide conformations in both low-dielectric solvent (chloroform) and high-dielectric solvent (DMSO) to experimentally study the solvent-dependent conformational change hypothesis. Taken together, the combined experimental and computational approaches can illuminate conformational ensembles of cyclic peptides in solution and help identify design opportunities for better permeability.

RDC-enhanced structure calculation of a β-heptapeptide in methanol

Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β-peptide with proteinogenic side chains in methanol. ¹ D_CH , ¹ D_NH , and ² D_HH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long-range definition in the backbone of the resulting 3₁₄ -helix and uncovers side-chain mobility. Experimental side-chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three-state model. Copyright © 2016 John Wiley & Sons, Ltd.

N-Confused porphyrins: complexation and 1H NMR studies

The complexation of 2-aza-21-carba-tetraphenylporphyrin and 2-aza-2-methyl-5,10,15,20-tetraphenyl-21-carbaporphyrin with nickel and zinc acetates in organic solvents has been investigated by UV-Vis spectroscopy and ¹H NMR.

Synthesis of a new quaternary phosphonium salt: NMR study of the conformational structure and dynamics

A novel phosphonium salt based on pyridoxine was synthesized. Conformational analysis of the compound in solution was performed using dynamic NMR experiments and calculations. The obtained results revealed some differences in the conformational transitions and the energy parameters of the conformational exchange of the studied compound in comparison to previously reported data for other phosphorus-containing pyridoxine derivatives. It was shown that increasing the substituent at the C-11 carbon leads to greater differences in the populations of stable states and the corresponding equilibrium energies. Copyright © 2015 John Wiley & Sons, Ltd.

Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products

Many cyclic peptide natural products are larger and structurally more complex than conventional small molecule drugs. Although some molecules in this class are known to possess favorable pharmacokinetic properties, there have been few reports on the membrane permeabilities of cyclic peptide natural products. Here, we present the passive membrane permeabilities of 39 cyclic peptide natural products, and interpret the results using a computational permeability prediction algorithm based on their known or calculated 3D conformations. We found that the permeabilities of these compounds, measured in a parallel artificial membrane permeability assay, spanned a wide range and demonstrated the important influence of conformation on membrane permeability. These results will aid in the development of these compounds as a viable drug paradigm.