Peptide Hydrolysis by Metal-Cyclen Complexes and Their Analogues: Insights from Theoretical Studies

Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1

Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.

Macrocyclic Ligand Coordinating Amide-Arm Hydrolysis Reaction Activation in Aqueous Solutions: Tetravalent Uranium Does It Better

Chelation of lanthanide and actinide cations within a suitable macrocyclic ligand often results in a rigid, kinetically inert, and thermodynamically stable complex. A benchmark for such cation-ligand suitability are cyclen-derived macrocyclic ligands, frequently used as large cation hosts for various applications. Herein, a comprehensive study of the 1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane ligand (DOTAM) chelates of UIV and CeIII and their properties in aqueous solutions is presented. By employing multiple analysis techniques, including X-ray crystallography, UV-vis absorbance, 1H NMR, UPLC-MS, cyclic voltammetry, and differential pulse voltammetry, the study has revealed that the two aqueous complexes undergo a spontaneous, gradual, and stepwise hydrolysis of each of the coordinated amides toward carboxylates. The coordination of UIV in the studied reaction has been shown to significantly enhance the reaction rate, leading to an acceleration of up to 6 orders of magnitude compared to the natural process of simple aqueous amides at room temperature. An attempt to describe the unusual chelated metal cation amide-activation feature, based on the relatively lower rigidity of the complex structure, is presented. Additionally, the electrochemical properties of the complex series are discussed in detail, along with the limitations of the analytical methods employed.

Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes

The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.

Probing Unexpected Reactivity in Radiometal Chemistry: Indium-111-Mediated Hydrolysis of Hybrid Cyclen-Hydroxypyridinone Ligands

Chelators based on hydroxypyridinones have utility in incorporating radioactive metal ions into diagnostic and therapeutic agents used in nuclear medicine. Over the course of our hydroxypyridinone studies, we have prepared two novel chelators, consisting of a cyclen (1,4,7,10-tetraazacyclododecane) ring bearing two pendant hydroxypyridinone groups, appended via methylene acetamide motifs at either the 1,4-positions (L¹) or 1,7-positions (L²) of the cyclen ring. In radiolabeling reactions of L¹ or L² with the γ-emitting radioisotope, [¹¹¹In]In³⁺, we have observed radiometal-mediated hydrolysis of a single amide group of either L¹ or L². The reaction of either [¹¹¹In]In³⁺ or [^natIn]In³⁺ with either L¹ or L², in aqueous alkaline solutions at 80 °C, initially results in formation of [In(L¹)]⁺ or [In(L²)]⁺, respectively. Over time, each of these species undergoes In³⁺-mediated hydrolysis of a single amide group to yield species in which In³⁺ remains coordinated to the resultant chelator, which consists of a cyclen ring bearing a single hydroxypyridinone group and a single carboxylate group. The reactivity toward hydrolysis is higher for the L¹ complex compared to that for the L² complex. Density functional theory calculations corroborate these experimental findings and importantly indicate that the activation energy required for the hydrolysis of L¹ is significantly lower than that required for L². This is the first reported example of a chelator undergoing radiometal-mediated hydrolysis to form a radiometalated complex. It is possible that metal-mediated amide bond cleavage is a source of instability in other radiotracers, particularly those in which radiometal complexation occurs in aqueous, basic solutions at high temperatures. This study highlights the importance of appropriate characterization of radiolabeled products.

Peptide Hydrolysis by Metal (Oxa)cyclen Complexes: Revisiting the Mechanism and Assessing Ligand Effects

The mechanism responsible for peptide bond hydrolysis by Co(III) and Cu(II) complexes with (oxa)cyclen ligands has been revisited by means of computational tools. We propose that the mechanism starts by substrate coordination and an outer-sphere attack on the amide C atom of a solvent water molecule assisted by the metal hydroxo moiety as a general base, which occurs through six-membered ring transition states. This new mechanism represents a more likely scenario than the previously proposed mechanisms that involved an inner-sphere nucleophilic attack through more strained four-membered rings transition states. The corresponding computed overall free-energy barrier of 25.2 kcal mol^-1 for hydrolysis of the peptide bond in Phe-Ala by a cobalt(III) oxacyclen catalyst (1) is consistent with the experimental values obtained from rate constants. Also, we assessed the influence of the nature of the ligand throughout a systematic replacement of N by O atoms in the (oxa)cyclen ligand. Increasing the number of coordinating O atoms accelerates the reaction by increasing the Lewis acidity of the metal ion. On the other hand, the higher reactivity observed for the copper(II) oxacyclen catalyst with respect to the analogous Co(III) complex can be attributed to the larger Brönsted basicity of the copper(II) hydroxo ligand. Ultimately, the detailed understanding of the ligand and metal nature effects allowed us to identify the double role of the metal hydroxo complexes as Lewis acids and Brönsted bases and to rationalize the observed reactivity trends.

Coligand modulated oxidative O-demethylation of a methyl ether appended tetradentate N-ligand in Co(ii) complexes

Two Co(ii) complexes of the formula CoL^OMeX₂ (X = Cl^- (1a); X = I^- (1b)), where L^OMe is 2-methoxy-N,N-bis(pyridin-2-ylmethyl) aniline, were synthesized and their structure, spectra and reactivity were studied. Upon oxidation of 1a and 1b, the ligand L^OMe undergoes demethylation at the metal centre resulting in the formation of Co(iii) complexes with modified phenoxide ligands. This is the very first example of oxidative O-demethylation reported at a Co(ii) centre. The oxidative behaviour exhibits a striking dependence on the nature of coligands coordinated to the metal centre. The Co(ii) complex 1a with stronger chloro coligands requires a strong oxidising agent like t-BuOOH for oxidative demethylation and the subsequent formation of a mononuclear Co(iii) complex with a demethylated ligand, CoL^O-Cl₂ (2). On the other hand, complex 1b with weaker iodo coligands undergoes oxidation in the presence of the weak oxidant O₂ to form a dihydroxo bridged binuclear Co(iii) complex [Co₂(L^O-)₂(OH)₂]²⁺ (3) with modified phenoxide ligands. The oxidation of 1b to 3 is monitored and the intermediate Co(ii) iodo aqua complex [CoL^OMeI(H₂O)]⁺ and Co(ii) diaqua complex [CoL^OMe(H₂O)₂]²⁺ are isolated and characterised.

Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes

In this study, mechanisms of phosphodiester hydrolysis catalyzed by six di- and tetravalent metal-cyclen (M-C) complexes (Zn-C, Cu-C, Co-C, Ce-C, Zr-C and Ti-C) have been investigated using DFT calculations. The activities of these complexes were studied using three distinct mechanisms: (1) direct attack ( DA ), (2) catalyst-assisted ( CA ), and (3) water-assisted ( WA ). All divalent metal complexes (Zn-C, Cu-C and Co-C) coordinated to the BNPP substrate in a monodentate fashion and activated its scissile phosphoester bond. However, all tetravalent metal complexes (Ce-C, Zr-C, and Ti-C) interacted with BNPP in a bidentate manner and strengthened this bond. The DA mechanism was energetically the most feasible for all divalent M-C complexes, while the WA mechanism was favored by the tetravalent complexes, except Ce-C. The divalent complexes were found to be more reactive than their tetravalent counterparts. Zn-C catalyzed the hydrolysis with the lowest barrier among all M-C complexes, while Ti-C was the most reactive tetravalent complex. The activities of Ce-C and Zr-C, except Ti-C, were improved with an increase in the coordination number of the metal ion. The structural and mechanistic information provided in this study will be very helpful in the development of more efficient metal complexes for this critical reaction.

Zn(ii)-cyclen complex-based liposomes for gene delivery: the advantage of Zn coordination

Zn-Coordination significantly improves the gene transfection efficiency and reduces the cytotoxicity of cyclen-based cationic liposomes.

Sulfonated Compounds Bind with Prostatic Acid Phosphatase (PAP248-286) to Inhibit the Formation of Amyloid Fibrils

The peptide segment of prostatic acid phosphatase (PAP248-286) aggregates to form SEVI (semen-derived enhancer of virus infection) amyloid fibrils. These are characteristic seminal amyloids that have the ability to promote the effect of HIV infection. In this paper, we explore the binding of sulfonated compounds with PAP248-286 through an in silico study. Three derivatives of suramin, NF110, NF279, and NF340, are selected. All of these sulfonated molecules bind to PAP248-286 and alter the conformation of the peptide, even though they have various structures, sizes, and configurations. The compounds bind with PAP248-286 through multiple interactions, such as hydrogen-bonding interactions, hydrophobic interactions, π-π stacking interactions, and electrostatic interactions. However, NF110, which has an X-shaped configuration, has the highest binding affinity of the three derivatives investigated. We also perform surface plasmon resonance and a Congo red assay to validate the results. The interactions between PAP248-286 and the sulfonated compounds are proposed to depend on the orientations of the sulfonate groups and the specific configurations of the compounds instead of the number of sulfonate groups. NF110 molecules occupy the exposed binding sites of PAP248-286, blocking interactions between the peptides. Therefore, these compounds are important in inhibiting the aggregation of PAP248-286. Herein, we provide useful information to develop new efficient microbicides to antagonize seminal amyloid fibrils and to block HIV transmission.

Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis

In this DFT study, activities of 11 different N₂O₄, N₂O₃, and NO₂ core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'_N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'_N2O3), and 2-(2-methoxy)ethanol (I'_NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimental information, these molecules were created by altering protonation states (singly protonated, doubly protonated, or doubly deprotonated) and number of their ligands. The energetics of the I'_N2O4, and I'_NO2 and their analogues predicted that both stepwise and concerted mechanisms occurred either with similar barriers, or the latter was more favorable than the former. They also showed that the doubly deprotonated form hydrolyzed the peptide bond with substantially lower barriers than the barriers for other protonation states. For NO₂ core possessing complexes, Zr-(NO₂)(OH^H)(H₂O/OH)_n for n = 1-3, the hydroxyl group containing molecules were found to be more reactive than their water ligand possessing counterparts. The barriers for these complexes reduced with an increase in the coordination number (6-8) of the Zr(IV) ion. Among all 11 molecules, the NO₂ core possessing and two hydroxyl group containing I'_DNO2-2H complex was found to be the most reactive complex with a barrier of 28.9 kcal/mol. Furthermore, barriers of 27.5, 28.9, and 32.0 kcal/mol for hydrolysis of Gly-Glu (negative), Gly-Gly (neutral), and Gly-Lys (positive) substrates, respectively, by this complex were in agreement with experiments. The activities of these complexes were explained in terms of basicity of their ligand environment and nucleophilicity of the Zr(IV) center using metal-ligand distances, charge on the metal ion, and the metal-nucleophile distance as parameters. These results provide a deeper understanding of the functioning of these complexes and will help design Zr(IV)-based synthetic metallopeptidases.

Significantly enhanced proteolytic activity of cyclen complexes by monoalkylation

The activity of Cu(ii) and Co(iii) cyclen complexes in the cleavage of proteins was remarkably improved by introducing long alkyl chains thus generating efficient proteolytic amphiphilic metal complexes.

Synthesis of a novel chitosan-based Ce(IV) complex with proteolytic activity in vitro toward edible biological proteins

The occurrence of enzymatic activities is attributed to proper spatial organization of functional groups from first principles. A novel chitosan-based Ce(IV) complex (CC[Ce(IV)]), an artificial metalloproteinase, was synthesized by attaching cyclen, Ce(IV), and chlorophyll-Cu(II) to a chitosan-based matrix. The enzymatic hydrolytic efficiency (HE) and the procedure of catalyzing myoglobin (Mb) by CC[Ce(IV)] in vitro were investigated using spectrophotometry, electrophoresis, and liquid chromatography. The results showed that the HE of Mb was up to 60% at 60°C within 24h, displaying a catalytic proficiency. The pseudo-first-order kinetic constant (kobs) for CC[Ce(IV)] treatment within 24h was 3.85×10(-2)h(-1), higher than that for α-chymotrypsin treatment, which was 2.63×10(-2)h(-1). Moreover, the peptide bond derived from Asp-Phe/Phe-Asp in Mb could be specifically cleaved by CC[Ce(IV)], which could simulate the functionality of α-chymotrypsin. This work provides an experimental basis for potential utilization of the chitosan-based Ce(IV) complexes in the food industry.

Kinetico-mechanistic studies of substitution reactions on cross-bridged cyclen Co(III) complexes with nucleosides and nucleotides

Kinetico-mechanistic studies on the substitution reactivity of the [Co{(μ-ET)cyclen}(H2O)2](3+) complex cation at pH values within the 6.0-7.0 range with biologically significant ligands have been carried out. The substitution processes have been found to occur exclusively on the mono-hydroxobridged [(Co{(μ-ET)cyclen}(H2O))2(μ-OH)](5+) species formed after equilibration of the cobalt complex in the relevant medium. The studies conducted on the substitution of the aqua/hydroxo ligands of this dinuclear species are indicative of a dominant role of outer-sphere complexation, involving hydrogen-bonding interactions. The values of the outer-sphere complex formation equilibrium constant are in line with the intervention of both the exiting aqua ligands and the NH groups at the encapsulating {(μ-ET)cyclen} ligand. These complexes result in the preferential formation of O- or N-bonded nucleotides depending on the structure of the base moiety of the ligand. Even the entry of the different donor bonded nucleotides is hampered by the hydrogen-bonding interaction with the dangling moiety of an already coordinated ligand. In general the overall substitution processes occur at a faster rate than those published for the fully alkylated encapsulating {(Me)2(μ-ET)cyclen} ligand derivative, as expected for the still available base-catalysing NH groups in the {(μ-ET)cyclen} ligand.

Kinetico-Mechanistic Studies of Nucleoside and Nucleotide Substitution Reactions of Co(III) Complexes of Fully Alkylated Cyclen

The solution chemistry of complex [Co{(Me)2(μ-ET)cyclen}(H2O)2](3+) containing a fully substituted tetraammine ligand designed for the avoidance of base-conjugated substitution mechanisms in the 6-8 pH range has been studied. The study should shed some light on the possible involvement of such Co(III) skeleton in inert interactions with biomolecules. The reactivity and speciation of the complex has been found similar to that of the parent cyclen derivative with the presence of mono- and bis-hydroxo-bridged species; at pH < 7.1, all reactivity has been found to be related to the aqua/hydroxo monomeric complexes. Under these pH conditions, the substitution reactions of the aqua/hydroxo ligands by chloride, inorganic phosphate, thymidine, cytidine 5'-monophosphate (5'-CMP), and thymidine-5'-monophosphate (5'-TMP) have been studied at varying conditions; ionic strength has been kept at 1.0 NaClO4 due to the high concentration of 2-(N-morpholino)ethanesulfonic acid (MES) or N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) used to ensure buffering. Except for chloride, the process occurs neatly in a one or two step process, showing dissociatively activated substitution mechanisms, having in general large ΔH(⧧), positive ΔS(⧧), and values of ΔV(⧧) close to those corresponding to the liberation of an aqua ligand to the reaction medium. The actuation of noticeable encounter-complex formation equilibrium constants has been found to be the determinant for the reactions with nucleosides and nucleotides, a clear indication of the relevance of hydrogen-bonding interactions in the reactivity of these molecules, even in this highly ionic strength medium. For the substitution of the active aqua/hydroxo ligands with 5'-TMP, the first substitution reaction produces an Nthymine-bound 5'-TMP complex that evolves to a bis-5'-TMP with an Nthymine,Ophosphate-bonding structure. The formation of outer-sphere complexes between the dangling phosphate group of the Nthymine-bound 5'-TMP and the thymine moiety of another entering 5'-TMP has been found to be responsible for this fact, which leaves only the phosphate group for coordination available.

Theoretical insights into the functioning of metallopeptidases and their synthetic analogues

CONSPECTUS: The selective hydrolysis of a peptide or amide bond (-(O═)C-NH-) by a synthetic metallopeptidase is required in a wide range of biological, biotechnological, and industrial applications. In nature, highly specialized enzymes known as proteases and peptidases are used to accomplish this daunting task. Currently, many peptide bond cleaving enzymes and synthetic reagents have been utilized to achieve efficient peptide hydrolysis. However, they possess some serious limitations. To overcome these inadequacies, a variety of metal complexes have been developed that mimic the activities of natural enzymes (metallopeptidases). However, in comparison to metallopeptidases, the hydrolytic reactions facilitated by their existing synthetic analogues are considerably slower and occur with lower catalytic turnover. This could be due to the following reasons: (1) they lack chemical properties of amino acid residues found within enzyme active sites; (2) they contain a higher metal coordination number compared with naturally occurring enzymes; and (3) they do not have access to second coordination shell residues that provide substantial rate enhancements in enzymes. Additionally, the critical structural and mechanistic information required for the development of the next generation of synthetic metallopeptidases cannot be readily obtained through existing experimental techniques. This is because most experimental techniques cannot follow the individual chemical steps in the catalytic cycle due to the fast rate of enzymes. They are also limited by the fact that the diamagnetic d(10) Zn(II) center is silent to electronic, electron spin resonance, and (67)Zn NMR spectroscopies. Therefore, we have employed molecular dynamics (MD), quantum mechanics (QM), and hybrid quantum mechanics/molecular mechanics (QM/MM) techniques to derive this information. In particular, the role of the metal ions, ligands, and microenvironment in the functioning of mono- and binuclear metal center containing enzymes such as insulin degrading enzyme (IDE) and bovine lens leucine aminopeptidase (BILAP), respectively, and their synthetic analogues have been investigated. Our results suggested that in the functioning of IDE, the chemical nature of the peptide bond played a role in the energetics of the reaction and the peptide bond cleavage occurred in the rate-limiting step of the mechanism. In the cocatalytic mechanism used by BILAP, one metal center polarized the scissile peptide bond through the formation of a bond between the metal and the carbonyl group of the substrate, while the second metal center delivered the hydroxyl nucleophile. The Zn(N3) [Zn(His, His, His)] core of matrix metalloproteinase was better than the Zn(N2O) [Zn(His, His, Glu)] core of IDE for peptide hydrolysis. Due to the synergistic interaction between the two metal centers, the binuclear metal center containing Pd2(μ-OH)([18]aneN6)](4+) complex was found to be ∼100 times faster than the mononuclear [Pd(H2O)4](2+) complex. A successful small-molecule synthetic analogue of a mononuclear metallopeptidase must contain a metal with a strong Lewis acidity capable of reducing the pKa of its water ligand to less than 7. Ideally, the metal center should include three ligands with low basicity. The steric effects or strain exerted by the microenvironment could be used to weaken the metal-ligand interactions and increase the activity of the metallopeptidase.

Synthesis of a chitosan-based functional biopolymer with both catalytic and binding groups for protein and DNA hydrolysis

Protein and DNA hydrolysis by chitosan-based biopolymer with catalytic and binding groups.