Macrocycles: lessons from the distant past, recent developments, and future directions

End-to-End Backbone Cyclization Enhances Passive Permeability of bRo5 Oligomeric Depsipeptides with Nonlinear Size Dependence

A majority of drugs are small molecules that satisfy Lipinski's Rule-of-Five (Ro5), but efforts to target topologically complex biomolecular interactions have reignited interest in nonconforming molecular therapeutics, dubbed "beyond Ro5 (bRo5)". Broadly useful design principles for bRo5 molecules are few in number, although several studies have highlighted the benefit to bioavailability and proteolytic stability that can result from the introduction of a constraining ring into conformationally mobile peptides. Here we show that a linear oligomeric depsipeptide (OD) template can be leveraged to link size to permeability, while the corresponding cyclic oligomeric depsipeptide (COD) series is used to determine the impact of cyclization as an added conformational constraint. Unexpectedly, certain macrocycle sizes confer a greater benefit to permeability than others.

Unifying principles for the design and evaluation of natural product-inspired compound collections

Natural products play a major role in the discovery of novel bioactive compounds. In this regard, the synthesis of natural product-inspired and -derived analogues is an active field that is further developing. Several strategies and principles for the design of such compounds have been developed to streamline their access and synthesis. This perspective describes how individual strategies or their elements can be combined depending on the project goal. Illustrative examples are shown that demonstrate the blurred lines between approaches and how they can work in concert to discover new biologically active molecules. Lastly, a general set of guidelines for choosing an appropriate strategy combination for the specific purpose is presented.

Expanding the Repertoire of Large Scaffolds with Syn and Anti Macrocyclic Metacyclophanes

Understanding how changes in structure translate to changes in molecular shape is key to catalyst optimization and molecular design in medicinal chemistry and materials. One key contributor to the molecular shape is the relative orientation of substituents on a scaffold. Macrocyclic metacyclophanes display their two arenes in a parallel or antiparallel fashion, resulting in anti or syn conformations that lead to disparate relative orientations of the aryl substituents. This work reports the synthesis of new 14- and 16-membered metacyclophanes and the elucidation of their anti/syn preferences by 1H NMR and computational conformational analysis. Most metacyclophanes studied herein display a strong anti or syn preference and, thus, have well-defined substituent orientations. We propose that anti/syn conformational preferences arise from the minimization of torsional strain along the backbone of the macrocycle, which leads to the prediction that metacyclophanes with remote aryl substituents will adopt the same conformation as their unsubstituted counterparts. Exit vector analysis also reveals that anti-metacyclophanes project their substituents into regions in three-dimensional space that are not accessed by other common large scaffolds, e.g., [2.2]paracyclophanes and ferrocenes. This work also demonstrates how ring size and functional groups, two parameters commonly optimized in macrocycle design, can be used to tune molecular shape.

Understanding the binding mechanisms of hydroxy-chalcone-based 24-membered macrocyclic bis-epoxide with beta-lactoglobulin

The lipocalin carrier protein, β-lactoglobulin (β-lg), stands out as a crucial protein in the food industry, known for its ability to effectively bind with hydrophobic small molecules. However, it was unclear how β-lg interacts with macrocyclic molecules. In this research, we focused on two key aspects. First, we synthesized a 24-membered macrocycle 4d by modifying a natural product chalcone to create a macrocycle by connecting two ortho-hydroxyl groups of each phenyl ring of two chalcone units with alkyl chains. To enhance solubility, we converted the chalcone CC bonds to epoxide rings. Second, we investigated the binding ability and mechanism of binding of the compound with the β-lg. The β-lg and 4d interaction shows an isoemissive point at 382 nm with Kb = 4.64 ± 0.02 × 105 at 298 K, indicating the excellent protein binding ability of 4d. Remarkably, despite its size, 4d binds to the protein without altering its conformation, suggesting the availability of a spacious binding site on the protein where the molecule fits well. Molecular docking analysis confirmed the presence of such a site at the mouth of the calyx. Additionally, our 200 ns molecular dynamics simulation demonstrated that 4d adopts a conformation to interact with the hydrophobic amino acids of the binding site, ultimately stabilizing the protein.

The effect of gem-difluorination on the conformation and properties of a model macrocyclic system

Conformational control of drug candidates to engineer improved potency and ADME properties is an ongoing area of research. Macrocyclic rings tend to offer a greater degree of rigidity than non-cyclised small molecules, and, as a result they are perfect platforms to instil conformational controls. In this study, the difluoroalkoxyphenyl moiety is examined as a tool to alter the conformation of macrocycles. A fluorinated and non-fluorinated macrocyclic matched pair is compared in terms of conformation preferences and related ADME properties. The synthesised macrocycles are found to give similar major conformations exhibiting a trans amide in the macrocyclic backbone. However, for the fluorinated macrocycle, the major trans amide conformation is in equilibrium with a cis amide minor conformation, seen by 1H NMR in a 4 : 1 ratio of trans/cis. The conformational fits for the minor fluorinated isomer demonstrate the out of plane preference of the difluoroalkoxy system encouraging the amide within the macrocycle backbone to adopt a cis conformation. The fluorinated macrocycle was less metabolically stable compared to the non-fluorinated, postulated to be a result of the interconversion of trans amide to the cis amide, which potentially could be more readily metabolised.

Facile synthesis of a new chiral polyimine macrocycle and its application for enantioseparation in high-performance liquid chromatography

Macrocyclic compounds such as crown ethers and cyclodextrins play an important role in the field of chromatography and show excellent separation performance. The design of simple and convenient methods for the efficient synthesis of novel chiral macrocycles for chromatographic separation is of great significance. In this work, a novel chiral polyimine macrocycle (PIMC) was designed and synthesized by the simply one-step reaction of 2,6-diformyl-4-tert-butylphenol with (S)-(-)-1,2-propanediamine. Then, it was bonded onto silica by the thiol-ene click reaction to construct a new chiral stationary phase (CSP) for high-performance liquid chromatography (HPLC). The chiral separation performance of the proposed CSP was examined by separating various racemates in the normal-phase (NP) and reversed-phase (RP) HPLC. In total, twelve and nine racemates, including ethers, esters, amines, alcohols, organic acids, ketones, and epoxides, were separated to varying degrees via NP-HPLC and RP-HPLC, respectively, Moreover, the CSP offered good chiral separation complementarity to Chiralcel OD-H and Chiralpak AD-H columns for resolution of these test racemates, and it can separate several racemic compounds that either cannot be separated or cannot be separated well be separated by the two commercially available columns. After the column was used for hundreds of injections, the relative standard deviations of the retention time and resolution were below 0.56 % and 0.45 %, respectively, showing the good reproducibility and stability of the CSP. This study provides a simple and convenient approach to synthesize a novel chiral macrocycle and CSP and also indicates the broad application prospects of such chiral PIMCs in HPLC chiral separation.

Understanding mechanisms of negative food effect for voclosporin using physiologically based pharmacokinetic modeling

Negative food effect refers to a reduction in bioavailability, when a drug is taken with food. Voclosporin, a highly lipophilic cyclic peptide drug for treatment of active lupus nephritis, has shown negative food effect in clinical trials. Here, the cause of the negative food effect of voclosporin was investigated using physiologically based pharmacokinetic (PBPK) modeling to understand the mechanism responsible for oral absorption of voclosporin. Voclosporin is a substrate for P-glycoprotein and CYP3A4, and it has been evaluated for intestinal membrane permeability in human induced pluripotent stem cell-derived intestinal epithelial cells (hiPSC-IECs). The membrane permeability in hiPSC-IECs is integrated into the PBPK model for simulating permeability accurately. The PBPK model simulated the systemic PK profile in fasted state in human. Then, the PBPK model with in vitro adsorption of voclosporin onto food simulated the systemic PK profile in fed state for food effect. In addition, the PBPK model for rats also simulated the plasma profile of voclosporin for the food effect. These results suggest that a possible cause of the negative food effect of voclosporin is the adsorption of voclosporin to food in gastrointestinal tract. These approaches could facilitate understanding of the mechanisms responsible for oral absorption of cyclic peptides.

Alder-ene reactions of arynes to form medium-sized and macrocyclic frameworks of sizes up to a 46-membered ring

Macrocyclization via the intramolecular Alder-ene reaction of arynes to construct carbo- and hetero-macrocycles fused with an indoline or isoindoline moiety is described. By installing ether, ester, alkene, and cyclic tethers at an appropriate location between the aryne and the ene donor, macrocycles up to a 46-membered ring could be constructed.

Macrocyclic-based strategy in drug design: From lab to the clinic

Macrocyclic compounds have emerged as potent tools in the field of drug design, offering unique advantages for enhancing molecular recognition, improving pharmacokinetic properties, and expanding the chemical space accessible to medicinal chemists. This review delves into the evolutionary trajectory of macrocyclic-based strategies, tracing their journey from laboratory innovations to clinical applications. Beginning with an exploration of the defining structural features of macrocycles and their impact on drug-like characteristics, this discussion progresses to highlight key design principles that have facilitated the development of diverse macrocyclic drug candidates. Through a series of illustrative representative case studies from approved macrocyclic drugs and candidates spanning various therapeutic areas, particular emphasis is placed on their efficacy in targeting challenging protein-protein interactions, enzymes, and receptors. Additionally, this review thoroughly examines how macrocycles effectively address critical issues such as metabolic stability, oral bioavailability and selectivity. Valuable insights into optimization strategies employed during both approved and clinical phases underscore successful translation of promising leads into efficacious therapies while providing valuable perspectives on harnessing the full potential of macrocycles in drug discovery and development endeavors.

Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents

Macrocycles are a promising class of compounds as therapeutics for difficult drug targets due to a favorable combination of properties: They often exhibit improved binding affinity compared to their linear counterparts due to their reduced conformational flexibility, while still being able to adapt to environments of different polarity. To assist in the rational design of macrocyclic drugs, there is need for computational methods that can accurately predict conformational ensembles of macrocycles in different environments. Molecular dynamics (MD) simulations remain one of the most accurate methods to predict ensembles quantitatively, although the accuracy is governed by the underlying force field. In this work, we benchmark four different force fields for their application to macrocycles by performing replica exchange with solute tempering (REST2) simulations of 11 macrocyclic compounds and comparing the obtained conformational ensembles to nuclear Overhauser effect (NOE) upper distance bounds from NMR experiments. Especially, the modern force fields OpenFF 2.0 and XFF yield good results, outperforming force fields like GAFF2 and OPLS/AA. We conclude that REST2 in combination with modern force fields can often produce accurate ensembles of macrocyclic compounds. However, we also highlight examples for which all examined force fields fail to produce ensembles that fulfill the experimental constraints.

Albumin host for supramolecular fluorescence recognition

Synthetic molecular sensors are crucial for real-time monitoring in biological systems and biotechnological applications, where detecting targets amidst potential interferents is essential. This task is particularly challenging in competitive environments that lacking chemically reactive functional groups, common in agricultural, biological, and environmental contexts. Consequently, scientific efforts have focused on developing sensitive and rapid analytical techniques, with fluorescent sensors emerging as prominent tools. Among these, the albumin-based supramolecular fluorescent indicator displacement assay (AS-FIDA) represents a significant advancement. Our research group has extensively contributed to this field, demonstrating the practical utility of various AS-FIDAs. We pioneered the use of albumin (ALB) as a host molecule in these synthetic chemical sensors, marking a notable advancement. AS-FIDA employs ALB as a versatile host molecule with multiple flexible and asymmetrical binding pockets capable of forming complexes with guest dyes, resulting in ALB@dye ensembles tailored for specific analyte recognition. Recent advancements in AS-FIDA have significantly expanded its applications. This review explores recent advances in ALB-based supramolecular sensors and sensor arrays for detecting biologically and environmentally significant molecules, such as pesticides, hormones, biomarkers, reactive species, mycotoxins, drugs, and carcinogens. The versatility of AS-FIDA positions it as a valuable tool in diverse settings, from laboratory research to practical applications in portable devices, smartphone-assisted on-site monitoring, imaging of living cells, and real sample analysis.

Macrocyclic receptors for anion recognition

Macrocyclic receptors have emerged as versatile and efficient molecular tools for the recognition and sensing of anions, playing a pivotal role in molecular recognition and supramolecular chemistry. The following review provides an overview of the recent advances in the design, synthesis, and applications of macrocyclic receptors specifically tailored for anion recognition. The unique structural features of macrocycles, such as their well-defined structures and pre-organised binding sites, contribute to their exceptional anion-binding capabilities that have led to their application across a broad range of the chemical and biological sciences.

Molecular complexity as a driving force for the advancement of organic synthesis

The generation of molecular complexity is a primary goal in the field of synthetic chemistry. In the context of retrosynthetic analysis, the concept of molecular complexity is central to identifying productive disconnections and the development of efficient total syntheses. However, this field-defining concept is frequently invoked on an intuitive basis without precise definition or appreciation of its subtleties. Methods for quantifying molecular complexity could prove useful for characterizing the state of synthesis in a more rigorous, reliable and reproducible fashion. As a first step to evaluating the importance of these methods to the state of the field, here we present our perspective on the development of molecular complexity quantification and its implications for chemical synthesis. The extension and application of these methods beyond computer-aided synthesis planning and medicinal chemistry to the traditional practice of 'complex molecule' synthesis could have the potential to unearth new opportunities and more efficient approaches for synthesis.

Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments

Small molecule ligands exhibit a diverse range of conformations in solution. Upon binding to a target protein, this conformational diversity is generally reduced. However, ligands can retain some degree of conformational flexibility even when bound to a receptor. In the Protein Data Bank (PDB), a small number of ligands have been modeled with distinct alternative conformations that are supported by X-ray crystallography density maps. However, the vast majority of structural models are fit to a single ligand conformation, potentially ignoring the underlying conformational heterogeneity present in the sample. We previously developed qFit-ligand to sample diverse ligand conformations and to select a parsimonious ensemble consistent with the density. While this approach indicated that many ligands populate alternative conformations, limitations in our sampling procedures often resulted in non-physical conformations and could not model complex ligands like macrocycles. Here, we introduce several improvements to qFit-ligand, including the use of routines within RDKit for stochastic conformational sampling. This new sampling method greatly enriches low energy conformations of small molecules and macrocycles. We further extended qFit-ligand to identify alternative conformations in PanDDA-modified density maps from high throughput X-ray fragment screening experiments. The new version of qFit-ligand improves fit to electron density and reduces torsional strain relative to deposited single conformer models and our previous version of qFit-ligand. These advances enhance the analysis of residual conformational heterogeneity present in ligand-bound structures, which can provide important insights for the rational design of therapeutic agents.

An analysis of the physicochemical properties of oral drugs from 2000 to 2022

Calculable physicochemical descriptors are a useful guide to assist compound design in medicinal chemistry. It is well established that controlling size, lipophilicity, hydrogen bonding, flexibility and shape, guided by descriptors that approximate to these properties, can greatly increase the chances of successful drug discovery. Many therapeutic targets and new modalities are incompatible with the optimal ranges of these properties and thus there is much interest in approaches to find oral drug candidates outside of this space. These considerations have been a focus for a while and hence we analysed the physicochemical properties of oral drugs approved by the FDA from 2000 to 2022 to assess if such concepts had influenced the output of the drug-discovery community. Our findings show that it is possible to find drug molecules that lie outside of the optimal descriptor ranges and that large molecules in particular (molecular weight >500 Da) can be oral drugs. The analysis suggests that this is more likely if lipophilicity, hydrogen bonding and flexibility are controlled. Crude physicochemical descriptors are useful in that regard but more accurate and robust means of understanding substructural classes, shape and conformation are likely to be required to improve the chances of success in this space.

Recent Progress on Transition Metal Catalyzed Macrocyclizations Based on C-H Bond Activation at Heterocyclic Scaffolds

Macrocycles are essential in protein-protein interactions and the preferential intake of bioactive scaffolds. Macrocycles are commonly synthesized by late-stage macrolactonizations, macrolactamizations, transition metal-catalyzed ring-closing metathesis, S-S bond-forming reactions, and copper-catalyzed alkyne-azide cycloaddition. Recently, transition metal-catalyzed C-H activation strategies have gained significant interest among chemists to synthesize macrocycles. This article provides a comprehensive overview of the transition metal-catalyzed macrocyclization via C-H bond functionalization of heterocycle-containing peptides, annulations, and heterocycle-ring construction through direct C-H bond functionalization. In the first part, palladium salt catalyzed coupling with indolyl C(sp3)-H and C(sp2)-H bonds for macrocyclization is reported. The second part summarizes rhodium-catalyzed macrocyclizations via site-selective C-H bond functionalization. Earth-abundant, less toxic 3d metal salt Mn-catalyzed cyclizations are reported in the latter part. This summary is expected to spark interest in emerging methods of macrocycle production among organic synthesis and chemical biology practitioners, helping to develop the discipline. We hope that this mini-review will also inspire synthetic chemists to explore new and broadly applicable C-C bond-forming strategies for macrocyclization via intramolecular C-H activation.

Preparation and evaluation of a 1,1'-bi-2-naphthol-based chiral macrocycle bonded silica chiral stationary phase for high performance liquid chromatography

Macrocycles play vital roles in supramolecular chemistry and chromatography. 1,1'-Bi-2-naphthol (BINOL)-based chiral polyimine macrocycles are an emerging class of chiral macrocycles that can be constructed by one-step aldehyde-amine condensation of BINOL derivatives with other building blocks. These macrocycles exhibit good characteristics, such as facile preparation, rigid cyclic structures, multiple chiral centers, and defined molecular cavities, that make them good candidates as new chiral recognition materials for chromatographic enantioseparations. In this study, a BINOL-based [2+2] chiral polyimine macrocycle was synthesized by one-step condensation of enantiopure (S)-2,2'-dihydroxy-[1,1'-binaphthalene]-3,3'-dicarboxaldehyde with (1R,2R)-1,2-diaminocyclohexane. The product was modified with 5-bromo-1-pentene and then attached to thiolated silica using click chemistry to construct a new chiral stationary phase (CSP). The enantioselectivity of the new CSP was explored by separating various racemates under normal phase (NP) and reversed phase (RP) high performance liquid chromatography (HPLC). Thirteen racemates and eight racemates were enantioseparated under the two separation modes, respectively, including chiral alcohols, phenols, esters, ketones, amines, and organic acids. Among them, nine racemates achieved baseline separation under NP-HPLC and seven racemates achieved baseline separation under RP-HPLC. High resolution separation was observed with benzoin (Rs = 5.10), epinephrine (Rs = 4.98), 3-benzyloxy-1,2-propanediol (Rs = 4.42), and 4,4'-dimethylbenzoin (Rs = 4.52) in NP-HPLC, and with 4-methylbenzhydrol (Rs = 4.72), benzoin ethyl ether (Rs = 3.79), 1-phenyl-1-pentanol (Rs = 3.68), and 1-(3-bromophenyl)ethanol (Rs = 3.60) in RP-HPLC. Interestingly, the CSP complemented Chiralcel OD-H, Chiralpak AD-H, and CYCLOBOND I 2000 RSP columns for resolution of these test racemates, separating several racemic compounds that could not be well separated by the three commercially available columns. The influences of injected sample amount on separation were also evaluated. It was found that the column exhibited excellent stability and reproducibility after hundreds of injections, and the relative standard deviations (n = 5) of the retention time and resolution were less than 0.49% and 0.69%, respectively. This study indicates that the BINOL-based chiral macrocycle has great potential for HPLC enantioseparation.

Macrocyclic bis-diphosphenes demonstrating bimetallic exo- and endo-cyclic binding modes

Macrocyclic bis-diphosphenes, formally heavier derivatives of macrocyclic azobenzenes, are accessed for the first time. These are synthesised in a reproducible fashion, through the nickel-mediated homocoupling of xanthene-derived NHC-stabilised bis-phosphinidene units. This gives direct access to target macrocyclic bis-diphosphenes 2, featuring exo-cyclic coordinated Ni0 fragments. The endo-cyclic binding mode in 3 is realised by NHC-abstraction using CuCl, so demonstrating two homometallic binding modes for this system. Additionally, reaction with CuCl in acetonitrile yields small amounts of a tetra-metallic NiII/CuI complex, which establishes simultaneous exo- and endo-cyclic metal binding. Fluctional solution state behavior in these systems is explored through variable temperature NMR spectroscopy, in addition to computational bonding analyses, giving the first insights into this novel class of compounds.

Solid-Phase Synthesis of Diverse Macrocycles by Regiospecific 2-Pyridone Formation: Scope and Applications

This study introduces a novel solid-phase macrocyclization method generating 2-pyridone rings. This method relies on the intramolecular condensation between secondary and tertiary dimethoxy-propionic amide units. This selective reaction leads to the formation of a single well-defined regioisomer. The method demonstrates remarkable efficiency in producing diverse peptidic and nonpeptidic bioactive targets, paving the way for the development of innovative macrocycle libraries featuring the 2-pyridone unit.

Cooperative Binding and Chirogenesis in an Expanded Perylene Bisimide Cyclophane

The encapsulation of more than one guest molecule into a synthetic cavity is a highly desirable yet a highly challenging task to achieve for neutral supramolecular hosts in organic media. Herein, we report a neutral perylene bisimide cyclophane, which has a tailored chiral cavity with an interchromophoric distance of 11.2 Å, capable of binding two aromatic guests in a π-stacked fashion. Detailed host-guest binding studies with a series of aromatic guests revealed that the encapsulation of the second guest in this cyclophane is notably more favored than the first one. Accordingly, for the encapsulation of the coronene dimer, a cooperativity factor (α) as high as 485 was observed, which is remarkably high for neutral host-guest systems. Furthermore, a successful chirality transfer, from the chiral host to encapsulated coronenes, resulted in a chiral charge-transfer (CT) complex and the rare observation of circularly polarized emission originating from the CT state for a noncovalent donor-acceptor assembly in solution. The involvement of the CT state also afforded an enhancement in the luminescence dissymmetry factor (glum) value due to its relatively large magnetic transition dipole moment. The 1:2 binding pattern and chirality-transfer were unambiguously verified by single-crystal X-ray diffraction analysis of the host-guest superstructures.

Identification of "Structural Pin" Interactions and their Significance for the Conformational Control of Macrocyclic Scaffolds

While peptide macrocycles with rigidified conformations have proven to be useful in the design of chemical probes of protein targets, conformational flexibility and rapid interconversion can be equally vital for biological activity and favorable physicochemical properties. This study introduces the concept of "structural pin", which describes a hydrogen bond that is largely responsible for stabilizing the entire macrocycle backbone conformation. Structural analysis of macrocycles using nuclear magnetic resonance (NMR), molecular modelling and X-ray diffraction indicates that disruption of the structural pin can drastically influence the conformation of the entire ring, resulting in novel states with increased flexibility. This finding provides a new tool to interrogate dynamic behaviour of macrocycles. Identification of structural pins offers a useful conceptual framework to understand positions that can either be modified to give flexible structures or retained to maintain the rigidity of the scaffold.

Rapid Peptide Cyclization Inspired by the Modular Logic of Nonribosomal Peptide Synthetases

Nonribosomal cyclic peptides (NRcPs) are structurally complex natural products and a vital pool of therapeutics, particularly antibiotics. Their structural diversity arises from the ability of the multidomain enzyme assembly lines, nonribosomal peptide synthetases (NRPSs), to utilize bespoke nonproteinogenic amino acids, modify the linear peptide during elongation, and catalyze an array of cyclization modes, e.g., head to tail, side chain to tail. The study and drug development of NRcPs are often limited by a lack of easy synthetic access to NRcPs and their analogues, with selective macrolactamization being a major bottleneck. Herein, we report a generally applicable chemical macrocyclization method of unprecedented speed and selectivity. Inspired by biosynthetic cyclization, it combines the deprotected linear biosynthetic precursor peptide sequence with a highly reactive C-terminus to produce NRcPs and analogues in minutes. The method was applied to several NRcPs of varying sequences, ring sizes, and cyclization modes including rufomycin, colistin, and gramicidin S with comparable success. We thus demonstrate that the linear order of modules in NRPS enzymes that determines peptide sequence encodes the key structural information to produce peptides conformationally biased toward macrocyclization. To fully exploit this conformational bias synthetically, a highly reactive C-terminal acyl azide is also required, alongside carefully balanced pH and solvent conditions. This allows for consistent, facile cyclization of exceptional speed, selectivity, and atom efficiency. This exciting macrolactamization method represents a new enabling technology for the biosynthetic study of NRcPs and their development as therapeutics.

Broad-spectrum activity of membranolytic cationic macrocyclic peptides against multi-drug resistant bacteria and fungi

The emergence of multidrug-resistant (MDR) strains causes severe problems in the treatment of microbial infections owing to limited treatment options. Antimicrobial peptides (AMPs) are drawing considerable attention as promising antibiotic alternative candidates to combat MDR bacterial and fungal infections. Herein, we present a series of small amphiphilic membrane-active cyclic peptides composed, in part, of various nongenetically encoded hydrophilic and hydrophobic amino acids. Notably, lead cyclic peptides 3b and 4b showed broad-spectrum activity against drug-resistant Gram-positive (MIC = 1.5-6.2 µg/mL) and Gram-negative (MIC = 12.5-25 µg/mL) bacteria, and fungi (MIC = 3.1-12.5 µg/mL). Furthermore, lead peptides displayed substantial antibiofilm action comparable to standard antibiotics. Hemolysis (HC50 = 230 µg/mL) and cytotoxicity (>70 % cell viability against four different mammalian cells at 100 µg/mL) assay results demonstrated the selective lethal action of 3b against microbes over mammalian cells. A calcein dye leakage experiment substantiated the membranolytic effect of 3b and 4b, which was further confirmed by scanning electron microscopy. The behavior of 3b and 4b in aqueous solution and interaction with phospholipid bilayers were assessed by employing nuclear magnetic resonance (NMR) spectroscopy in conjunction with molecular dynamics (MD) simulations, providing a solid structural basis for understanding their membranolytic action. Moreover, 3b exhibited stability in human blood plasma (t1/2 = 13 h) and demonstrated no signs of resistance development against antibiotic-resistant S. aureus and E. coli. These findings underscore the potential of these newly designed amphiphilic cyclic peptides as promising anti-infective agents, especially against Gram-positive bacteria.

Synthesis, structural, multitargeted molecular docking analysis of anti-cancer, anti-tubercular, DNA interactions of benzotriazole based macrocyclic ligand

Biologically important macromolecule 1, 1', 3, 3' Bis - [2,3,5,6-Tetramethyl-p-phenylenebis(methylene)] dibenzotriazlinium dibromide hydrate (BTD) was synthesized and characterized using FT-IR, NMR and single-crystal XRD (SCXRD). SCXRD revealed that the compound was crystallized as a monoclinic system and associated through weak intermolecular interactions like H-bonding and π- π stacking interactions. These weak intermolecular interactions in BTD were studied using Crystal Explorer and Gaussian. The calculated energies for the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) showed the stability and reactivity of the title compound. Molecular electrostatic potential (MEP) surface analysis was used to investigate the crystal's nucleophilic and electrophilic reactive sites. The molecular shape and intermolecular interactions in the crystal structure were determined using Hirshfeld surface analysis and fingerprint plots. Anticancer, anti-bacterial and DNA binding ability of BTD were investigated by experimental and theoretical techniques. The obtained results suggest that BTD possesses better anti-cancer, anti-bacterial and DNA binding abilities. The mode of action of antibiotic and anticancer approach was discussed. This provides promising therapeutic advantages for further development.

Synthesis and Functionalization of Azetidine-Containing Small Macrocyclic Peptides

Cyclic peptides are increasingly important structures in drugs but their development can be impeded by difficulties associated with their synthesis. Here, we introduce the 3-aminoazetidine (3-AAz) subunit as a new turn-inducing element for the efficient synthesis of small head-to-tail cyclic peptides. Greatly improved cyclizations of tetra-, penta- and hexapeptides (28 examples) under standard reaction conditions are achieved by introduction of this element within the linear peptide precursor. Post-cyclization deprotection of the amino acid side chains with strong acid is realized without degradation of the strained four-membered azetidine. A special feature of this chemistry is that further late-stage modification of the resultant macrocyclic peptides can be achieved via the 3-AAz unit. This is done by: (i) chemoselective deprotection and substitution at the azetidine nitrogen, or by (ii) a click-based approach employing a 2-propynyl carbamate on the azetidine nitrogen. In this way, a range of dye and biotin tagged macrocycles are readily produced. Structural insights gained by XRD analysis of a cyclic tetrapeptide indicate that the azetidine ring encourages access to the less stable, all-trans conformation. Moreover, introduction of a 3-AAz into a representative cyclohexapeptide improves stability towards proteases compared to the homodetic macrocycle.

Cascade ring expansion reactions for the synthesis of medium-sized rings and macrocycles

This Feature Article discusses recent advances in the development of cascade ring expansion reactions for the synthesis of medium-sized rings and macrocycles. Cascade ring expansion reactions have much potential for use in the synthesis of biologically important medium-sized rings and macrocycles, most notably as they don't require high dilution conditions, which are commonly used in established end-to-end macrocyclisation methods. Operation by cascade ring expansion method can allow large ring products to be accessed via rearrangements that proceed exclusively by normal-sized ring cyclisation steps. Ensuring that there is adequate thermodynamic driving force for ring expansion is a key challenge when designing such methods, especially for the expansion of normal-sized rings into medium-sized rings. This Article is predominantly focused on methods developed in our own laboratory, with selected works by other groups also discussed. Thermodynamic considerations, mechanism, reaction design, route planning and future perspective for this field are all covered.

The macrocycle inhibitor landscape of SLC-transporter

In the past years the interest in Solute Carrier Transporters (SLC) has increased due to their potential as drug targets. At the same time, macrocycles demonstrated promising activities as therapeutic agents. However, the overall macrocycle/SLC-transporter interaction landscape has not been fully revealed yet. In this study, we present a statistical analysis of macrocycles with measured activity against SLC-transporter. Using a data mining pipeline based on KNIME retrieved in total 825 bioactivity data points of macrocycles interacting with SLC-transporter. For further analysis of the SLC inhibitor profiles we developed an interactive KNIME workflow as well as an interactive map of the chemical space coverage utilizing parametric t-SNE models. The parametric t-SNE models provide a good discrimination ability among several corresponding SLC subfamilies' targets. The KNIME workflow, the dataset, and the visualization tool are freely available to the community.

Chemical cyclization of tyrosine-containing peptides via in situ generated triazolinedione peptides

Tyr-derived cyclic peptide natural products are formed by enzymatic manifolds that oxidatively cross-link embedded phenolic side chains of tyrosine (Tyr) and 4-hydroxyphenylglycine residues during their controlled production. Bioactive Tyr-derived cyclic peptides, such as the arylomycins and vancomycins, continue to motivate the development of enzymatic and chemical strategies for their de novo assembly and modification. However, chemical access to these structurally diverse natural cycles can be challenging and step intensive. Therefore, we developed an oxidative procedure to selectively convert Tyr-containing N4-substituted 1,2,4-triazolidine-3,5-dione peptides (urazole peptides) into stable Tyr-linked cyclic peptides. We show that Tyr-containing urazole peptides are simple to prepare and convert into reactive N4-substituted 1,2,4-triazoline-3,5-dione peptides by oxidation, which then undergo spontaneous cyclization under mildly basic aqueous conditions to form a cross-linkage with the phenol side chain of embedded Tyr residues. Using this approach, we have demonstrated access to over 25 Tyr-linked cyclic peptides (3- to 11-residue cycles) with good tolerance of native residue side chain functionalities. Importantly, this method is simple to perform, and product formation can be quickly confirmed by mass spectrometric and 1H NMR spectroscopic analyses.

Tetrazine cyclized peptides for one-bead-one-compound library: Synthesis and sequencing

While most FDA-approved peptide drugs are cyclic, robust cyclization chemistry of peptides and the deconvolution of the cyclic peptide sequences using tandem mass spectrometry render cyclic peptide drug discovery difficult. In this chapter, the protocol for the successful synthesis of tetrazine-linked cyclic peptide library in solid phase, which shows both robust cyclization and easy sequence deconvolution, is described. The protocol for the linearization and cleavage of cyclic peptides from the solid phase by simple UV light irradiation, followed by accurate sequencing using tandem mass spectrometry, is described. We describe the troubleshooting for this dithiol bis-arylation reaction and for the successful cleavage of the aryl cyclic peptide into linear form. This method for efficient solid-phase macrocyclization can be used for the rapid production of loop-based peptides and screening for inhibition of protein-protein interactions, by using the covalent inverse electron-demand Diels Alder reaction to supplement the non-covalent interaction between a protein and its peptide binder, isolating highly selective peptides in the process.

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.

Expanding the scope of the successive ring expansion strategy for macrocycle and medium-sized ring synthesis: unreactive and reactive lactams

New methods are described that expand the scope of the Successive Ring Expansion (SuRE) with respect to synthetically challenging lactams. A protocol has been developed for use with 'unreactive' lactams, enabling SuRE reactions to be performed on subsrates that fail under previously established conditions. Ring expansion is also demonstarted on 'reactive' lactams derived from iminosugars for the first time. The new SuRE methods were used to prepare a diverse array of medium-sized and macrocyclic lactams and lactones, which were evaluted in an anti-bacterial assay against E. coli BW25113WT.

Investigating the diastereoselective synthesis of a macrocycle under Curtin-Hammett control

This work sheds new light on the stereoselective synthesis of chiral macrocycles containing twisted aromatic units, valuable π-conjugated materials for recognition, sensing, and optoelectronics. For the first time, we use the Curtin-Hammett principle to investigate a chiral macrocyclisation reaction, revealing the potential for supramolecular π-π interactions to direct the outcome of a dynamic kinetic resolution, favouring the opposite macrocyclic product to that expected under reversible, thermodynamically controlled conditions. Specifically, a dynamic, racemic perylene diimide dye (1 : 1 P : M) is strapped with an enantiopure (S)-1,1'-bi-2-naphthol group (P-BINOL) to form two diastereomeric macrocyclic products, the homochiral macrocycle (PP) and the heterochiral species (PM). We find there is notable selectivity for the PM macrocycle (dr = 4 : 1), which is rationalised by kinetic templation from intramolecular aromatic non-covalent interactions between the P-BINOL π-donor and the M-PDI π-acceptor during the macrocyclisation reaction.

Cell penetration of oxadiazole-containing macrocycles

Passive membrane permeability is an important property in drug discovery and biological probe design. To elucidate the cell-penetrating ability of oxadiazole-containing (Odz) peptides, we employed the Chloroalkane Penetration Assay. The present study demonstrates that Odz cyclic peptides can be highly cell-penetrant depending on the position of specific side chains and the chloroalkane tag. Solution NMR shows that Odz cyclic peptides adopt a β-turn conformation. However, despite observing high cell penetration, we observed low passive permeability in experiments with artificial membranes. These findings highlight the complexity of controlling cell penetration for conformationally sensitive macrocycles and suggest that Odz cyclic peptides may provide a framework for designing cell-penetrant cyclic peptides.

Targeted sampling of natural product space to identify bioactive natural product-like polyketide macrolides

Polyketide or polyketide-like macrolides (pMLs) continue to serve as a source of inspiration for drug discovery. However, their inherent structural and stereochemical complexity challenges efforts to explore related regions of chemical space more broadly. Here, we report a strategy termed the Targeted Sampling of Natural Product space (TSNaP) that is designed to identify and assess regions of chemical space bounded by this important class of molecules. Using TSNaP, a family of tetrahydrofuran-containing pMLs are computationally assembled from pML inspired building blocks to provide a large collection of natural product-like virtual pMLs. By scoring functional group and volumetric overlap against their natural counterparts, a collection of compounds are prioritized for targeted synthesis. Using a modular and stereoselective synthetic approach, a library of polyketide-like macrolides are prepared to sample these unpopulated regions of pML chemical space. Validation of this TSNaP approach by screening this library against a panel of whole-cell biological assays, reveals hit rates exceeding those typically encountered in small molecule libraries. This study suggests that the TSNaP approach may be more broadly useful for the design of improved chemical libraries for drug discovery.

A Modular Strategy for the Synthesis of Macrocycles and Medium-Sized Rings via Cyclization/Ring Expansion Cascade Reactions

Macrocycles and medium-sized rings are important in many scientific fields and technologies but are hard to make using current methods, especially on a large scale. Outlined herein is a strategy by which functionalized macrocycles and medium-sized rings can be prepared using cyclization/ring expansion (CRE) cascade reactions, without resorting to high dilution conditions. CRE cascade reactions are designed to operate exclusively via kinetically favorable 5-7-membered ring cyclization steps; this means that the problems typically associated with classical end-to-end macrocyclization reactions are avoided. A modular synthetic approach has been developed to facilitate the simple assembly of the requisite linear precursors, which can then be converted into an extremely broad range of functionalized macrocycles and medium-sized rings using one of nine CRE protocols.

Divergent Cascade Ring-Expansion Reactions of Acryloyl Imides

Macrocyclic and medium-sized ring ketones, lactones and lactams can all be made from common acryloyl imide starting materials through divergent, one-pot cascade ring-expansion reactions. Following either conjugate addition with an amine or nitromethane, or osmium(VIII)-catalysed dihydoxylation, rearrangement through a four-atom ring expansion takes place spontaneously to form the ring expanded products. A second ring expansion can also be performed following a second iteration of imide formation and alkene functionalisation/ring expansion. In the dihydroxylation series, three- or four-atom ring expansion can be performed selectively, depending on whether the reaction is under kinetic or thermodynamic control.

The Role of Attractive Non-Covalent Interactions in Peptide Macrocyclization

The efficiency of macrocyclization reactions relies on the appropriate conformational preorganization of a linear precursor, ensuring that reactive ends are in spatial proximity prior to ring closure. Traditional peptide cyclization approaches that reduce the extent of terminal ion pairing often disfavor cyclization-conducive conformations and can lead to undesired cyclodimerization or oligomerization side reactions, particularly when they are performed without high dilution. To address this challenge, synthetic strategies that leverage attractive noncovalent interactions, such as zwitterionic attraction between chain termini during macrocyclization, offer a potential solution by reducing the entropic penalty associated with linear peptides adopting precyclization conformations. In this study, we investigate the role of (N-isocyanoimino)triphenylphosphorane (Pinc) in facilitating the cyclization of linear peptides into conformationally rigid macrocycles. The observed moderate diastereoselectivity is consistent with the preferential Si-facial addition of Pinc, where the isocyanide adds to the E-iminium ion on the same face as the l-proline amide group. The resulting peptide chain reveals that the activated phosphonium ylide of Pinc brings the reactive ends close together, promoting cyclization by enclosing the carboxylate within the interior of the pentapeptide and preventing the formation of byproducts. For shorter peptides with modified peptide backbones, the cyclization mechanism and outcome are redirected, as nucleophilic motifs such as thiazole and imidazole can covalently trap nitrilium intermediates. The isolation of the intermediate in the unproductive macrocyclization pathway, along with nuclear magnetic resonance and density functional theory studies, provides insights into heterocycle-dependent selectivity. The Pinc-driven macrocyclization process has generated diverse collections of cyclic molecules, and our models offer a comprehensive understanding of observed trends, facilitating the development of other heterocycle-forming macrocyclization reactions.

Exploring the synthetic approaches and clinical prowess of established macrocyclic pharmaceuticals

Macrocyclic compounds, characterized by cyclic structures, often originate from either modified forms of unicyclic canonical molecules or natural products. Within the field of medicinal chemistry, there has been a growing fascination with drug-like macrocycles in recent years, primarily due to compelling evidence indicating that macrocyclization can significantly influence both the biological and physiochemical properties, as well as the selectivity, when compared to their acyclic counterparts. The approval of contemporary pharmaceutical agents like Lorlatinib underscore the notable clinical relevance of drug-like macrocycles. Nonetheless, the synthesis of these drug-like macrocycles poses substantial challenges, primarily stemming from the complexity of ring-closing reactions, which are inherently dependent on the size and geometry of the bridging linker, impacting overall yields. Nevertheless, macrocycles offer a promising avenue for expanding the synthetic toolkit in medicinal chemistry, enabling the creation of bioactive compounds. To shed light on the subject, we delve into the clinical prowess of established macrocyclic drugs, spanning various therapeutic areas, including oncology, and infectious diseases. Case studies of clinically approved macrocyclic agents illustrate their profound impact on patient care and disease management. As we embark on this journey through the world of macrocyclic pharmaceuticals, we aim to provide a comprehensive overview of their synthesis and clinical applications, shedding light on the pivotal role they play in modern medicine.

Spontaneous and Selective Macrocyclization in Nitroaldol Reaction Systems

Through a dynamic polymerization and self-sorting process, a range of lowellane macrocycles have been efficiently generated in nitroaldol systems composed of aromatic dialdehydes and aliphatic or aromatic dinitroalkanes. All identified macrocycles show a composition of two repeating units, resulting in tetra-β-nitroalcohols of different structures. The effects of the building block structure on the macrocyclization process have been demonstrated, and the influence from the solvent has been explored. In general, the formation of the lowellanes was amplified in response to phase-change effects, although solution-phase structures were, in some cases, favored.

Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability

The biological activities and pharmacological properties of peptides and peptide mimetics are determined by their conformational states. Therefore, a detailed understanding of the conformational landscape is crucial for rational drug design. Nuclear magnetic resonance (NMR) is the only method for structure determination in solution. However, it remains challenging to determine the structures of peptides using NMR because of very weak nuclear Overhauser effects (NOEs), the semiquantitative nature of the rotating frame Overhauser effect (ROE), and the low number of NOEs/ROEs in N-methylated peptides. In this study, we introduce a new approach to investigating the structures of modified macrocyclic peptides. We utilize exact NOEs (eNOEs) in viscous solvent mixtures to replicate various cellular environments. eNOEs provide detailed structural information for highly dynamic modified peptides. Structures of high precision were obtained for cyclosporin A, with a backbone atom rmsd of 0.10 Å. Distinct conformational states in different environments were identified for omphalotin A (OmphA), a fungal nematotoxic and multiple backbone N-methylated macrocyclic peptides. A model for cell-permeation is presented for OmphA, based on its structures in polar, apolar, and mixed polarity solvents. During the transition from a polar to an apolar environment, OmphA undergoes a rearrangement of its H-bonding network, accompanied by a cis to trans isomerization of the ω torsion angle within a type VIa β-turn. We hypothesize that the kinetics of these conformational transitions play a crucial role in determining the membrane-permeation capabilities of OmphA.

Streamlined Protein-Protein Interface Loop Mimicry

Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.

Total and chemoenzymatic synthesis of the lipodepsipeptide rhizomide A

Rhizomides are a family of depsipeptide macrolactones synthesized by a non-ribosomal peptide synthetase (NRPS) encoded in the genome of Paraburkholderia rhizoxinica str. HKI 454. In this study, the total and chemoenzymatic synthesis of the depsipeptide rhizomide A is described. Rhizomide A was generated through macrolactamization while thelinear C-terminal N-acetylcysteamine (SNAC) thioester substrate was synthesized through a C-terminal thioesterification strategy. It was shown that the rhizomide A thioesterase (RzmA-TE) is an active macrocyclization catalyst, allowing the chemoenzymatic synthesis of rhizomide A.This work further showcases the biocatalytic power of TEs in accessing complex macrocyclic natural products.

Metallosupramolecular polymers: current status and future prospects

Metallo-supramolecular polymers have gained increasing attention and witnessed continuous development as a vibrant new research interest in the domain of soft materials. These nonconventional polymers have found widespread application in materials and biology owing to their well-defined and diversified topologies and the distinct dynamic nature of the metallosupramolecular interactions against various stimuli. Because of the intriguing redox, photonic, electronic, and magnetic properties, these stimuli-responsive supramolecular structures have attracted considerable interest for optoelectronic device fabrication. However, it still remains challenging to develop stimuli responsive systems with offbeat applications. Furthermore, achieving spatiotemporal control remains elusive with thermoresponsive and sono-responsive metallosupramolecular polymers, which encounter the disadvantage of poor precision control. Additionally, controlling the morphology of these soft materials on the mesoscale, both in solution and on substrates, has many challenges. In this review, we discuss the recent developments and future directions for the construction of stimuli responsive metallosupramolecular systems targeting practical applications. Furthermore, we discuss the synthetic methodologies that have been used to regulate the mesoscale morphology of these materials, such as coordination modulation and pseudomorphic replication. Finally, we briefly cover the burgeoning field of programmed synthesis of metallosupramolecular polymers, emphasizing techniques, such as living polymerization and chemical fuel-driven transiently active systems, which we believe will be the major research directions in the future.

Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles

Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.

An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides

Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.

High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment

Knowledge of the putative bound-state conformation of a molecule is an essential prerequisite for the successful application of many computer-aided drug design methods that aim to assess or predict its capability to bind to a particular target receptor. An established approach to predict bioactive conformers in the absence of receptor structure information is to sample the low-energy conformational space of the investigated molecules and derive representative conformer ensembles that can be expected to comprise members closely resembling possible bound-state ligand conformations. The high relevance of such conformer generation functionality led to the development of a wide panel of dedicated commercial and open-source software tools throughout the last decades. Several published benchmarking studies have shown that open-source tools usually lag behind their commercial competitors in many key aspects. In this work, we introduce the open-source conformer ensemble generator CONFORGE, which aims at delivering state-of-the-art performance for all types of organic molecules in drug-like chemical space. The ability of CONFORGE and several well-known commercial and open-source conformer ensemble generators to reproduce experimental 3D structures as well as their computational efficiency and robustness has been assessed thoroughly for both typical drug-like molecules and macrocyclic structures. For small molecules, CONFORGE clearly outperformed all other tested open-source conformer generators and performed at least equally well as the evaluated commercial generators in terms of both processing speed and accuracy. In the case of macrocyclic structures, CONFORGE achieved the best average accuracy among all benchmarked generators, with RDKit's generator coming close in second place.

Instant Macrocyclizations via Multicomponent Reactions

Macrocycles fascinate chemists due to both their structure and their applications. However, we still lack efficient and sustainable synthetic methods, giving us straightforward access to them. Herein, a rapid macrocyclization utilizing a two-step, one-pot approach based on orthogonal multicomponent reaction (MCR) tactics is introduced. This synthetic protocol, which is based on Ugi and Groebke-Blackburn-Bienaymé reactions with isocyanides tethered to alkyl tosylates, yields medium sized macrocycles that are otherwise difficult to achieve. Single crystal structures reveal conformational reorganization via intramolecular hydrogen bonding, and modeling studies profile the synthesized libraries.

Diazaborine-Mediated Bicyclization of Native Peptides with Inducible Reversibility

Multicyclic peptides are appealing candidates for peptide-based drug discovery. While various methods are developed for peptide cyclization, few allow multicyclization of native peptides. Herein we report a novel cross-linker DCA-RMR1, which elicits facile bicyclization of native peptides via N-terminus Cys-Cys cross-linking. The bicyclization is fast, affords quantitative conversion, and tolerates various side chain functionalities. Importantly, the resulting diazaborine linkage, while stable at a neutral pH, can readily reverse upon mild acidification to give pH-responsive peptides.

First 24-Membered Macrocyclic 1,10-Phenanthroline-2,9-Diamides-An Efficient Switch from Acidic to Alkaline Extraction of f-Elements

A reaction of acyl chlorides derived from 1,10-phenanthroline-2,9-dicarboxylic acids with piperazine allows the preparation of the corresponding 24-membered macrocycles in good yield. The structural and spectral properties of these new macrocyclic ligands were thoroughly investigated, revealing promising coordination properties towards f-elements (Am, Eu). It was shown that the prepared ligands can be used for selective extraction of Am(III) from alkaline-carbonate media in presence of Eu(III) with an SF_Am/Eu up to 40. Their extraction efficiency is higher than calixarene-type extraction of the Am(III) and Eu(III) pair. Composition of macrocycle-metal complex with Eu(III) was investigated by luminescence and UV-vis spectroscopy. The possibility of such ligands to form complexes of L:Eu = 1:2 stoichiometry is revealed.

Aggregation-Induced Catalysis: Asymmetric Catalysis with Chiral Aggregates

So far, there have been 4 methods to control chirality including the use of chiral auxiliaries, reagents, solvents, and catalysts documented in literature and textbooks. Among them, asymmetric catalysts are normally divided into homogeneous and heterogeneous catalysis. In this report, we present a new type of asymmetric control-asymmetric catalysis via chiral aggregates that would not belong to the above categories. This new strategy is represented by catalytic asymmetric dihydroxylation reaction of olefins in which chiral ligands are aggregated by taking advantage of typical aggregation-induced emission systems containing tetrahydrofuran and H₂O cosolvents. It was proven that the chiral induction can be enhanced from er of 78:22 to 97:3 simply by changing the ratios of these 2 cosolvents. The formation of chiral aggregates of asymmetric dihydroxylation ligands, (DHQD)₂PHAL and (DHQ)₂PHAL, has been proven by aggregation-induced emission and a new analytical tool-aggregation-induced polarization established by our laboratory. In the meanwhile, chiral aggregates were found to be formed either by adding NaCl into tetrahydrofuran/H₂O systems or by increasing concentrations of chiral ligands. The present strategy also showed promising reverse control of enantioselectivity in the Diels-Alder reaction. This work is anticipated to be extended broadly to general catalysis, especially to asymmetric catalysis in the future.