Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.

We describe a new template-based method for docking flexible ligands such as macrocycles to proteins. It combines Monte-Carlo energy minimization on the manifold, a fast manifold search method, with BRIKARD for complex flexible ligand searching, and with the MELD accelerator of Replica-Exchange Molecular Dynamics simulations for atomistic degrees of freedom. Here we test the method in the Drug Design Data Resource blind Grand Challenge competition. This method was among the best performers in the competition, giving sub-angstrom prediction quality for the majority of the targets.

Rigid Peptide Macrocycles from On-Resin Glaser Stapling.

Peptide macrocycles are widely utilized in the development of high affinity ligands, including stapled α-helices. The linear rigidity of a 1,3-diynyl linkage provides an optimal distance (7 Å) between ß-carbons of the i,i+4 amino acid side chains, thus suggesting its utility in stabilizing α-helical structures. Here, we report the development of an on-resin strategy for an intramolecular Glaser reaction between two alkyne-terminated side chains by using copper chloride, an essential bpy-diol ligand, and diisopropylethylamine at room temperature. The efficiency of this ligation was illustrated by the synthesis of (i,i+4)-, (i,i+5)-, (i,i+6)-, and (i,i+7)-stapled BCL-9 α-helical peptides using the unnatural amino acid propargyl serine. Overall, this procedurally simple method relies on inexpensive and widely available reagents to generate low molecular weight 23-, 26-, 29-, and 32-membered peptide macrocycles.

A "Motif-Oriented" Total Synthesis of Nannocystin Ax. Preparation and Biological Assessment of Analogues.

The highly cytotoxic cyclodepsipeptides of the nannocystin family are known to bind to the eukaryotic translation elongation factor 1α (EF-1α). Analysis of the docking pose, as proposed by a previous in silico study, suggested that the trisubstituted alkene moiety and the neighboring methyl ether form a domain that might be closely correlated with biological activity. This hypothesis sponsored a synthetic campaign which was designed to be "motif-oriented": specifically, a sequence of ring closing alkyne metathesis (RCAM) followed by hydroxy-directed trans-hydrostannation of the resulting cycloalkyne was conceived, which allowed this potentially anchoring substructure to be systematically addressed at a late stage. This inherently flexible approach opened access to nannocystin Ax (1) itself as well as to 10 non-natural analogues. While the biological data confirmed the remarkable potency of this class of compounds and showed that the domain in question is indeed an innate part of the pharmacophore, the specific structure/activity relationships can only partly be reconciled with the original in silico docking study; therefore, we conclude that this model needs to be carefully revisited.

Molecular Rearrangement of an Aza-Scorpiand Macrocycle Induced by pH: A Computational Study.

Rearrangements and their control are a hot topic in supramolecular chemistry due to the possibilities that these phenomena open in the design of synthetic receptors and molecular machines. Macrocycle aza-scorpiands constitute an interesting system that can reorganize their spatial structure depending on pH variations or the presence of metal cations. In this study, the relative stabilities of these conformations were predicted computationally by semi-empirical and density functional theory approximations, and the reorganization from closed to open conformations was simulated by using the Monte Carlo multiple minimum method.

Biological Characterization and in Vivo Assessment of the Activity of a New Synthetic Macrocyclic Antifungal Compound.

We recently identified a novel family of macrocyclic amidinoureas showing potent antifungal activity against Candida spp. In this study, we demonstrate the fungicidal effect of these compounds as well as their killing activity in a dose-dependent manner. Transcriptional analysis data indicate that our molecules induce a significant change in the transcriptome involving ATP binding cassette (ABC) transporter genes. Notably, experiments against Candida albicans mutants lacking those genes showed resistance to the compound, suggesting the involvement of ABC transporters in the uptake or intracellular accumulation of the molecule. To probe the mode of action, we performed fluorescence microscopy experiments on fungal cells treated with an ad-hoc synthesized fluorescent derivative. Fluorescence microscopy images confirm the ability of the compound to cross the membrane and show a consistent accumulation within the cytoplasm. Finally, we provide data supporting the in vivo efficacy in a systemic infection murine model setup with a drug-resistant strain of C. albicans.

Cyanide Scavenging by a Cobalt Schiff-Base Macrocycle: A Cost-Effective Alternative to Corrinoids.

The complex of cobalt(II) with the ligand 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]heptadeca-1(17)2,11,13,15-pentaene (CoN4[11.3.1]) has been shown to bind two molecules of cyanide in a cooperative fashion with an association constant of 2.7 (±0.2) × 10(5). In vivo, irrespective of whether it is initially administered as the Co(II) or Co(III) cation, EPR spectroscopic measurements on blood samples show that at physiological levels of reductant (principally ascorbate) CoN4[11.3.1] becomes quantitatively reduced to the Co(II) form. However, following addition of sodium cyanide, a dicyano Co(III) species is formed, both in blood and in buffered aqueous solution at neutral pH. In keeping with other cobalt-containing cyanide-scavenging macrocycles like cobinamide and cobalt(III) meso-tetra(4-N-methylpyridyl)porphine, we found that CoN4[11.3.1] exhibits rapid oxygen turnover in the presence of the physiological reductant ascorbate. This behavior could potentially render CoN4[11.3.1] cytotoxic and/or interfere with evaluations of the antidotal capability of the complex toward cyanide through respirometric measurements, particularly since cyanide rapidly inhibits this process, adding further complexity. A sublethal mouse model was used to assess the effectiveness of CoN4[11.3.1] as a potential cyanide antidote. The administration of CoN4[11.3.1] prophylactically to sodium cyanide-intoxicated mice resulted in the time required for the surviving animals to recover from "knockdown" (unconsciousness) being significantly decreased (3 ± 2 min) compared to that of the controls (22 ± 5 min). All observations are consistent with the demonstrated antidotal activity of CoN4[11.3.1] operating through a cyanide-scavenging mechanism, which is associated with a Co(II) → Co(III) oxidation of the cation. To test for postintoxication neuromuscular sequelae, the ability of mice to remain in position on a rotating cylinder (RotaRod test) was assessed during and after recovery. While intoxicated animals given CoN4[11.3.1] did recover ∼30 min more quickly than controls given only toxicant, there were no indications of longer-term problems in either group, as determined by continuing the RotaRod testing up to 24 h after the intoxications and routine behavioral observations for a further week.

Bayesian inference of conformational state populations from computational models and sparse experimental observables.

We present a Bayesian inference approach to estimating conformational state populations from a combination of molecular modeling and sparse experimental data. Unlike alternative approaches, our method is designed for use with small molecules and emphasizes high-resolution structural models, using inferential structure determination with reference potentials, and Markov Chain Monte Carlo to sample the posterior distribution of conformational states. As an application of the method, we determine solution-state conformational populations of the 14-membered macrocycle cineromycin B, using a combination of previously published sparse Nuclear Magnetic Resonance (NMR) observables and replica-exchange molecular dynamic/Quantum Mechanical (QM)-refined conformational ensembles. Our results agree better with experimental data compared to previous modeling efforts. Bayes factors are calculated to quantify the consistency of computational modeling with experiment, and the relative importance of reference potentials and other model parameters.

Tuning photoinduced processes of covalently bound isoalloxazine and anthraquinone bichromophores.

We present here the synthesis of several new isoalloxazine cyclophanes containing electroactive anthraquinones linked by aliphatic chains of different lengths. Such structural changes provide different interchromophoric orientations leading to the tuning of the rate of the photoinduced electron transfer process from the anthraquinone unit towards the isoalloxazine singlet excited state. Molecular modelling studies were undertaken in order to determine the minimal energy of the proposed structures using Monte Carlo calculations (Amber, Macromodel v.8.1). The compounds have been fully characterised by NMR spectroscopy and the solid state structures of some of the macrocycles have been elucidated. The photophysical studies have been carried out in order to investigate the influence of π-π stacking on the optical properties of the macrocycles.

A liquid-liquid extraction procedure followed by a low temperature purification step for the analysis of macrocyclic lactones in milk by liquid chromatography-tandem mass spectrometry and fluorescence detection.

In this work a method is proposed and demonstrated for the analysis of the macrocyclic lactones abamectin, doramectin, eprinomectin, ivermectin and moxidectin in bovine milk by liquid chromatography coupled to mass spectrometry (LC-MS/MS) and liquid chromatography with fluorescence detection (LC-FL). The method is based on liquid-liquid extraction followed by a low temperature purification (LLE-LTP) step. Moreover, the proposed method was validated according to the Commission Decision 2002/657/EC, using LC-MS/MS and LC-FL for confirmatory and quantitative analysis, respectively. For LC-MS/MS the recovery rates observed ranged from 101.2 to 141.6% with coefficient of variation from 2.6 to 19.8%. For LC-FL the recovery rates observed ranged from 100.2 to 105% and coefficient of variations from 2.9 to 8.8%. Matrix effects were negligible due to the low temperature purification step. The quantification limits were far below the maximum limits established by regulations of all countries consulted. The proposed method proved to be simple, easy, and adequate for high-throughput analysis of a large number of samples per day at low cost.

LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops.

We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is based on perturbing an existing conformation along a molecular dynamics trajectory using initial atomic velocities with kinetic energy concentrated on the low-frequency vibrational modes, followed by energy minimization. A novel Chebyshev polynomial filter is used to heavily dampen the high-frequency components of a randomly generated Maxwell-Boltzmann velocity vector. The method is very efficient, even for large systems; it is straightforward to implement and requires only standard force-field energy and gradient evaluations. The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks.

Terbium-macrocycle complexes as chemical sensors: detection of an aspirin metabolite in urine using a salicylurate-specific receptor site.

Salicylurate (SU) is the major metabolite in urine of acetylsalicylic acid (aspirin) and can be used as a metric to monitor aspirin pharmacokinetics and as an indicator of appendicitis, anemia, and liver disease. Detection in urine and plasma currently requires solvent extraction or other sample handling prior to analysis. We present a simple method to quantify SU in urine via chelation to a terbium binary complex with the macrocycle 1,4,7,10-tetraazacyclododecane-1,7-bisacetate (DO2A). Binding of SU to form the [Tb(DO2A)(SU)](-) ternary complex triggers intense luminescence under UV excitation due to an absorbance-energy transfer-emission mechanism. Here we report characterization of the [Tb(DO2A)(SU)](-) ternary complex and application of this sensitized lanthanide luminescence method to quantify SU in urine samples following a low-dose aspirin regimen.

Spectral properties of self-assembled squaraine-tetralactam: a theoretical assessment.

Using several theoretical approaches relying on the time-dependent density functional theory, we have computed the electronic spectrum in the visible range of a squaraine dye, either isolated or embedded into a tetralactam macrocycle. The amplitude of the bathochromic displacement induced by the complexation is well-reproduced by the most accurate models. This total shift is split into specific components, allowing us to unravel the most-important contributions (geometry modifications, polarisations...). This study constitutes a further step in the investigation of environmental effects on dyes' absorption spectra.

Examination of the structural features that favor the columnar self-assembly of bis-urea macrocycles.

Second-generation self-assembling bis-urea macrocycles were designed that form columnar structures in the solid state. The new macrocycles were constructed from more flexible building blocks yielding greater solubility and a more efficient synthesis. In addition, heteroatoms in the form of ether oxygens were incorporated in the walls of the macrocycles to provide additional recognition sites for guest encapsulation. We observed reduced fidelity of the stacking motif and in some cases the intermolecular urea-urea hydrogen bonds were disrupted by the formation of intramolecular hydrogen bonds. We also observed new offset assembly motifs that maintained the urea-urea interaction. These results suggest that the stacking of the arene units in the rigid first-generation systems was an important factor in guiding the formation of the columnar stacks.

Assessment of macrocyclic triamine ligands as synthons for organometallic 99mTc radiopharmaceuticals.

In a search of coordination molecules suitable to the fac-{(99m)Tc(CO)3}(+) core as a synthon for (99m)Tc-radiopharmaceuticals, nonradioactive rhenium complexes of two macrocyclic triamine compounds with different chelate ring structures, 1,4,7-triazacyclononane (9N3) and 1,5,9-triazacyclododecane (12N3), were synthesized and characterized. (99m)Tc-labeled 9N3 and 12N3 compounds were also prepared using [(99m)Tc(OH 2)3(CO)3](+) and were characterized by both in vitro and in vivo studies. 9N3 produced a single rhenium complex, whereas 12N3 generated two major complexes. The crystallographic data and infrared absorption wavenumber assigned to the C-O stretch suggested that the coordination geometry of 9N3 would be more suitable to fac-{Re(CO)3}(+) than that of 12N3. In contrast, both 9N3 and 12N3 provided a single (99m)Tc-labeled compound. However (99m)Tc-labeled 9N3 exhibited higher stability than (99m)Tc-labeled 12N3 in rat plasma and in the presence of histidine at an elevated temperature. In biodistribution studies, both (99m)Tc-labeled compounds did not show any specific accumulation of radioactivity in any organs except for the excretory organs such as the liver and kidney. These findings showed that 9N3 would constitute a macrocyclic chelating molecule of choice to prepare (99m)Tc radiopharmaceuticals using a fac-{(99m)Tc(CO)3}(+) core.

X-ray diffraction and theoretical studies for the quantitative assessment of intermolecular arene-perfluoroarene stacking interactions.

The arene-perfluoroarene stacking interaction was studied by experimental and theoretical methods. A series of compounds with different possibilities for formation of this recognition motif in the solid state were synthesized, and their crystal structures determined by single-crystal X-ray diffraction. The crystal packing of these compounds, as well as the packing of related compounds retrieved from crystallographic databases, were analyzed with quantitative crystal potentials: total lattice energies and the cohesive energies of closest molecular pairs in the crystals were calculated. The arene-perfluoroarene recognition motif emerges as a dominant interaction in the non-hydrogen-bonding compounds studied here, to the point that asymmetric dimers formed over the stacking motif carry over to asymmetric units made of two molecules in the crystal both for pure compounds and for molecular complexes; however, inter-ring distances and angles range from 3.70 to 4.85 A and from 5 to 21 degrees , respectively. Pixel energy partitioning reveals that whenever aromatic rings stack, the largest cohesive energy contribution comes from dispersion, which roughly amounts to 20 kJ mol(-1) per phenyl ring, while the coulombic term is minor but significant enough to make a difference between the arene-arene or perfluoroarene-perfluoroarene interactions on the one hand, and arene-perfluoroarene interactions on the other, whereby the latter are favored by about 10 kJ mol(-1) per phenyl ring. No evidence of special interaction which can be attributed to HF confrontation was recognizable.