An approach to computer-aided inhibitor design: Application to cathepsin L

Summary We have developed an approach to search for molecules that can be used as lead compounds in designing an inhibitor for a given proteolytic enzyme when the 3D structure of a homologous protein is known. This approach is based on taking the cast of the binding pocket of the protease and comparing its dimensions with that of the dimensions of small molecules. Herein the 3D structure of papain is used to model cathepsin L using the comparative modeling technique. The cast of the binding pocket is computed using the crystal structure of papain because the structures of papain and the model of cathepsin L are found to be similar at the binding site. The dimensions of the cast of the binding site of papain are used to screen for molecules from the Cambridge Structural Database (CSD) of small molecules. Twenty molecules out of the 80 000 small molecules in the CSD are found to have dimensions that are accommodated by the papain binding pocket. Visual comparison of the shapes of the cast and the 20 screened molecules resulted in identifying brevotoxin b, a toxin isolated from the red tide dinoflagellate Ptycho brevis (previously classified as Gymonodium breve), as the structure that best fits the binding pocket of papain. We tested the proteolytic activity of papain and cathepsin L in the presence of brevotoxin b and found inhibition of papain and cathepsin L with K_is of 25 M and 0.6 M, respectively. We also compare our method with a more elaborate method in the literature, by presenting our results on the computer search for inhibitors of the HIV-1 protease.     

Macrocyclic Protease Inhibitors with Reduced Peptide Character

There is a real need for simple structures that define a β‐strand conformation, a secondary structure that is central to peptide–protein interactions. For example, protease substrates and inhibitors almost universally adopt this geometry on active site binding. A planar pyrrole is used to replace two amino acids of a peptide backbone to generate a simple macrocycle that retains the required geometry for active site binding. The resulting β‐strand templates have reduced peptide character and provide potent protease inhibitors with the attachment of an appropriate amino aldehyde to the C‐terminus. Picomolar inhibitors of cathepsin L and S are reported and the mode of binding of one example to the model protease chymotrypsin is defined by X‐ray crystallography.     

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Peptide cation-radical fragment ions of the z-type, [^●AXAR⁺], [^●AXAK⁺], and [^●XAR⁺], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS³-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO─NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [y_n]⁺ type. Compared with collision-induced dissociation, UVPD yielded less side-chain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second (B) excited electronic states in the peptide ion R-CH^●-CONH- chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH⁺-C^●(O^–)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic C_α and amide nitrogen positions.

Open image in new window

Graphical Abstract ?

     

An Electrochemical Study of Immobilized Ruthenocene in Aqueous Media

The voltammetric exploration of ruthenocene RuCp₂ in aqueous solution via abrasive modification on a basal plane pyrolytic graphite electrode is reported. It is found that ruthenocene undergoes a one‐electron electrochemically irreversible oxidation to ruthenocenium, which then rapidly dimerizes to form [RuCp₂] . Then, depending on the anion in solution, either disproportionates to [RuCp₂]²⁺ and subsequently decomposes to ruthenium oxide, or is anion stabilized. SEM images and cyclic voltammetry of the electrode surface indicates that in the presence of smaller anions the dimer is not stabilized, whereas for larger anions, such as sodium toluene sulfonate, the dimer is stabilized and decomposition is inhibited.     

Genomics-driven discovery of chiral triscatechol siderophores with enantiomeric Fe(iii) coordination

Ferric complexes of triscatechol siderophores may assume one of two enantiomeric configurations at the iron site. Chirality is known to be important in the iron uptake process, however an understanding of the molecular features directing stereospecific coordination remains ambiguous. Synthesis of the full suite of (DHB^L/DLys^L/DSer)₃ macrolactone diastereomers, which includes the siderophore cyclic trichrysobactin (CTC), enables the effects that the chirality of Lys and Ser residues exert on the configuration of the Fe(iii) complex to be defined. Computationally optimized geometries indicate that the Λ/Δ configurational preferences are set by steric interactions between the Lys sidechains and the peptide backbone. The ability of each (DHB^L/DLys^L/DSer)₃ diastereomer to form a stable Fe(iii) complex prompted a genomic search for biosynthetic gene clusters (BGCs) encoding the synthesis of these diastereomers in microbes. The genome of the plant pathogen Dickeya chrysanthemi EC16 was sequenced and the genes responsible for the biosynthesis of CTC were identified. A related but distinct BGC was identified in the genome of the opportunistic pathogen Yersinia frederiksenii ATCC 33641; isolation of the siderophore from Y. frederiksenii ATCC 33641, named frederiksenibactin (FSB), revealed the triscatechol oligoester, linear-(DHB^LLys^LSer)₃. Circular dichroism (CD) spectroscopy establishes that Fe(iii)–CTC and Fe(iii)–FSB are formed in opposite enantiomeric configuration, consistent with the results of the ferric complexes of the cyclic (DHB^L/DLys^L/DSer)₃ diastereomers.

Synthesis and genome mining leverage access to diastereomers of the siderophore cyclic trichrysobactin. Computational modeling and CD spectroscopy address effects that ligand-based stereochemistry exerts on the configuration at Fe(iii).     

Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

It is shown that y-type ions, after losing C-terminal H₂O or NH₃, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH₂ heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH₂) are reported. Results from isotope labeling, tandem mass spectrometry (MSⁿ), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-“like” ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed. ?      

Manipulation of Electrostatic and Saccharide Linker Interactions in the Design of Efficient Glycopolypeptide‐Based Cholera Toxin Inhibitors

Multivalent, glycopolymer inhibitors designed for the treatment of disease and pathogen infection have shown improvements in binding correlated with general changes in glycopolymer architecture and composition. We have previously demonstrated that control of glycopolypeptide backbone extension and ligand spacing significantly impacts the inhibition of the cholera toxin B subunit pentamer (CT B₅) by these polymers. In the studies reported here, we elucidate the role of backbone charge and linker length in modulating the inhibition event. Peptides of the sequence AXPXG (where X is a positive, neutral or negative amino acid), equipped with the alkyne functionality of propargyl glycine, were designed and synthesized via solid‐phase peptide synthetic methods and glycosylated via Cu(I)‐catalyzed alkyne‐azide cycloaddition reactions. The capacity of the glycopeptides to inhibit the binding of the B₅ subunit of cholera toxin was evaluated. These studies indicated that glycopeptides with a negatively charged backbone show improved inhibition of the binding event relative to the other glycopeptides. In addition, variations in the length of the linker between the peptide and the saccharide ligand also affected the inhibition of CT by the glycopeptides. Our findings suggest that, apart from appropriate saccharide spacing and polypeptide chain extension, saccharide linker conformation and the systematic placement of charges on the polypeptide backbone are also significant variables that can be tuned to improve the inhibitory potencies of glycopolypeptide‐based multivalent inhibitors.

     

Dinuclear complexes of cobalt(II) with N,N′-substituted dithioxamides derived from α-aminoacids

Summary The coordination behaviour of N,N-bis(1-carboxymethyl)dithioxamide (GLYDTO), N,N-bis(1-carboxyethyl)dithioxamide (ALADTO), N,N-bis(1-carboxy-2-methylpropyl) dithioxamide (VALDTO) and N,N-bis(1-carboxy-3-methylbutyl)dithioxamide (LEUDTO) has been investigated by isolating and characterizing the dinuclear, neutral cobalt(II) complexes, [Co₂(L-4H)(H₂O)₂] (L = GLYDTO, ALADTO, VALDTO or LEUDTO) and [Co₂(L-4H)(H₂O)₆] (L = ALADTO or VALDTO). All ligands were characterized by mass, i.r., and ¹H- and ¹³C-n.m.r. spectroscopy. The complexes possess distorted octahedral structures as revealed by the magnetic and electronic (diffuse reflectance) spectral data. The i.r. data indicate that the ligands are bis-tridentate, bis-dianions coordinated to each metal ion through the carboxylate oxygen, deprotonated thioamide nitrogen and thiocarbonyl sulphur atoms.     

Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs

BACKGROUND: The lysosomal cysteine proteases of the papain family are some of the best studied proteolytic enzymes. Small-molecule inhibitors and fluorogenic substrate mimics have been used to probe the physiological roles of these proteases. A high degree of homology between family members and overlap in substrate specificity have made elucidating individual protease function, expression and activity difficult. RESULTS: Using peptide vinyl sulfones and epoxide as templates, we have generated probes that can be tagged with radioactive iodine. The resulting compounds covalently label various cathepsins and several unidentified polypeptides likely to be proteases. MB-074 was found to be a highly selective probe of cathepsin B activity. Probes that labeled several cathepsins were used to examine the specificity and cell permeability of the CA-074 family of inhibitors. Although CA-074 reportedly acts in vivo, we find it is unable to penetrate cells. Esterifying CA-074 resulted in a cell-permeable inhibitor with dramatically reduced activity and specificity for cathepsin B. The probes were also used to monitor protease activity in primary human tumor tissue and cells derived from human placenta. CONCLUSIONS: We have generated a highly selective cathepsin B probe and several less specific reagents for the study of cathepsin biology. The reagents have several advantages over commonly used fluorogenic substrates, allowing inhibitor targets to be identified in a pool of total cellular enzymes. We have used the probes to show that cathepsin activity is regulated in tumor tissues and during differentiation of placental-derived cytotrophoblasts to invasive cells required for establishing blood circulation in a developing embryo.     

Efficient Covalent Bond Formation in Gas-Phase Peptide–Peptide Ion Complexes with the Photoleucine Stapler

Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* _n L _m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N₂ from the L* diazirine rings underwent insertion into X?H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific ¹³C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)⁺ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]⁺ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide–peptide ion interactions in the gas phase.

Open image in new window

Graphical Abstract ?

     

Development of Reduced Peptide Bond Pseudopeptide Michael Acceptors for the Treatment of Human African Trypanosomiasis

Human African Trypanosomiasis (HAT) is an endemic protozoan disease widespread in the sub-Saharan region that is caused by T. b. gambiense and T. b. rhodesiense. The development of molecules targeting rhodesain, the main cysteine protease of T. b. rhodesiense, has led to a panel of inhibitors endowed with micro/sub-micromolar activity towards the protozoa. However, whilst impressive binding affinity against rhodesain has been observed, the limited selectivity towards the target still remains a hard challenge for the development of antitrypanosomal agents. In this paper, we report the synthesis, biological evaluation, as well as docking studies of a series of reduced peptide bond pseudopeptide Michael acceptors (SPR10–SPR19) as potential anti-HAT agents. The new molecules show K_i values in the low-micro/sub-micromolar range against rhodesain, coupled with k_2nd values between 1314 and 6950 M⁻¹ min⁻¹. With a few exceptions, an appreciable selectivity over human cathepsin L was observed. In in vitro assays against T. b. brucei cultures, SPR16 and SPR18 exhibited single-digit micromolar activity against the protozoa, comparable to those reported for very potent rhodesain inhibitors, while no significant cytotoxicity up to 70 µM towards mammalian cells was observed. The discrepancy between rhodesain inhibition and the antitrypanosomal effect could suggest additional mechanisms of action. The biological characterization of peptide inhibitor SPR34 highlights the essential role played by the reduced bond for the antitrypanosomal effect. Overall, this series of molecules could represent the starting point for further investigations of reduced peptide bond-containing analogs as potential anti-HAT agents     

Rapid,Traceless, AgI‐Promoted Macrocyclization of Peptides Possessing an N‐Terminal Thioamide

Peptide macrocyclization is often a slow process, plagued by epimerization and cyclodimerization. Herein, we describe a new method for peptide macrocyclization employing the Ag^I‐promoted transformation of peptide thioamides. The Ag^I has a dual function: chemoselectively activating the thioamide and tethering the N‐terminal thioamide to the C‐terminal carboxylate. Extrusion of Ag₂S generates an isoimide intermediate, which undergoes acyl transfer to generate the native cyclic peptide, resulting in a rapid, traceless macrocylization process. Cyclic peptides are furnished in high yields within 1 hour, free of epimerization and cyclodimerization.     

Rapid,Traceless, AgI‐Promoted Macrocyclization of Peptides Possessing an N‐Terminal Thioamide

Peptide macrocyclization is often a slow process, plagued by epimerization and cyclodimerization. Herein, we describe a new method for peptide macrocyclization employing the Ag^I‐promoted transformation of peptide thioamides. The Ag^I has a dual function: chemoselectively activating the thioamide and tethering the N‐terminal thioamide to the C‐terminal carboxylate. Extrusion of Ag₂S generates an isoimide intermediate, which undergoes acyl transfer to generate the native cyclic peptide, resulting in a rapid, traceless macrocylization process. Cyclic peptides are furnished in high yields within 1 hour, free of epimerization and cyclodimerization.     

Synthesis of a new N,N-ethane-1,2-bis(4-methoxyphenyl)carbothioamide ligand and its Cu(I) and Ag(I) complexes

[Cu(H₂L)(PPh₃)₂]NO₃ · 0.5H₂O (2) and [Ag(H₂L)(PPh₃)₂]NO₃ · 0.5H₂O (3) complexes of a new flexible thioamide ligand; N,N′-ethane-1,2-bis(4-methoxyphenyl)carbothioamide H₂L (1) have been synthesized using PPh₃ as a coligand. The synthesized compounds have been characterized with the help of elemental analyses, IR, ¹H, ¹³C and ³¹P NMR spectroscopy. The ligand and its Cu(I) complex have been studied by single crystal X-ray crystallography. The ligand acts as a neutral S-donor and forms a nine-membered chelate ring in [Cu(H₂L)(PPh₃)₂]NO₃ · 0.5H₂O. The molecular packing is stabilized by an anionic cavity formed by intermolecular hydrogen bonding between the basal plane of the complex molecule and the nitrate ions. The square shaped columnar channel has dimensions of 5.489(25) [N(11)–H(11A)?O(13)?H(21A)N(21)] × 3.693(7) [N(11)–C(11)–C(21)–N(21)] Å.     

A Tricyclic Template Derived from (2S,4R)-4-Hydroxyproline for the Synthesis of Protein Loop Mimetics

A tricyclic diketopiperazine, formally derived by coupling (2S,4S)-4-aminoproline (Pro(NH₂)) and (2S,4R)-4-(carboxymethyl)proline (Pro(CH₂COOH)), is synthesized starting from readily available (2S,4R)-4-hydroxyproline. The resulting tricyclic template has carboxy and amino groups to which a peptide chain may be attached. The Fmoc-protected template 5 is incorporated into the cyclic molecule cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵-) ( 6 ) where Pro(NH₂)⁷ = Pro(CH₂COOH)⁸ represents the template, using solid-phase peptide synthesis with cyclization in solution. The molecule is shown by NMR and dynamic simulated annealing methods to adopt a preferred conformation in aqueous solution, which includes an extended backbone at the residues Asn²-Pro³-Asn⁴, and a type-Iβ-turn at . These studies show that this novel template may be used in the synthesis of cyclic peptide and protein mimetics having defined secondary structure in aqueous environments.     

Determination of an opiate pentapeptide by on-line reversed phase preconcentration and ligand exchange chromatography with spectrofluorometric detection

Summary In order to study the occurrence of the opiate pentapeptide -[D-Ala^2,4, Tyr⁵] CM-5-NH₂ in the 10^–9–10^–5 M concentration range, we have developed a new method consisting of extraction of the peptide from its buffered aqueous medium onto a reversed phase cartridge of 50 L void volume, followed by on-line injection onto a Cu(II) modified silica gel column. The acetonitrile-rich mobile phase allows detection of the natural fluorescence of the peptide at the picomole level.     

Ynamide‐Mediated Thiopeptide Synthesis

Exploration of the full potential of thioamide substitution as a tool in the chemical biology of peptides and proteins has been hampered by insufficient synthetic strategies for the site‐specific introduction of a thioamide bond into a peptide backbone. A novel ynamide‐mediated two‐step strategy for thiopeptide bond formation with readily available monothiocarboxylic acids as thioacyl donors is described. The α‐thioacyloxyenamide intermediates formed from the ynamides and monothiocarboxylic acids can be purified, characterized, and stored. The balance between their activity and stability enables them to act as effective thioacylating reagents to afford thiopeptide bonds under mild reaction conditions. Amino acid functional groups such as OH, CONH₂, and indole NH groups need not be protected during thiopeptide synthesis. The modular nature of this strategy enables the site‐specific incorporation of a thioamide bond into peptide backbones in both solution and the solid phase.     

Reversible inhibition of the oxidase-like activity of Fe single-atom nanozymes for drug detection

Mechanism research of nanozymes has always been of great interest since their emergence as outstanding mimics of friable natural enzymes. An important but rarely mentioned issue in mechanism research of nanozymology is the inhibitory effect of nanozymes. And conventional nanozymes with various active sites hinder the mechanism research, while single-atom Fe–N–C nanozymes with similar active sites to natural enzymes exhibit structural advantages. Herein, we synthesized Fe single-atom nanozymes (Fe-SANs) with ultrahigh oxidase-like activity and found that a common analgesic-antipyretic drug 4-acetamidophenol (AMP) had inhibitory effects for the oxidase-like activity of Fe-SANs. We investigated the inhibitory effects in detail and demonstrated that the inhibition type was reversible mixed-inhibition with inhibition constants (K_i and ) of 0.431 mM and 0.279 mM, respectively. Furthermore, we put forward a colorimetric method for AMP detection based on nanozyme inhibition. The research on the inhibitory effects of small molecules on nanozymes expands the scope of analysis based on nanozymes and the inhibition mechanism study may offer some insight into investigating the interaction between nanozymes and inhibitors.

Inhibitory effects of paracetamol on the oxidase-like activity of Fe single-atom nanozymes.     

Copper(II)‐Mediated Transformation of a Tridentate Non‐Innocent Ligand into a Tetradentate Salen‐Type Innocent Ligand

A non‐innocent ligand, H₄L, was synthesized by introducing a ? CH₂NH₂ group at the ortho carbon atom to the aniline moiety of 2‐anilino‐4,6‐di‐tert‐butylphenol. The new ligand was characterized by IR and NMR spectroscopy and mass spectrometry techniques. Upon treatment with CuCl₂ ? 2 H₂O, this non‐innocent ligand provided a mononuclear four‐coordinate salen‐type Cu^II complex by complete modification of the ligand backbone. The complex was characterized by IR spectroscopy, mass spectrometry, X‐ray single‐crystal diffraction, electron paramagnetic resonance (EPR) spectroscopy, and UV/Vis/near‐IR spectroscopy techniques. X‐ray crystallographic analysis showed an asymmetric environment around the Cu^II center with a small (≈12°) twist between the two biting planes. Analysis of the X‐band EPR spectrum also supported the asymmetric environment and also indicated the presence of an unpaired electron on the d orbital. The UV/Vis/near‐IR spectrum showed strong absorption bands for metal‐to‐ligand charge transfer and ligand‐to‐metal charge transfer along with a Cu^II‐centered d–d transition. Mechanistic investigation of the formation of complex 1 indicated that modification of the ligand backbone proceeded through ligand‐centered amine to imine oxidation as well as through C? N bond‐breaking processes. During these processes, 3,5‐di‐tert‐butyl‐1,2‐benzoquinone and 2‐aminobenzylidene were produced. Ammonia, generated in situ through hydrolysis of the imine to the aldehyde, reacted with 3,5‐di‐tert‐butyl‐1,2‐benzoquinone to form the corresponding 3,5‐di‐tert‐butyl‐1,2‐iminobenzoquinone moiety, which upon two‐electron reduction in the reaction medium formed 3,5‐di‐tert‐butyl‐1,2‐aminophenol. This aminophenol underwent condensation with the H₂L5 ligand that was formed by self‐condensation of two molecules of 2‐aminobenzaldehyde and provided the modified ligand backbone.