Thermolysin: kinetic study with oligopeptides

Production of marine bacterial metalloprotease A69 and evaluation of its potential in preparing soybean peptides with angiotensin-converting enzyme-inhibitory activity

BACKGROUND

Marine bacteria secrete a variety of proteases, which are a good source to explore proteases with application value. However, only a few marine bacterial proteases with a potential in bioactive peptides preparation have been reported.

RESULTS

The metalloprotease A69 from the marine bacterium Anoxybacillus caldiproteolyticus 1A02591 was successfully expressed in the food safe bacterium Bacillus subtilis as a secreted enzyme. A technique to efficiently produce protease A69 in a 15-L bioreactor was established, with a production of 8988 U mL-1 . Based on optimizing the hydrolysis parameters of A69 on soybean protein, a process for soybean protein peptides (SPs) preparation was set up, in which soybean protein was hydrolyzed by A69 at 4000 U g-1 and 60 °C for 3 h. The prepared SPs had a high content (> 90%) of peptides with a molecular mass less than 3000 Da and contained 18 amino acids. The prepared SPs showed high angiotensin-converting enzyme (ACE)-inhibitory activity, with an IC50 value of 0.135 mg mL-1 . Moreover, three ACE-inhibitory peptides, RPSYT, VLIVP and LAIPVNKP, were identified from the SPs using liquid chromatography-mass spectrometry analysis.

CONCLUSION

The marine bacterial metalloprotease A69 has a promising potential for preparing SPs with good nutritional and potential antihypertensive effects, laying a good foundation for its industrial production and application. © 2023 Society of Chemical Industry.

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.

Specificity-directed design of a FRET-quenched heptapeptide for assaying thermolysin-like proteases

Thermolysin (TL) is an industrially important zinc endopeptidase, and the prototype of the M4 family of metallopeptidases. The catalytic function of TL and its relatives is typically assessed using chromogenic or more sensitive fluorescent peptides, with the latter substrates relying on Förster resonance energy transfer (FRET). Here, we demonstrate that a FRET-quenched heptapeptide designed on the basis of the enzyme's substrate specificity (Dabcyl-FKFLGKE-EDANS) is efficiently cleaved by TL and dispase (a TL-like protease) in between the Phe3 and Leu4 residues. The specificity constants (determined at pH 7.4 and 25 °C) for TL and dispase (3.6 × 10⁶ M^-1 s^-1 and 4.6 × 10⁶ M^-1 s^-1, respectively) were found to be amongst the highest documented for any TL substrate. Maximal peptide cleavage rates were achieved at pH 6.5 and a temperature of 65 °C. In view of the sensitivity of the assay, concentrations as low as 10 pM TL could be detected. Furthermore, the rate of hydrolysis of Dabcyl-FKFLGKE-EDANS was slow or immeasurable with some other unrelated metallo-, serine- and cysteine proteases, suggesting that the peptide has the potential to serve as a selective substrate for TL and TL-like proteases.

Screening of Angiotensin-I Converting Enzyme Inhibitory Peptides Derived from Caulerpa lentillifera

Peptides with angiotensin-I converting enzyme (ACE) inhibitory activity have received considerable interest due to their potential as antihypertensive agents and consumer concern over the safety of synthetic drugs. The objective of this study was to isolate ACE inhibitory (ACEI) peptides from Caulerpa lentillifera (known commonly as sea grape) protein hydrolysate. In this study, short-chain peptides were obtained after hydrolysis by various enzymes and subsequently by ultrafiltration. Thermolysin hydrolysate showed the highest ACEI activity. Bioassay-guided fractionation was performed using reversed-phase high performance liquid chromatography (RP-HPLC) to uncover the fraction 9 with the highest ACE inhibitory activity from thermolysin hydrolysate. Peptides in this fraction were further identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis coupled with de novo sequencing, which gave two oligopeptides, FDGIP (FP-5) and AIDPVRA (AA-7). The identities and activities of these two peptides were further confirmed using synthetic peptides. Their IC50 values were determined as 58.89 ± 0.68 µM and 65.76 ± 0.92 µM, respectively. Moreover, the inhibition kinetics revealed that both FP-5 and AA-7 are competitive inhibitors. These activities were further explained using molecular docking simulation. The present study is the first report about ACEI peptides derived from Caulerpa lentillifera and it shows the potential for preventing hypertension and for functional food development.

Protein disulfide isomerase does not act as an unfoldase in the disassembly of cholera toxin

Cholera toxin (CT) is composed of a disulfide-linked A1/A2 heterodimer and a ring-like, cell-binding B homopentamer. The catalytic A1 subunit must dissociate from CTA2/CTB₅ to manifest its cellular activity. Reduction of the A1/A2 disulfide bond is required for holotoxin disassembly, but reduced CTA1 does not spontaneously separate from CTA2/CTB₅: protein disulfide isomerase (PDI) is responsible for displacing CTA1 from its non-covalent assembly in the CT holotoxin. Contact with PDI shifts CTA1 from a protease-resistant conformation to a protease-sensitive conformation, which is thought to represent the PDI-mediated unfolding of CTA1. Based solely on this finding, PDI is widely viewed as an ‘unfoldase’ that triggers toxin disassembly by unfolding the holotoxin-associated A1 subunit. In contrast with this unfoldase model of PDI function, we report the ability of PDI to render CTA1 protease-sensitive is unrelated to its role in toxin disassembly. Multiple conditions that promoted PDI-induced protease sensitivity in CTA1 did not support PDI-mediated disassembly of the CT holotoxin. Moreover, preventing the PDI-induced shift in CTA1 protease sensitivity did not affect PDI-mediated disassembly of the CT holotoxin. Denatured PDI could still convert CTA1 into a protease-sensitive state, and equal or excess molar fractions of PDI were required for both efficient conversion of CTA1 into a protease-sensitive state and efficient disassembly of the CT holotoxin. These observations indicate the ‘unfoldase’ property of PDI does not play a functional role in CT disassembly and does not represent an enzymatic activity.

Deciphering Design Principles of Förster Resonance Energy Transfer-Based Protease Substrates: Thermolysin-Like Protease from Geobacillus stearothermophilus as a Test Case

Protease activity is frequently assayed using short peptides that are equipped with a Förster resonance energy transfer (FRET) reporter system. Many frequently used donor-acceptor pairs are excited in the ultraviolet range and suffer from low extinction coefficients and quantum yields, limiting their usefulness in applications where a high sensitivity is required. A large number of alternative chromophores are available that are excited in the visible range, for example, based on xanthene or cyanine core structures. These alternatives are not only larger in size but also more hydrophobic. Here, we show that the hydrophobicity of these chromophores not only affects the solubility of the resulting FRET-labeled peptides but also their kinetic parameters in a model enzymatic reaction. In detail, we have compared two series of 4-8 amino acid long peptides, designed to serve as substrates for the thermolysin-like protease (TLP-ste) from Geobacillus stearothermophilus. These peptides were equipped with a carboxyfluorescein donor and either Cy5 or its sulfonated derivative Alexa Fluor 647 as the acceptor. We show that the turnover rate k _cat is largely unaffected by the choice of the acceptor fluorophore, whereas the K _M value is significantly lower for the Cy5- than for the Alexa Fluor 647-labeled substrates. TLP-ste is a rather nonspecific protease with a large number of hydrophobic amino acids surrounding the catalytic site, so that the fluorophore itself may form additional interactions with the enzyme. This hypothesis is supported by the result that the difference between Cy5- and Alexa Fluor 647-labeled substrates becomes less pronounced with increasing peptide length, that is, when the fluorophore is positioned at a larger distance from the catalytic site. These results suggest that fluorophores may become an integral part of FRET-labeled peptide substrates and that K _M and k _cat values are generally only valid for a specific combination of the peptide sequence and FRET pair.

Drug induced self-assembly of triblock copolymers into polymersomes for the synergistic dual-drug delivery of platinum drugs and paclitaxel

Co-delivery of two drugs in one nanoparticle is increasingly used to overcome, for example, multi-drug resistance in cancer therapy and therefore suitable drug carriers need to be developed.

Mechanisms of peptide hydrolysis by aspartyl and metalloproteases

Peptide hydrolysis has been involved in a wide range of biological, biotechnological, and industrial applications.

Peptide Hydrolysis in Thermolysin: Ab Initio QM/MM Investigation of the Glu143-Assisted Water Addition Mechanism

Thermolysin (TLN) is one of the best-studied zinc metalloproteases. Yet the mechanism of action is still under debate. In order to investigate the energetic feasibility of the currently most favored mechanism, we have docked a tripeptide to the active site of TLN and computed the free energy profile at the quantum mechanics/molecular mechanics level of theory. The mechanism consists of three distinct steps:  (i) a Zn-bound water molecule is deprotonated by Glu143 and attacks the carbonyl bond of the substrate; (ii) Glu143 transfers the proton to the amide nitrogen atom; (iii) the nitrogen atom is protonated and the peptide bond is irreversibly broken. The free energy barriers for steps i and iii have almost equal heights, 14.8 and 14.7 kcal/mol, respectively, and are in good agreement with the effective experimental activation barrier obtained for similar substrates, 12.1-13.6 kcal/mol. Transition state stabilization for nucleophilic attack is achieved by formation of a weak coordination bond between the substrate carbonyl oxygen atom and the Zn ion and of three strong hydrogen bonds between the substrate and protonated His231 and two solvent molecules. The transition state for the nucleophilic attack (step i) is more tightly bonded than the enzyme-substrate complex, implying that TLN complies with Pauling's hypothesis regarding transition-state stabilization. Glu143, at first unfavorably oriented for protonation of the amide nitrogen atom, displayed large structural fluctuations that facilitated reorganization of the local hydrogen-bond network and transport of the proton to the leaving group on the nanosecond time scale. The present simulations give further evidence that Glu143 is a highly effective proton shuttle which should be assigned a key role in any reaction mechanism proposed for TLN.

Ligand binding to a high-energy partially unfolded protein

The conformational energy landscape of a protein determines populations of all possible conformations of the protein and also determines the kinetics of the conversion between the conformations. Interaction with ligands influences the conformational energy landscapes of proteins and shifts populations of proteins in different conformational states. To investigate the effect of ligand binding on partial unfolding of a protein, we use Escherichia coli dihydrofolate reductase (DHFR) and its functional ligand NADP(+) as a model system. We previously identified a partially unfolded form of DHFR that is populated under native conditions. In this report, we determined the free energy for partial unfolding of DHFR at varying concentrations of NADP(+) and found that NADP(+) binds to the partially unfolded form as well as the native form. DHFR unfolds partially without releasing the ligand, though the binding affinity for NADP(+) is diminished upon partial unfolding. Based on known crystallographic structures of NADP(+) -bound DHFR and the model of the partially unfolded protein we previously determined, we propose that the adenosine-binding domain of DHFR remains folded in the partially unfolded form and interacts with the adenosine moiety of NADP(+) . Our result demonstrates that ligand binding may affect the conformational free energy of not only native forms but also high-energy non-native forms.

Product inhibition in native-state proteolysis

The proteolysis kinetics of intact proteins by nonspecific proteases provides valuable information on transient partial unfolding of proteins under native conditions. Native-state proteolysis is an approach to utilize the proteolysis kinetics to assess the energetics of partial unfolding in a quantitative manner. In native-state proteolysis, folded proteins are incubated with nonspecific proteases, and the rate of proteolysis is determined from the disappearance of the intact protein. We report here that proteolysis of intact proteins by nonspecific proteases, thermolysin and subtilisin deviates from first-order kinetics. First-order kinetics has been assumed for the analysis of native-state proteolysis. By analyzing the kinetics of proteolysis with varying concentrations of substrate proteins and also with cleavage products, we found that the deviation from first-order kinetics results from product inhibition. A kinetic model including competitive product inhibition agrees well with the proteolysis time course and allows us to determine the uninhibited rate constant for proteolysis as well as the apparent inhibition constant. Our finding suggests that the likelihood of product inhibition must be considered for quantitative assessment of proteolysis kinetics.

LC-MS/MS coupled with QSAR modeling in characterising of angiotensin I-converting enzyme inhibitory peptides from soybean proteins

The importance of soy products in reducing the risk of cardiovascular disease is well documented. Our previous computation study has indicated the presence of several potent ACE inhibitory peptides within soybean proteins which needs to be identified. The aim of the study was to identify ACE inhibitory peptides from soy proteins using LC-MS/MS coupled with quantitative structure-activity relationship (QSAR) model. Soybean protein hydrolysate digested by thermolysin showed an IC50 value of 53.6 μg/mL, decreased slightly to 51.8 μg/mL after adding pepsin, and increased to 115.6 μg/mL after adding trypsin. A total of 34 peptides were characterised from LC-MS/MS. Five novel tripeptides, IVF, LLF, LNF, LSW and LEF, with predicted IC50 values lower than 10 μM were synthesized and validated. The results showed that soybean is an excellent source of ACE inhibitory peptides.

Effects of site-directed mutagenesis in the N-terminal domain of thermolysin on its stabilization

The thermolysin variant G8C/N60C/S65P in which the triple mutation in the N-terminal domain, Gly8→Cys/Asn60→Cys/Ser65→Pro, is undertaken increases stability [Yasukawa, K. and Inouye, K. (2007) Improving the activity and stability of thermolysin by site-directed mutagenesis. Biochim. Biophys. Acta 1774, 1281-1288] and its mechanism is examined in this study. The apparent denaturing temperatures based on ellipticity at 222 nm of the wild-type thermolysin (WT), G8C/N60C, S65P and G8C/N60C/S65P were 85, >95, 88 and >95°C, respectively. The first-order rate constants, k(obs), of the thermal inactivation of WT and variants at 10 mM CaCl₂ increased with increasing thermal treatment temperatures (70-95°C), and those at 80°C decreased with increasing CaCl₂ concentrations (1-100 mM). The k(obs) values were in the order of WT > S65P > G8C/N60C≒G8C/N60C/S65P at all temperatures and CaCl₂ concentrations. These results indicate that the mutational combination, Gly8→Cys/Asn60→Cys and Ser65→Pro, increases stability only as high as Gly8→Cys/Asn60→Cys does. Assuming that irreversible inactivation of thermolysin occurs only in the absence of calcium ions, the dissociation constants, K(d), to the calcium ions of WT, G8C/N60C, S65P and G8C/N60C/S65P were 47, 8.9, 17 and 7.2 mM, respectively, suggesting that Gly8→Cys/Asn60→Cys and Ser65→Pro stabilize thermolysin by improving its affinity to calcium ions, most probably the one at the Ca²⁺-binding site III in the N-terminal domain.

Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.

A mutant leucine aminopeptidase from Streptomyces cinnamoneus with enhanced L-aspartyl L-amino acid methyl ester synthetic activity

L-aspartyl L-amino acid methyl ester was synthesized using a mutant of a thermostable leucine aminopeptidase from Streptomyces cinnamoneus, D198 K SSAP, obtained in previously. A peptide of high-intensity sweetener, L-aspartyl-L-phenylalanine methyl ester, was selected as a model for demonstrating the synthesis of L-aspartyl L-amino acid methyl ester. The hydrolytic activities of D198 K SSAP toward L-aspartyl-L-phenylalanine and its methyl ester were, respectively, 74-fold and fourfold higher than those of wild type. Similarly, the initial rate of the enzyme for L-aspartyl-L-phenylalanine methyl ester synthesis was over fivefold higher than that of wild-type SSAP in 90% methanol (v/v) in a one-pot reaction. Furthermore, other L-aspartyl L-amino acid methyl esters were synthesized efficiently using D198 K SSAP. Results show that the substitution of Asp198 of SSAP with Lys is effective for synthesizing L-aspartyl L-amino acid methyl ester.

One-pot synthesis of diverse DL-configuration dipeptides by a Streptomyces D-stereospecific amidohydrolase

The synthesis of diverse DL-configuration dipeptides in a one-pot reaction was demonstrated by using a function of the aminolysis reaction of a D-stereospecific amidohydrolase from Streptomyces sp., a clan SE, S12 family peptidase categorized as a peptidase with D-stereospecificity. The enzyme was able to use various aminoacyl derivatives, including L-aminoacyl derivatives, as acyl donors and acceptors. Investigations of the specificity of the peptide synthetic activity revealed that the enzyme preferentially used D-aminoacyl derivatives as acyl donors. In contrast, L-amino acids and their derivatives were preferentially used as acyl acceptors. Consequently, the synthesized dipeptides had a DL-configuration when D- and L-aminoacyl derivatives were mixed in a one-pot reaction. This report also describes that the enzyme produced cyclo(D-Pro-L-Arg), a specific inhibitor of family 18 chitinase, with a conversion rate for D-Pro benzyl ester and L-Arg methyl ester to cyclo(D-Pro-L-Arg) of greater than 65%. Furthermore, based on results of cyclo(D-Pro-L-Arg) synthesis, we propose a reaction mechanism for cyclo(D-Pro-L-Arg) production.

Determining protease substrate selectivity and inhibition by label-free supramolecular tandem enzyme assays

An analytical method has been developed for the continuous monitoring of protease activity on unlabeled peptides in real time by fluorescence spectroscopy. The assay is enabled by a reporter pair comprising the macrocycle cucurbit[7]uril (CB7) and the fluorescent dye acridine orange (AO). CB7 functions by selectively recognizing N-terminal phenylalanine residues as they are produced during the enzymatic cleavage of enkephalin-type peptides by the metalloendopeptidase thermolysin. The substrate peptides (e.g., Thr-Gly-Ala-Phe-Met-NH(2)) bind to CB7 with moderately high affinity (K ≈ 10(4) M(-1)), while their cleavage products (e.g., Phe-Met-NH(2)) bind very tightly (K > 10(6) M(-1)). AO signals the reaction upon its selective displacement from the macrocycle by the high affinity product of proteolysis. The resulting supramolecular tandem enzyme assay effectively measures the kinetics of thermolysin, including the accurate determination of sequence specificity (Ser and Gly instead of Ala), stereospecificity (d-Ala instead of l-Ala), endo- versus exopeptidase activity (indicated by differences in absolute fluorescence response), and sensitivity to terminal charges (-CONH(2) vs -COOH). The capability of the tandem assay to measure protease inhibition constants was demonstrated on phosphoramidon as a known inhibitor to afford an inhibition constant of (17.8 ± 0.4) nM. This robust and label-free approach to the study of protease activity and inhibition should be transferable to other endo- and exopeptidases that afford products with N-terminal aromatic amino acids.

Enzyme Triggered Gelation of Arginine Containing Ionic-Peptides

We have investigated the possibility of using the protease enzyme thermolysin to catalyse the synthesis and gelation of ionic-complementary peptides from non-gelling peptide precursors. In the described system, thermolysin was added at a fixed concentration (0.3 mg mL−1) to solutions (25 - 100 mg mL−1) of a short tetra-peptide FEFR. Initially, the protease partially hydrolysed the tetrapeptide into di-peptides in all samples. Subsequently, longer peptide sequences were found to form through reverse-hydrolysis and their stability was found to be dependent on their self-assembling properties. The sequences that self-assembled into anti-parallel β-sheet rich fibres became the stable products for the reverse hydrolysis reaction, while the others formed were unstable and disappeared with increasing incubation time. Ultimately, the main product of the system was octa-peptide, which suggests that it represents the thermodynamically favoured product of this dynamic library.

Synthesis and inhibition properties of a series of pyranose derivatives towards a Zn-metalloproteinase from Saccharomonospora canescens

The Zn-proteinase, isolated from Saccharomonospora canescens (NPS), shares many common features with thermolysin, but considerable differences are also evident, as far as the substrate recognition site is concerned. In substrates of general structure AcylAlaAlaPhe 4NA, this neutral proteinase cleaves only the arylamide bond (non-typical activity of Zn-proteinases), while thermolysin attacks the peptide bond Ala-Phe. Phosphoramidon is a powerful tight binding inhibitor for thermolysin and significantly less specific towards NPS. The K(i)-values (65 μM for NPS vs 0.034 μM for thermolysin) differ nearly 2000-folds. This implies significant differences in the specificity of the corresponding subsites. The carbohydrate moiety is supposed to accommodate in the S₁-subsite and the series of arabinopyranosides and glucopyranosides (12 compounds), which are assayed as inhibitors in a model system: NPS with SucAlaAlaPhe4NA as a substrate could be considered as mapping the S₁-subsite of NPS. Members of the series with an additional ring (3,4-epithio, 3,4-anhydro-derivatives) turned out to be reasonably good competitive inhibitors (K(i)≈0.1-0.2 mM are of the same order as the K(i) value for phosphoramidon). The structure of these compounds (8, 9, 11 and 12) seems to fit the size of the S₁-subsite and due to an appropriately oriented OH-group in addition, to protect the active site Zn(2+).

Enzymatic catalyzed synthesis and triggered gelation of ionic peptides

We investigate the possibility of using the protease thermolysin to drive the synthesis and gelation of ionic-complementary peptides from nongelling precursors. In this system, short peptide fragments are continuously interconverted to form a dynamic peptide library, which eventually favors synthesis of peptides that are thermodynamically stabilized by molecular self-assembly. Thermolysin was added at a fixed concentration (0.3 mg mL(-1)) to solutions (0-300 mg mL(-1)) of the short tetrapeptide FEFK. Initially, the protease partially hydrolyzed the tetrapeptide into dipeptides in all samples. Subsequently, longer peptide sequences were found to form through reverse-hydrolysis. The stability of the different sequences was found to be dependent on their self-assembling properties. The sequences that self-assembled into antiparallel beta-sheet rich fibers became the stable products for the reverse hydrolysis reaction, while the others formed were unstable and disappeared with increasing incubation time. Ultimately, the main product of the system was octapeptide, which suggests that it represents the thermodynamically favored product of this dynamic library. Its concentration dictated the gelation behavior of the sample, and gels with moduli up to 25 kPa where obtained depending on the initial concentration of tetrapeptide.

The aminolysis reaction of streptomyces S9 aminopeptidase promotes the synthesis of diverse prolyl dipeptides

Prolyl dipeptide synthesis by S9 aminopeptidase from Streptomyces thermocyaneoviolaceus (S9AP-St) has been demonstrated. In the synthesis, S9AP-St preferentially used l-Pro-OBzl as the acyl donor, yielding synthesized dipeptides having an l-Pro-Xaa structure. In addition, S9AP-St showed broad specificity toward the acyl acceptor. Furthermore, S9AP-St produced cyclo (l-Pro-l-His) with a conversion ratio of substrate to cyclo (l-Pro-l-His) higher than 40%.

Discovery of potent thermolysin inhibitors using structure based virtual screening and binding assays

In the present work, 22 compounds of the U.S. NCI compound library (size 273K) were identified as putative thermolysin binders by structure based virtual screening with the ICM software (ICM-VLS). In vitro competitive binding assays confirmed that 12 were thermolysin binders. Thermolysin binding modes of the 12 compounds were studied by docking using ICM and Molegro Virtual Docker (MVD). The most potent inhibitor had an IC(50) value of 6.4 x 10(-8) mM (NSC250686, 1 beta-D-arabinofuranosyl-N(4)-lauroylcytosine). The structure of this compound is quite different from the other 11 compounds. Nine out of the 12 compounds contained a similar chemical skeleton (3-nitrobenzamide derivatives) and have IC(50) values ranging from 697.48 to 0.047 mM. The ICM-VLS score and the activity profiles (pIC(50) values) were compared and found to be somewhat linearly correlated (R(2) = 0.78). Kinetic studies showed that, except for NSC285166 (oxyquinoline), the compounds are competitive thermolysin inhibitors.

Improving the activity and stability of thermolysin by site-directed mutagenesis

In previous site-directed mutagenesis study on thermolysin, mutations which increase the catalytic activity or the thermal stability have been identified. In this study, we attempted to generate highly active and stable thermolysin by combining the mutations so far revealed to be effective. Three mutant enzymes, L144S (Leu144 in the central alpha-helix located at the bottom of the active site cleft is replaced with Ser), G8C/N60C/S65P (Gly8, Asn60, and Ser65 in the N-terminal region are replaced with Cys, Cys, and Pro, respectively, to introduce a disulfide bridge between the positions 8 and 60), and G8C/N60C/S65P/L144S, were constructed by site-directed mutagenesis. In the hydrolysis of N-[3-(2-furyl)acryloyl]-glycyl-L-leucine amide (FAGLA) and N-carbobenzoxy-L-aspartyl-L-phenylalanine methyl ester (ZDFM), the k(cat)/K(m) values of L144S and G8C/N60C/S65P/L144S were 5- to 10-fold higher than that of the wild-type enzyme. The rate constants for thermal inactivation at 70 degrees C and 80 degrees C of G8C/N60C/S65P and G8C/N60C/S65P/L144S decreased to 50% of that of the wild-type enzyme. These results indicate that G8C/N60C/S65P/L144S is more active and stable than the wild-type thermolysin. Thermodynamic analysis suggests that the single mutation of Leu144-->Ser and the triple mutation of Gly8-->Cys, Asn60-->Cys, and Ser65-->Pro are independent.

Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A

Zinc proteases are ubiquitous and the zinc ion plays a central function in the catalytic mechanism of these enzymes. A novel class of mechanism-based inhibitors takes advantage of the zinc ion chemistry in carboxypeptidase A (CPA) to promote covalent attachment of an inhibitor to the carboxylate of Glu-270, resulting in irreversible inhibition of the enzyme. The effect of the active site zinc ion on irreversible inactivation of CPA was probed by molecular orbital (MO) calculations on a series of active site models and the Cl(-) + CH(3)Cl S(N)2 reaction fragment. Point charge models representing the active site reproduced energetics from full MO calculations at 12.0 A separation between the zinc and the central carbon of the S(N)2 reaction, but at 5.0 A polarization played an important role in moderating barrier suppression. ONIOM MO/MO calculations that included the residues within 10 A of the active site zinc suggest that about 75% of the barrier suppression arises from the zinc ion and its ligands. A model of the pre-reactive complex of the 2-benzyl-3-iodopropanoate inactivator with CPA was constructed from the X-ray structure of l-phenyl lactate bound in the active site of the enzyme. The model was fully solvated and minimized by using the AMBER force field to generate the starting structure for the ONIOM QM/MM calculations. Optimization of this structure led to the barrierless S(N)2 displacement of the iodide of the inhibitor by Glu-270, assisted by interaction of the zinc ion with the leaving group. The resulting product is in good agreement with the X-ray structure of the covalently modified enzyme obtained by irreversible inhibition of CPA by 2-benzyl-3-iodopropanoate.

Engineering, expression, purification, and production of recombinant thermolysin

Thermolysin [EC 3.4.24.27] is a thermostable neutral zinc metalloproteinase originally identified in the culture broth of Bacillus thermoproteolyticus Rokko. Since the discovery in 1962, the enzyme has been extensively studied regarding its structure and catalytic mechanism. Today, thermolysin is a representative of zinc metalloproteinase and an attractive target in protein engineering to understand the catalytic mechanism, thermostability, and halophilicity. Thermolysin is used in industry, especially for the enzymatic synthesis of N-carbobenzoxy L-Asp-L-Phe methyl ester (ZDFM), a precursor of an artificial sweetener, aspartame. Generation of genetically engineered thermolysin with higher activity in the synthesis of ZDFM has been highly desired. In accordance with the expansion of studies on thermolysin, various strategies for its expression and purification have been devised and successfully used. In this review, we aim to outline recombinant thermolysins associated with their engineering, expression, purification, and production.

Effects of water-miscible solvents and polyhydroxy compounds on the structure and enzymatic activity of thermolysin

The effect of organic solvents (n-propanol, isopropanol, dimethylformamide and dimethylsulfoxide) on the structure, activity and stability of thermolysin was the focus of this investigation. Results show the ability of the solvents to cause mixed inhibition of thermolysin, which was indicated by kinetic and structural studies (near-UV CD spectra and intrinsic fluorescence). Inhibitory effect of the solvents increased with increments in solvents logP. Thermoinactivation of thermolysin was studied at 80 degrees C in 50% of solvents and showed that with the increase in solvent hydrophobicity, thermal stability of the enzyme decreased. For the stabilization of thermolysin at high temperature, additives such as glycerol, sorbitol and trehalose were employed. In the presence of DMF with a relatively low logP, trehalose was shown to be a good stabilizer, whereas glycerol had a marked stabilization effect in the presence of n-propanol and isopropanol with a relatively high logP. Consequently, it was concluded that the stabilizing effect of additives can be correlated with the logP of solvents.