Design of Ligand Binding to an Engineered Protein Cavity Using Virtual Screening and Thermal Up-shift Evaluation

Summary Proteins could be used to carry and deliver small compounds. As a tool for designing ligand binding sites in protein cores, a three-step virtual screening method is presented that has been optimised using existing data on T4 lysozyme complexes and tested in a newly engineered cavity in flavodoxin. The method can pinpoint, in large databases, ligands of specific protein cavities. In the first step, physico-chemical filters are used to screen the library and discard a majority of compounds. In the second step, a flexible, fast docking procedure is used to score and select a smaller number of compounds as potential binders. In the third step, a finer method is used to dock promising molecules of the hit list into the protein cavity, and an optimised free energy function allows discarding the few false positives by calculating the affinity of the modelled complexes. To demonstrate the portability of the method, several cavities have been designed and engineered in the flavodoxin from Anabaena PCC 7119, and the W66F/L44A double mutant has been selected as a suitable host protein. The NCI database has then been screened for potential binders, and the binding to the engineered cavity of five promising compounds and three tentative non-binders has been experimentally tested by thermal up-shift assays and spectroscopic titrations. The five tentative binders (some apolar and some polar), unlike the three tentative non-binders, are shown to bind to the host mutant and, importantly, not to bind to the wild type protein. The three-step virtual screening method developed can thus be used to identify ligands of buried protein cavities. We anticipate that the method could also be used, in a reverse manner, to identify natural or engineerable protein cavities for the hosting of ligands of interest.     

Ferroxidase Activity in Eukaryotic Ferritin is Controlled by Accessory‐Iron‐Binding Sites in the Catalytic Cavity

Ferritins are iron‐storage nanocage proteins that catalyze the oxidation of Fe²⁺ to Fe³⁺ at ferroxidase sites. By a combination of structural and spectroscopic techniques, Asp140, together with previously identified Glu57 and Glu136, is demonstrated to be an essential residue to promote the iron oxidation at the ferroxidase site. However, the presence of these three carboxylate moieties in close proximity to the catalytic centers is not essential to achieve binding of the Fe²⁺ substrate to the diferric ferroxidase sites with the same coordination geometries as in the wild‐type cages.     

Direct Detection of DNA and DNA‐Ligand Interaction by Impedance Spectroscopy

In this work we present an impedimetric detection system for DNA‐ligand interactions. The sensor system consists of thiol‐modified single‐stranded DNA chemisorbed to gold. Impedance measurements in the presence of the redox system ferri‐/ferrocyanide show an increase in charge transfer resistance (R_ct) after hybridisation of a complementary target. Different amounts of capture strands, used for gold electrode modification, result in surface coverages between 3 and 15 pmol/cm² ssDNA. The relative change in R_ct upon hybridisation increases with increasing amount of capture probe on the electrode from 1.5‐ to 4.5‐fold. Impedimetric detection of binding events of a metal‐intercalator ([Ru(phen)₃]²⁺) and a groove binder (spermine) to double‐stranded DNA is demonstrated. Binding of [Ru(phen)₃]²⁺ and spermine exhibits a decrease in charge transfer resistance. Here, the ligand’s interaction leads to electrostatic shielding of the negatively charged DNA backbone. The impedance changes have been evaluated in dependence on the concentration of both DNA binders. Furthermore, the association of a single‐stranded binding protein (SSBP) is found to cause an increase in charge transfer resistance only when incubated with single‐stranded DNA. The specific binding of an anti‐dsDNA antibody to the dsDNA‐modified electrode surface decreases in contrast the interfacial impedance.     

Site‐Resolved Backbone and Side‐Chain Intermediate Dynamics in a Carbohydrate‐Binding Module Protein Studied by Magic‐Angle Spinning NMR Spectroscopy

Magic‐angle spinning solid‐state NMR spectroscopy has been applied to study the dynamics of CBM3b–Cbh9A from Clostridium thermocellum (ctCBM3b), a cellulose binding module protein. This 146‐residue protein has a nine‐stranded β‐sandwich fold, in which 35 % of the residues are in the β‐sheet and the remainder are composed of loops and turns. Dynamically averaged ¹H‐¹³C dipolar coupling order parameters were extracted in a site‐specific manner by using a pseudo‐three‐dimensional constant‐time recoupled separated‐local‐field experiment (dipolar‐chemical shift correlation experiment; DIPSHIFT). The backbone‐Cα and Cβ order parameters indicate that the majority of the protein, including turns, is rigid despite having a high content of loops; this suggests that restricted motions of the turns stabilize the loops and create a rigid structure. Water molecules, located in the crystalline interface between protein units, induce an increased dynamics of the interface residues thereby lubricating crystal water‐mediated contacts, whereas other crystal contacts remain rigid.     

Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β‐Hairpins

A popular strategy in the de novo design of stable β‐sheet structures for various biomedical applications is the incorporation of aromatic pairs at the non‐hydrogen‐bonding (NHB) position. However, it is important to explicitly understand how aryl pair packing at the NHB region is coordinated with backbone structural rearrangements, and to delineate the benefits and drawbacks associated with stereopositional choice of dissimilar aromatic pairs. Here, we probe the consequences of flipped Trp/Tyr pairs by using engineered permutants at the NHB position of dodecapeptide β‐hairpins, proximal and distal to the turn. Extensive conformational analysis of these peptides using NMR and CD spectroscopy reveal that a classic Edge‐to‐Face and Face‐to‐Edge geometry at the proximal and distal aromatic pairs, respectively, in YW‐WY, is the most stabilizing. Such a preferred packing geometry in YW‐WY results in a highly twisted β‐sheet backbone, with Trp always providing a ‘Face’ orientation to its dissimilar aromatic partner Tyr. Flipping the proximal and/or distal aromatic pair distorts the ideal T‐shaped geometry, and results in alternate aryl arrangements that can adversely affect strand twist and β‐sheet stability. Our study reveals the existence of a strong stereopositional influence on the packing of dissimilar aromatic pairs. Our findings highlight the importance of modeling physical interaction forces while designing protein and peptide structures for functional applications.     

Oxime Side‐Chain Cross‐Links in an α‐Helical Coiled‐Coil Protein: Structure,Thermodynamics, and Folding‐Templated Synthesis of Bicyclic Species

Covalent side‐chain cross‐links are a versatile method to control peptide folding, particularly when α‐helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein–protein complex. A series of sequence variants of the dimeric coiled coil GCN4‐p1 bearing oxime bridges at solvent‐exposed positions were prepared and biophysically characterized. Triggered unmasking of a side‐chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X‐ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α‐helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.     

Addressing Challenges in Palladium‐Catalyzed Cross‐Coupling Reactions Through Ligand Design

The development of palladium‐catalyzed cross‐coupling reactions has revolutionized the synthesis of organic molecules on both bench‐top and industrial scales. While significant research effort has been directed toward evaluating how modifying various reaction parameters can influence the outcome of a given cross‐coupling reaction, the design and implementation of novel ancillary ligand frameworks has played a particularly important role in advancing the state‐of‐the‐art. This Review seeks to highlight notable examples from the recent chemical literature, in which newly developed ancillary ligands have enabled more challenging substrate transformations to be addressed with greater selectivity and/or under increasingly mild conditions. Throughout, the importance and subtlety of ligand effects in palladium‐catalyzed cross‐coupling reactions are described, in an effort to inspire further development and understanding within the field of ancillary ligand design.     

Position‐Dependent Effects of Fluorinated Amino Acids on the Hydrophobic Core Formation of a Heterodimeric Coiled Coil

Systematic model investigations of the molecular interactions of fluorinated amino acids within native protein environments substantially improve our understanding of the unique properties of these building blocks. A rationally designed heterodimeric coiled coil peptide (VPE/VPK) and nine variants containing amino acids with variable fluorine content in either position a16 or d19 within the hydrophobic core were synthesized and used to evaluate the impact of fluorinated amino acid substitutions within different hydrophobic protein microenvironments. The structural and thermodynamic stability of the dimers were examined by applying both experimental (CD spectroscopy, FRET, and analytical ultracentrifugation) and theoretical (MD simulations and MM‐PBSA free energy calculations) methods. The coiled coil environment imposes position‐dependent conformations onto the fluorinated side chains and thus affects their packing and relative orientation towards their native interaction partners. We find evidence that such packing effects exert a significant influence on the contribution of fluorine‐induced polarity to coiled coil folding.     

Water‐in‐Oil Micro‐Emulsion Enhances the Secondary Structure of a Protein by Confinement

A scheme is presented in which an organic solvent environment in combination with surfactants is used to confine a natively unfolded protein inside an inverse microemulsion droplet. This type of confinement allows a study that provides unique insight into the dynamic structure of an unfolded, flexible protein which is still solvated and thus under near‐physiological conditions. In a model system, the protein osteopontin (OPN) is used. It is a highly phosphorylated glycoprotein that is expressed in a wide range of cells and tissues for which limited structural analysis exists due to the high degree of flexibility and large number of post‐translational modifications. OPN is implicated in tissue functions, such as inflammation and mineralisation. It also has a key function in tumour metastasis and progression. Circular dichroism measurements show that confinement enhances the secondary structural features of the protein. Small‐angle X‐ray scattering and dynamic light scattering show that OPN changes from being a flexible protein in aqueous solution to adopting a less flexible and more compact structure inside the microemulsion droplets. This novel approach for confining proteins while they are still hydrated may aid in studying the structure of a wide range of natively unfolded proteins.     

Ligand binding affinity prediction by linear interaction energy methods

A recent method for estimating ligand binding affinities is extended. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. This type of method may be useful for computational prediction of ligand binding strengths, e.g., in drug design applications.     

α‐L‐Fucosidase Inhibition by Pyrrolidine–Ferrocene Hybrids: Rationalization of Ligand‐Binding Properties by Structural Studies

Enhanced metabolism of fucose through fucosidase overexpression is a signature of some cancer types, thus suggesting that fucosidase‐targetted ligands could play the role of drug‐delivery vectors. Herein, we describe the synthesis of a new series of pyrrolidine–ferrocene conjugates, consisting of a L ‐fuco‐configured dihydroxypyrrolidine as the fucosidase ligand armed with a cytotoxic ferrocenylamine moeity. Three‐dimensional structures of several of these fucosidase inhibitors reveal transition‐state‐mimicking ³E conformations. Elaboration with the ferrocenyl moiety results in sub‐micromolar inhibitors of both bovine and bacterial fucosidases, with the 3D structure of the latter revealing electron density indicative of highly mobile alkylferrocene compounds. The best compounds show a strong antiproliferative effect, with up to 100 % inhibition of the proliferation of MDA‐MB‐231 cancer cells at 50 μM .     

Micelle‐Triggered β‐Hairpin to α‐Helix Transition in a 14‐Residue Peptide from a Choline‐Binding Repeat of the Pneumococcal Autolysin LytA

Choline‐binding modules (CBMs) have a ββ‐solenoid structure composed of choline‐binding repeats (CBR), which consist of a β‐hairpin followed by a short linker. To find minimal peptides that are able to maintain the CBR native structure and to evaluate their remaining choline‐binding ability, we have analysed the third β‐hairpin of the CBM from the pneumococcal LytA autolysin. Circular dichroism and NMR data reveal that this peptide forms a highly stable native‐like β‐hairpin both in aqueous solution and in the presence of trifluoroethanol, but, strikingly, the peptide structure is a stable amphipathic α‐helix in both zwitterionic (dodecylphosphocholine) and anionic (sodium dodecylsulfate) detergent micelles, as well as in small unilamellar vesicles. This β‐hairpin to α‐helix conversion is reversible. Given that the β‐hairpin and α‐helix differ greatly in the distribution of hydrophobic and hydrophilic side chains, we propose that the amphipathicity is a requirement for a peptide structure to interact and to be stable in micelles or lipid vesicles. To our knowledge, this “chameleonic” behaviour is the only described case of a micelle‐induced structural transition between two ordered peptide structures.     

Tuning the Stability and Reactivity of Metal‐bound Alkylperoxide by Remote Site Substitution of the Ligand

An alkylperoxonickel(II) complex with hydrotris(3,5‐diisopropyl‐4‐bromo‐1‐pyrazolyl)borate, [Ni^II(OOtBu)(Tp^iPr2,Br)] ( 3a ), is synthesized, and its chemical properties are compared with those of the prototype non‐brominated ligand derivative [Ni^II(OOtBu)(Tp^iPr2)] ( 3b ; Tp^iPr2=hydrotris(3,5‐diisopropyl‐1‐pyrazolyl)borate). Same synthetic procedures for the prototype 3b and its precursors can be employed to the synthesis of the Tp^iPr2,Br analogues. The dimeric nickel(II)‐hydroxo complex, [(Ni^IITp^iPr2,Br)₂(μ‐OH)₂] ( 2a ), can be synthesized by the base hydrolysis of the labile complexes [Ni^II(Y)(Tp^iPr2,Br)] (Y=NO₃ ( 1a ), OAc ( 1a′ )), which are obtained by the metathesis of NaTp^iPr2,Br with the corresponding nickel(II) salts, and the following dehydrative condensation of 2a with the stoichiometric amount of tert‐butylhydroperoxide yields 3a . The unique structural characteristics of the prototype 3b , that is, highly distorted geometry of the nickel center and intermediate coordination mode of the O O moiety between η¹ and η², are kept in the brominated ligand analogue 3a . The introduction of the electron‐withdrawing substitutents on the distal site of Tp^R affects the thermal stability and reactivity of the nickel(II)‐alkylperoxo species.     

Replacement of Water Molecules in a Phosphate Binding Site by Furanoside‐Appended lin‐Benzoguanine Ligands of tRNA‐Guanine Transglycosylase (TGT)

The enzyme tRNA‐guanine transglycosylase has been identified as a drug target for the foodborne illness shigellosis. A key challenge in structure‐based design for this enzyme is the filling of the polar ribose‐34 pocket. Herein, we describe a novel series of ligands consisting of furanoside‐appended lin‐benzoguanines. They were designed to replace a conserved water cluster and differ by the functional groups at C(2) and C(3) of the furanosyl moiety being either OH or OMe. The unfavorable desolvation of Asp102 and Asp280, which are located close to the ribose‐34 pocket, had a significant impact on binding affinity. While the enzyme has tRNA as its natural substrate, X‐ray co‐crystal structures revealed that the furanosyl moieties of the ligands are not accommodated in the tRNA ribose‐34 site, but at the location of the adjacent phosphate group. A remarkable similarity of the position of the oxygen atoms in these two structures suggests furanosides as a potential phosphate isoster.     

The Influence of the Amide Linkage in the FeIII‐Binding Properties of Catechol‐Modified Rosamine Derivatives

The two new fluorescent ligands RosCat1 and RosCat2 contain catechol receptors connected to rosamine platforms through an amide linkage and were synthesized by using microwave‐assisted coupling reactions of carboxyl‐ or amine‐substituted rosamines with the corresponding catechol units and subsequent deprotection. RosCat1 possesses a reverse amide, whereas RosCat2 has the usual oriented amide bond (HNCO vs. CONH, respectively). The ligands were characterized by means of NMR spectroscopy, mass‐spectrometry, and DFT calculations and X‐ray crystallography studies for RosCat1 . The influence of the amide linkage on the photophysical properties of the fluorescent ligands was assessed in different solvents and showed a higher fluorescence quantum yield for RosCat1 . The coordination chemistry of these ligands with a Fe^III center has been rationalized by mass‐spectrometric analysis and semiempirical calculations. Octahedral Fe^III complexes were obtained by the chelation of three RosCat1 or RosCat2 ligands. Interestingly, the unconventional amide connectivity in RosCat1 imposes the formation of an eight‐membered ring on the chelate complex through a “salicylate‐type” mode of coordination.     

Enhancing CO2 Separation Ability of a Metal–Organic Framework by Post‐Synthetic Ligand Exchange with Flexible Aliphatic Carboxylates

A series of porous metal–organic frameworks having flexible carboxylic acid pendants in their pores (UiO‐66‐ADn: n=4, 6, 8, and 10, where n denotes the number of carbons in a pendant) has been synthesized by post‐synthetic ligand exchange of terephthalate in UiO‐66 with a series of alkanedioic acids (HO₂C(CH₂)_n?2CO₂H). NMR, IR, PXRD, TEM, and mass spectral data have suggested that a terephthalate linker in UiO‐66 was substituted by two alkanedioate moieties, resulting in free carboxyl pendants in the pores. When post‐synthetically modified UiO‐66 was partially digested by adjusting the amount of added HF/sample, NMR spectra indicated that the ratio of alkanedioic acid/terephthalic acid was increased with smaller amounts of acid, implying that the ligand substitution proceeded from the outer layer of the particles. Gas sorption studies indicated that the surface areas and the pore volumes of all UiO‐66‐ADns were decreased compared to those of UiO‐66, and that the CO₂ adsorption capacities of UiO‐66‐ADn (n=4, 8) were similar to that of UiO‐66. In the case of UiO‐66‐AD6, the CO₂ uptake capacity was 34 % higher at 298 K and 58 % higher at 323 K compared to those of UiO‐66. It was elucidated by thermodynamic calculations that the introduction of flexible carboxyl pendants of appropriate length has two effects: 1) it increases the interaction enthalpy between the host framework and CO₂ molecules, and 2) it mitigates the entropy loss upon CO₂ adsorption due to the formation of multiple configurations for the interactions between carboxyl groups and CO₂ molecules. The ideal adsorption solution theory (IAST) selectivity for CO₂ adsorption over that of CH₄ was enhanced for all of the UiO‐66‐ADns compared to that of UiO‐66 at 298 K. In particular, UiO‐66‐AD6 showed the most strongly enhanced CO₂ uptake capacity and significantly increased selectivity for CO₂ adsorption over that of CH₄ at ambient temperature, suggesting that it is a promising material for sequestering CO₂ from landfill gas.